diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java
index 8ab3f29fb3..f384f2ba65 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java
@@ -22,8 +22,12 @@
import static org.junit.Assert.*;
+import java.io.BufferedReader;
import java.io.File;
+import java.io.FileReader;
import java.io.IOException;
+import java.io.Reader;
+import java.io.StringReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
@@ -47,6 +51,7 @@
import org.biojava.nbio.structure.ecod.EcodDomain;
import org.biojava.nbio.structure.ecod.EcodFactory;
import org.biojava.nbio.structure.ecod.EcodInstallation;
+import org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser;
import org.junit.Ignore;
import org.junit.Rule;
import org.junit.Test;
@@ -277,12 +282,47 @@ public void testFilterByHierarchy() throws IOException {
assertEquals(expected,actual);
}
+ /**
+ * Checks that the current release can still be read.
+ *
+ * The version is read from the file's header without parsing the domains, so this
+ * additionally parses the first few thousand lines of the same file. That is enough to
+ * notice a column change — which is what ECOD did at v294.1, unnoticed for months —
+ * without building the three million domains the whole file now holds.
+ */
@Test
public void testVersion() throws IOException {
EcodDatabase ecod3 = EcodFactory.getEcodDatabase("latest");
String version = ecod3.getVersion();
assertNotNull(version);
assertNotEquals("latest", version);
+ System.out.println("latest version of ECOD is "+version);
+
+ File domainsFile = new File(((EcodInstallation) ecod3).getCacheLocation(),
+ "ecod.latest.domains.txt");
+ assertTrue("No local copy of the domains file at "+domainsFile, domainsFile.exists());
+
+ EcodParser parser = new EcodParser(firstLines(domainsFile, 5000));
+ assertEquals(version, parser.getVersion());
+ assertFalse("No domains parsed from ECOD "+version
+ + "; the distribution format has probably changed",
+ parser.getDomains().isEmpty());
+ }
+
+ /**
+ * @return a reader over the first {@code maxLines} lines of the file
+ */
+ private static Reader firstLines(File f, int maxLines) throws IOException {
+ StringBuilder head = new StringBuilder();
+ try (BufferedReader in = new BufferedReader(new FileReader(f))) {
+ String line;
+ int n = 0;
+ while (n < maxLines && (line = in.readLine()) != null) {
+ head.append(line).append('\n');
+ n++;
+ }
+ }
+ return new StringReader(head.toString());
}
/**
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java
index de6c072719..6ea23aef8a 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestSeqResParsing.java
@@ -53,7 +53,7 @@ public void test11GS() throws IOException, StructureException{
s = StructureIO.getStructure(pdbID);
assertNotNull(s);
- assertTrue(s.getChains().size() > 0);
+ assertFalse(s.getChains().isEmpty());
Chain c = s.getChainByIndex(0);
assertTrue(c.getSeqResGroups().size() > 2);
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 0b8cb53791..e0db50f1db 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
biojava
org.biojava
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
biojava-modfinder
biojava-modfinder
@@ -31,7 +31,7 @@
org.biojava
biojava-structure
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
jar
compile
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java
index 187e113924..e038f57cd3 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ModifiedCompoundXMLConverter.java
@@ -69,7 +69,7 @@ public static String toXML(ModifiedCompound mc) throws IOException{
Set linkages = mc.getAtomLinkages();
- if ( linkages.size() > 0 ) {
+ if (!linkages.isEmpty()) {
int pos = -1;
for ( StructureAtomLinkage link: linkages){
pos ++;
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java
index c9575a5444..0d94d36e6e 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java
@@ -285,7 +285,7 @@ public void identify(final List chains,
if (residues.isEmpty()) {
String pdbId = "?";
- if ( chains.size() > 0) {
+ if (!chains.isEmpty()) {
Structure struc = chains.get(0).getStructure();
if ( struc != null)
pdbId = struc.getPDBCode();
diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java
index 34376307a0..ba8e6d2a3d 100644
--- a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java
+++ b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java
@@ -32,7 +32,8 @@
import java.net.URL;
import java.util.List;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.fail;
@@ -100,11 +101,11 @@ public void testAcetylation() throws IOException {
List sites = Site.parseSites(localFile);
- assertTrue(sites.size() > 0);
+ assertFalse(sites.isEmpty());
for (Site s : sites) {
- assertTrue(s.getResidue() != null);
+ assertNotNull(s.getResidue());
}
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 001e3e52f1..eb9e3564c1 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
org.biojava
biojava
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
biojava-ontology
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/WeakValueHashMap.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/WeakValueHashMap.java
index 7762642c76..c508cdc206 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/WeakValueHashMap.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/WeakValueHashMap.java
@@ -58,12 +58,12 @@ public WeakValueHashMap() {
private void diddleReferenceQueue() {
// Avoid making behind-the-scenes modifications while iterators exist.
- if (iteratorRefs.size() > 0) {
+ if (!iteratorRefs.isEmpty()) {
Reference ref;
while ((ref = iteratorRefQueue.poll()) != null) {
iteratorRefs.remove(ref);
}
- if (iteratorRefs.size() > 0) {
+ if (!iteratorRefs.isEmpty()) {
return;
}
}
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 12e4941d55..1527d691f4 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
biojava
org.biojava
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
biojava-protein-comparison-tool
@@ -36,23 +36,23 @@
org.biojava
biojava-alignment
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
org.biojava
biojava-core
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
org.biojava
biojava-structure
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
org.biojava
biojava-structure-gui
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
net.sourceforge.jmol
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 82107e8058..827c708a2b 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
biojava
org.biojava
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
biojava-protein-disorder
jar
@@ -63,7 +63,7 @@
org.biojava
biojava-core
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 24644c8ffe..21e01ce42e 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
biojava
org.biojava
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
4.0.0
biojava-structure-gui
@@ -27,13 +27,13 @@
org.biojava
biojava-structure
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
compile
org.biojava
biojava-core
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
compile
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java
index 9e3c825910..c5542b4edc 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java
@@ -229,7 +229,7 @@ public void keyReleased(KeyEvent e) {
list.ensureIndexIsVisible(list.getSelectedIndex() - 1);
return;
} else if (e.getKeyCode() == KeyEvent.VK_ENTER
- && list.getSelectedIndex() != -1 && suggestions.size() > 0) {
+ && list.getSelectedIndex() != -1 && !suggestions.isEmpty()) {
setText((String) list.getSelectedValue());
@@ -365,7 +365,7 @@ public String doInBackground() {
setFont(regular);
- if (suggestions.size() > 0) {
+ if (!suggestions.isEmpty()) {
list.setListData(suggestions);
list.setSelectedIndex(0);
list.ensureIndexIsVisible(0);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java
index 136f184584..8e1a975205 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/SCOPAutoSuggestProvider.java
@@ -111,7 +111,7 @@ private List getPossibleScopDomains(String userInput) {
if ( stop.get())
return domains;
- if ( domains == null || domains.size() < 1){
+ if ( domains == null || domains.isEmpty()){
if ( userInput.length() > 5){
// e.g. d4hhba
@@ -127,11 +127,11 @@ private List getPossibleScopDomains(String userInput) {
if (DEBUG)
System.out.println("domains: " + domains);
- if ( domains == null || domains.size() < 1) {
+ if ( domains == null || domains.isEmpty()) {
if ( userInput.length() > 0 ){
List descs = scop.filterByClassificationId(userInput);
- if ( descs == null || descs.size() < 1){
+ if ( descs == null || descs.isEmpty()){
descs = scop.filterByDescription(userInput);
}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java
index d1ce5c0e30..feec8b0366 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/RasmolCommandListener.java
@@ -74,7 +74,7 @@ public void actionPerformed(ActionEvent event) {
// check last command in history
// if equivalent, don't add,
// otherwise add
- if (history.size()>0){
+ if (!history.isEmpty()){
String txt=history.get(history.size()-1);
if (! txt.equals(cmd)) {
history.add(cmd);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java
index 06542e5271..75da6c8e28 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java
@@ -126,7 +126,7 @@ private void setPrefSize() {
public void setAligMap(List apos){
this.apos = apos;
- if ( apos.size() == 0)
+ if (apos.isEmpty())
return;
AlignedPosition last = apos.get(apos.size()-1);
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 5392798310..647ab49c72 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
biojava
org.biojava
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
biojava-structure
biojava-structure
@@ -51,13 +51,13 @@
org.biojava
biojava-alignment
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
compile
org.biojava
biojava-core
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
compile
@@ -87,7 +87,7 @@
com.fasterxml.jackson.core
jackson-databind
- 2.13.4.2
+ 2.18.9
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
index b0d7253507..bd5a01b885 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
@@ -62,7 +62,7 @@ public boolean equals(Object obj) {
if ((this.surname == null) ? (other.surname != null) : !this.surname.equals(other.surname)) {
return false;
}
- return !((this.initials == null) ? (other.initials != null) : !this.initials.equals(other.initials));
+ return (this.initials == null) ? other.initials == null : this.initials.equals(other.initials);
}
@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
index 2f534b2828..4e2d3e340a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
@@ -424,7 +424,7 @@ public boolean isHeavyAtom() {
* @return true if Element is not Hydrogen and not Carbon.
*/
public boolean isHeteroAtom() {
- return !(this == C || this == H);
+ return this != C && this != H;
}
/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java
index 9158906d23..341483f31b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java
@@ -83,7 +83,7 @@ public String toPDB() {
@Override
public void toPDB(StringBuffer buf) {
- if (groups == null || groups.size() < 1) {
+ if (groups == null || groups.isEmpty()) {
return;
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java
index 373bcf1611..0933198d7b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java
@@ -102,7 +102,7 @@ public static void cluster(AlternativeAlignment[] aligs, int cutoff){
}
clusters.add(currentCluster);
- if ( remainList.size() == 0) {
+ if ( remainList.isEmpty()) {
break;
}
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
index 6c045ba48e..83f16b7982 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
@@ -1450,7 +1450,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str
//afpChain.setTotalRmsdOpt(rmsd);
//System.out.println("rmsd: " + rmsd);
- if(!(nAtom= strLen * 0.95 && !isRmsdLenAssigned) {
rmsdLen=rmsd;
isRmsdLenAssigned=true;
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
index 4f57161268..cab98b0113 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
@@ -1455,7 +1455,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str
//afpChain.setTotalRmsdOpt(rmsd);
//System.out.println("rmsd: " + rmsd);
- if(!(nAtom= strLen * 0.95 && !isRmsdLenAssigned) {
rmsdLen=rmsd;
isRmsdLenAssigned=true;
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
index e0423b6f8f..43da1d7c06 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
@@ -127,7 +127,7 @@ public void setAlignRes(List> alignRes) {
public int length() {
if (alignRes == null)
return 0;
- if (alignRes.size() == 0)
+ if (alignRes.isEmpty())
return 0;
return alignRes.get(0).size();
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
index cbbb3ae895..344ee3c239 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
@@ -179,7 +179,7 @@ public int size() {
// Get the size from the variables that can contain the information
if (parent != null)
return parent.size();
- else if (getBlocks().size() == 0) {
+ else if (getBlocks().isEmpty()) {
throw new IndexOutOfBoundsException(
"Empty BlockSet: number of Blocks == 0.");
} else
@@ -194,7 +194,7 @@ public int getCoreLength() {
}
protected void updateLength() {
- if (getBlocks().size() == 0) {
+ if (getBlocks().isEmpty()) {
throw new IndexOutOfBoundsException(
"Empty BlockSet: number of Blocks == 0.");
}
@@ -207,7 +207,7 @@ protected void updateLength() {
}
protected void updateCoreLength() {
- if (getBlocks().size() == 0) {
+ if (getBlocks().isEmpty()) {
throw new IndexOutOfBoundsException(
"Empty BlockSet: number of Blocks == 0.");
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
index 738eee30c5..06c93a4403 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
@@ -207,7 +207,7 @@ public int getCoreLength() {
* lengths.
*/
protected void updateLength() {
- if (getBlockSets().size() == 0) {
+ if (getBlockSets().isEmpty()) {
throw new IndexOutOfBoundsException(
"Empty MultipleAlignment: blockSets size == 0.");
} // Otherwise try to calculate it from the BlockSet information
@@ -223,7 +223,7 @@ protected void updateLength() {
* BlockSet core lengths.
*/
protected void updateCoreLength() {
- if (getBlockSets().size() == 0) {
+ if (getBlockSets().isEmpty()) {
throw new IndexOutOfBoundsException(
"Empty MultipleAlignment: blockSets size == 0.");
} // Otherwise try to calculate it from the BlockSet information
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
index 052f147fc6..29c7012801 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
@@ -153,7 +153,7 @@ public MultipleMcOptimizer(MultipleAlignment seedAln,
for (Block b : toDelete) {
for (BlockSet bs : msa.getBlockSets()) {
bs.getBlocks().remove(b);
- if (bs.getBlocks().size() == 0)
+ if (bs.getBlocks().isEmpty())
emptyBs.add(bs);
}
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
index 771b8b5f68..5033576df0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
@@ -205,7 +205,7 @@ public static String toTransformMatrices(MultipleAlignment alignment) {
List btransforms = alignment.getBlockSet(bs)
.getTransformations();
- if (btransforms == null || btransforms.size() < 1)
+ if (btransforms == null || btransforms.isEmpty())
continue;
if (alignment.getBlockSets().size() > 1) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
index 7ac77a602e..fe1c9c411b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
@@ -117,7 +117,7 @@ public void setSubunitMap(Map subunitMap) {
"Subunit Map index higher than Subunit List size.");
// Update the relation enum
- if (subunitMap.size() == 0) {
+ if (subunitMap.isEmpty()) {
relation = QsRelation.DIFFERENT;
} else if (subunitMap.keySet().size() == subunits1.size()) {
if (subunitMap.values().size() == subunits2.size()) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
index c6791f4ed2..e535a87508 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -1313,7 +1313,7 @@ public static Group[] prepareGroupsForDisplay(AFPChain afpChain, Atom[] ca1, Ato
if ( afpChain.getBlockNum() > 0){
// Superimpose ligands relative to the first block
- if( hetatms2.size() > 0 ) {
+ if(!hetatms2.isEmpty()) {
if ( afpChain.getBlockRotationMatrix().length > 0 ) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
index 1435191c2c..71b8a3da22 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -228,7 +228,7 @@ public Structure getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean
throws StructureException, IOException {
return getBiologicalAssembly(new PdbId(pdbId), bioAssemblyId, multiModel);
}
-
+
/**
* Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the
* assembly from the biounit annotations found in {@link Structure#getPDBHeader()}
@@ -284,7 +284,7 @@ public Structure getBiologicalAssembly(PdbId pdbId, int bioAssemblyId, boolean m
asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms();
- if (transformations == null || transformations.size() == 0) {
+ if (transformations == null || transformations.isEmpty()) {
throw new StructureException("Could not load transformations to recreate biological assembly id " + bioAssemblyId + " of " + pdbId);
}
@@ -339,7 +339,7 @@ public Structure getBiologicalAssembly(String pdbId, boolean multiModel) throws
asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms();
- if (transformations == null || transformations.size() == 0) {
+ if (transformations == null || transformations.isEmpty()) {
throw new StructureException("Could not load transformations to recreate biological assembly id " + bioAssemblyId + " of " + pdbId);
}
@@ -385,7 +385,7 @@ public List getBiologicalAssemblies(String pdbId, boolean multiModel)
List transformations =
asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms();
- if (transformations == null || transformations.size() == 0) {
+ if (transformations == null || transformations.isEmpty()) {
logger.info("Could not load transformations to recreate biological assembly id {} of {}. Assembly " +
"id will be missing in biological assemblies.", bioAssemblyId, pdbId);
continue;
@@ -807,7 +807,7 @@ public Structure getStructureForPdbId(String id) throws IOException, StructureEx
public Structure getStructureForPdbId(PdbId pdbId) throws IOException {
if (pdbId == null)
return null;
-
+
while (checkLoading(pdbId)) {
// waiting for loading to be finished...
try {
@@ -833,7 +833,7 @@ public Structure getStructureForPdbId(PdbId pdbId) throws IOException {
protected Structure loadStructureFromCifByPdbId(String pdbId) throws IOException {
return loadStructureFromCifByPdbId(new PdbId(pdbId));
}
-
+
protected Structure loadStructureFromCifByPdbId(PdbId pdbId) throws IOException {
logger.debug("Loading structure {} from mmCIF file {}.", pdbId, path);
Structure s;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java
index 759ee61931..e8d5434578 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/MultipleAlignmentXMLParser.java
@@ -169,7 +169,7 @@ else if ("ScoresCache".equals(child.getNodeName())){
}
}
//Because if it is 0 means that there were no transformations
- if (transforms.size() != 0){
+ if (!transforms.isEmpty()){
bs.setTransformations(transforms);
}
return bs;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
index 0f46b7f416..ed576b9abe 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
@@ -27,7 +27,6 @@
import org.slf4j.LoggerFactory;
import javax.vecmath.Point3d;
-import javax.vecmath.Vector3d;
import java.util.*;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
@@ -101,12 +100,56 @@ public void run() {
}
}
- static class IndexAndDistance {
- final int index;
- final double dist;
- IndexAndDistance(int index, double dist) {
- this.index = index;
- this.dist = dist;
+ /**
+ * The neighbors of a single atom, as parallel primitive arrays of neighbor atom indices and their distances to
+ * the central atom, sorted by increasing distance.
+ *
+ * Parallel primitive arrays are used rather than an array of index-distance objects because there are ~30
+ * neighbors per atom: for a large structure that would mean millions of small short-lived objects.
+ */
+ static class Neighbors {
+
+ /** The neighbor atom indices, ordered by increasing distance to the central atom */
+ final int[] indices;
+ /** The distances to the central atom, in increasing order and parallel to {@link #indices} */
+ final double[] dists;
+
+ private Neighbors(int[] indices, double[] dists) {
+ this.indices = indices;
+ this.dists = dists;
+ }
+
+ /**
+ * Creates a Neighbors from the first count elements of the given buffers, copying them to exact-size arrays
+ * and sorting them by increasing distance.
+ * @param indicesBuffer the neighbor indices, only the first count elements are used
+ * @param distsBuffer the neighbor distances, only the first count elements are used
+ * @param count the number of neighbors
+ * @return the sorted neighbors
+ */
+ static Neighbors createSorted(int[] indicesBuffer, double[] distsBuffer, int count) {
+ int[] indices = Arrays.copyOf(indicesBuffer, count);
+ double[] dists = Arrays.copyOf(distsBuffer, count);
+ // Sorting by closest to farthest away neighbors achieves faster runtimes when checking for occluded
+ // sphere sample points in calcSingleAsa. This follows the ideas exposed in
+ // Eisenhaber et al, J Comp Chemistry 1994 (https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.540160303)
+ // This is essential for performance: it brings down the number of occlusion checks to
+ // an average of n_sphere_points/10 per atom, producing ~ x4 performance gain overall.
+ // An insertion sort is used because the arrays are small (~30 elements on average) and because it avoids
+ // both the boxing of a comparator-based sort and the object allocation an index-distance array would need.
+ for (int i = 1; i < count; i++) {
+ double dist = dists[i];
+ int index = indices[i];
+ int j = i - 1;
+ while (j >= 0 && dists[j] > dist) {
+ dists[j + 1] = dists[j];
+ indices[j + 1] = indices[j];
+ j--;
+ }
+ dists[j + 1] = dist;
+ indices[j + 1] = index;
+ }
+ return new Neighbors(indices, dists);
}
}
@@ -116,9 +159,16 @@ static class IndexAndDistance {
private final double[] radii;
private final double probe;
private final int nThreads;
- private Vector3d[] spherePoints;
+ /**
+ * The sphere points to sample, as a flat array of interleaved x,y,z coordinates (thus of size 3 x nSpherePoints).
+ * A flat array of primitives (rather than an array of Vector3d objects) is used for performance: it keeps the
+ * points contiguous in memory and avoids a pointer dereference per point in the innermost loop of
+ * {@link #calcSingleAsa(int)}.
+ */
+ private double[] spherePoints;
+ private int nSpherePoints;
private double cons;
- private IndexAndDistance[][] neighborIndices;
+ private Neighbors[] neighbors;
private boolean useSpatialHashingForNeighbors;
@@ -239,7 +289,8 @@ private void initSpherePoints(int nSpherePoints) {
logger.debug("Will use {} sphere points", nSpherePoints);
// initialising the sphere points to sample
- spherePoints = generateSpherePoints(nSpherePoints);
+ this.nSpherePoints = nSpherePoints;
+ this.spherePoints = generateSpherePoints(nSpherePoints);
cons = 4.0 * Math.PI / nSpherePoints;
}
@@ -285,10 +336,10 @@ public double[] calculateAsas() {
long start = System.currentTimeMillis();
if (useSpatialHashingForNeighbors) {
logger.debug("Will use spatial hashing to find neighbors");
- neighborIndices = findNeighborIndicesSpatialHashing();
+ neighbors = findNeighborIndicesSpatialHashing();
} else {
logger.debug("Will not use spatial hashing to find neighbors");
- neighborIndices = findNeighborIndices();
+ neighbors = findNeighborIndices();
}
long end = System.currentTimeMillis();
logger.debug("Took {} s to find neighbors", (end-start)/1000.0);
@@ -334,109 +385,126 @@ void setUseSpatialHashingForNeighbors(boolean useSpatialHashingForNeighbors) {
* Returns list of 3d coordinates of points on a unit sphere using the
* Golden Section Spiral algorithm.
* @param nSpherePoints the number of points to be used in generating the spherical dot-density
- * @return the array of points as Vector3d objects
+ * @return a flat array of interleaved x,y,z coordinates, of size 3 x nSpherePoints
*/
- private Vector3d[] generateSpherePoints(int nSpherePoints) {
- Vector3d[] points = new Vector3d[nSpherePoints];
+ private double[] generateSpherePoints(int nSpherePoints) {
+ double[] points = new double[3 * nSpherePoints];
double inc = Math.PI * (3.0 - Math.sqrt(5.0));
double offset = 2.0 / nSpherePoints;
for (int k=0;k thisNbIndices = new ArrayList<>(initialCapacity);
+ int count = 0;
for (int i = 0; i < atomCoords.length; i++) {
if (i == k) continue;
double dist = atomCoords[i].distance(atomCoords[k]);
- if (dist < radius + radii[i]) {
- thisNbIndices.add(new IndexAndDistance(i, dist));
+ if (areNeighbors(k, i, dist)) {
+ if (count == indicesBuffer.length) {
+ indicesBuffer = Arrays.copyOf(indicesBuffer, count * 2);
+ distsBuffer = Arrays.copyOf(distsBuffer, count * 2);
+ }
+ indicesBuffer[count] = i;
+ distsBuffer[count] = dist;
+ count++;
}
}
- IndexAndDistance[] indicesArray = thisNbIndices.toArray(new IndexAndDistance[0]);
- nbsIndices[k] = indicesArray;
+ nbs[k] = Neighbors.createSorted(indicesBuffer, distsBuffer, count);
}
- return nbsIndices;
+ return nbs;
}
/**
- * Returns the 2-dimensional array with neighbor indices for every atom,
+ * Returns the neighbors of every atom, sorted by increasing distance,
* using spatial hashing to avoid all to all distance calculation.
- * @return 2-dimensional array of size: n_atoms x n_neighbors_per_atom
+ * @return array of size n_atoms
*/
- IndexAndDistance[][] findNeighborIndicesSpatialHashing() {
-
- // looking at a typical protein case, number of neighbours are from ~10 to ~50, with an average of ~30
- int initialCapacity = 60;
+ Neighbors[] findNeighborIndicesSpatialHashing() {
List contactList = calcContacts();
- Map> indices = new HashMap<>(atomCoords.length);
+
+ // A first pass to count the neighbors per atom, so that exact-size arrays can be allocated in the second
+ // pass. Atom indices are dense, so plain arrays are used rather than a map: that avoids boxing the indices
+ // and the repeated hashing, which are significant given that there are ~30 contacts per atom.
+ int[] counts = new int[atomCoords.length];
for (Contact contact : contactList) {
// note contacts are stored 1-way only, with j>i
int i = contact.getI();
int j = contact.getJ();
-
- List iIndices;
- List jIndices;
- if (!indices.containsKey(i)) {
- iIndices = new ArrayList<>(initialCapacity);
- indices.put(i, iIndices);
- } else {
- iIndices = indices.get(i);
- }
- if (!indices.containsKey(j)) {
- jIndices = new ArrayList<>(initialCapacity);
- indices.put(j, jIndices);
- } else {
- jIndices = indices.get(j);
- }
-
- double radius = radii[i] + probe + probe;
- double dist = contact.getDistance();
- if (dist < radius + radii[j]) {
- iIndices.add(new IndexAndDistance(j, dist));
- jIndices.add(new IndexAndDistance(i, dist));
+ if (areNeighbors(i, j, contact.getDistance())) {
+ counts[i]++;
+ counts[j]++;
}
}
- // convert map to array for fast access
- IndexAndDistance[][] nbsIndices = new IndexAndDistance[atomCoords.length][];
- for (Map.Entry> entry : indices.entrySet()) {
- List list = entry.getValue();
- IndexAndDistance[] indexAndDistances = list.toArray(new IndexAndDistance[0]);
- nbsIndices[entry.getKey()] = indexAndDistances;
+ int[][] indices = new int[atomCoords.length][];
+ double[][] dists = new double[atomCoords.length][];
+ for (int i = 0; i < atomCoords.length; i++) {
+ // note that some atoms might have no neighbors at all, in which case these are empty arrays
+ indices[i] = new int[counts[i]];
+ dists[i] = new double[counts[i]];
}
- // important: some atoms might have no neighbors at all: we need to initialise to empty arrays
- for (int i=0; i calcContacts() {
private double calcSingleAsa(int i) {
Point3d atom_i = atomCoords[i];
- int n_neighbor = neighborIndices[i].length;
- IndexAndDistance[] neighbor_indices = neighborIndices[i];
- // Sorting by closest to farthest away neighbors achieves faster runtimes when checking for occluded
- // sphere sample points below. This follows the ideas exposed in
- // Eisenhaber et al, J Comp Chemistry 1994 (https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.540160303)
- // This is essential for performance. In my tests this brings down the number of occlusion checks in loop below to
- // an average of n_sphere_points/10 per atom i, producing ~ x4 performance gain overall
- Arrays.sort(neighbor_indices, Comparator.comparingDouble(o -> o.dist));
+ // note the neighbors are already sorted by increasing distance (see Neighbors#createSorted), which is
+ // essential for the performance of the occlusion checks in the loop below
+ Neighbors nbs = neighbors[i];
+ int[] neighbor_indices = nbs.indices;
+ double[] neighbor_dists = nbs.dists;
+ int n_neighbor = neighbor_indices.length;
double radius_i = probe + radii[i];
@@ -476,36 +542,47 @@ private double calcSingleAsa(int i) {
int[] numDistsCalced = null;
if (logger.isDebugEnabled()) numDistsCalced = new int[n_neighbor];
- // now we precalculate anything depending only on i,j in equation 3 in Eisenhaber 1994
- double[] sqRadii = new double[n_neighbor];
- Vector3d[] aj_minus_ais = new Vector3d[n_neighbor];
+ // Now we precalculate anything depending only on i,j in equation 3 in Eisenhaber 1994.
+ // The per-neighbor data is laid out in a single flat array as quadruplets
+ // [aj_minus_ai.x, aj_minus_ai.y, aj_minus_ai.z, cutoff], so that the innermost loop below is a purely
+ // sequential scan over contiguous primitives, with no object dereferencing. That matches the access
+ // pattern of the early break and is significantly faster than an array of Vector3d objects.
+ double[] nbData = new double[4 * n_neighbor];
for (int nbArrayInd =0; nbArrayInd> 2]++;
- if (dotProd > sqRadii[nbArrayInd]) {
+ if (dotProd > nbData[off + 3]) {
is_accessible = false;
break;
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
index 3f0f44158b..4201f8d5ca 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
@@ -31,8 +31,6 @@
import java.io.*;
import java.net.URL;
-import java.nio.file.Files;
-import java.nio.file.StandardCopyOption;
import java.text.DateFormat;
import java.text.DecimalFormat;
import java.text.ParseException;
@@ -54,7 +52,7 @@ public class CathInstallation implements CathDatabase{
public static final String nodeListFileName = "cath-names-v%s.txt";
public static final String domallFileName = "cath-domain-boundaries-v%s.txt";
- public static final String CATH_DOWNLOAD_URL = "http://download.cathdb.info/cath/releases/";
+ public static final String CATH_DOWNLOAD_URL = "https://download.cathdb.info/cath/releases/";
public static final String CATH_DOWNLOAD_ALL_RELEASES_DIR = "all-releases";
public static final String CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR = "cath-classification-data";
@@ -352,13 +350,15 @@ private void parseCathDomainList() throws IOException {
parseCathDomainList(buffer);
}
- private void parseCathDomainList(BufferedReader bufferedReader) throws IOException{
+ protected void parseCathDomainList(BufferedReader bufferedReader) throws IOException{
String line;
- // int counter = 0;
+ int counter = 0;
while ( (line = bufferedReader.readLine()) != null ) {
if ( line.startsWith("#") ) continue;
+ if ( line.trim().isEmpty() ) continue;
CathDomain cathDomain = parseCathListFileLine(line);
- // counter++;
+ if ( cathDomain == null ) continue;
+ counter++;
String pdbId = cathDomain.getPdbIdAndChain().substring(0,4); // includes chain letter
@@ -374,6 +374,9 @@ private void parseCathDomainList(BufferedReader bufferedReader) throws IOExcepti
domainMap.put( cathDomain.getDomainName(), cathDomain );
}
+ if (counter == 0) {
+ throw new IOException("Could not parse any CATH domains from the domain list file.");
+ }
}
private void parseCathNames() throws IOException {
@@ -388,7 +391,9 @@ private void parseCathNames(BufferedReader bufferedReader) throws IOException{
//int counter = 0;
while ( (line = bufferedReader.readLine()) != null ) {
if ( line.startsWith("#") ) continue;
+ if ( line.trim().isEmpty() ) continue;
CathNode cathNode = parseCathNamesFileLine(line);
+ if ( cathNode == null ) continue;
cathTree.put(cathNode.getNodeId(), cathNode);
}
}
@@ -415,6 +420,7 @@ private void parseCathDomainDescriptionFile(BufferedReader bufferedReader) throw
StringBuilder sseqs = null;
while ( (line = bufferedReader.readLine()) != null ) {
if ( line.startsWith("#") ) continue;
+ if ( line.trim().isEmpty() ) continue;
if ( line.startsWith("FORMAT") ) {
cathDescription = new CathDomain();
cathDescription.setFormat( line.substring(10) );
@@ -506,8 +512,11 @@ private void parseCathDomainDescriptionFile(BufferedReader bufferedReader) throw
}*/
private CathDomain parseCathListFileLine(String line) {
+ String [] token = line.trim().split("\\s+");
+ if (token.length < 12) {
+ return null;
+ }
CathDomain cathDomain = new CathDomain();
- String [] token = line.split("\\s+");
cathDomain.setDomainName(token[0]);
cathDomain.setClassId(Integer.parseInt(token[1]));
cathDomain.setArchitectureId(Integer.parseInt(token[2]));
@@ -524,8 +533,12 @@ private CathDomain parseCathListFileLine(String line) {
}
private CathNode parseCathNamesFileLine(String line) {
+ String[] token = line.trim().split("\\s+",3);
+ if (token.length < 3) {
+ LOGGER.debug("Invalid line in cath names file, was expecting 3 tokens but got {} tokens: {}", token.length, line);
+ return null;
+ }
CathNode cathNode = new CathNode();
- String[] token = line.split("\\s+",3);
cathNode.setNodeId( token[0] );
int idx = token[0].lastIndexOf(".");
if ( idx == -1 ) idx = token[0].length();
@@ -546,8 +559,8 @@ private void parseCathDomall(BufferedReader bufferedReader) throws IOException{
String line;
while ( ((line = bufferedReader.readLine()) != null) ) {
if ( line.startsWith("#") ) continue;
- if ( line.length() == 0 ) continue;
- String[] token = line.split("\\s+");
+ if ( line.trim().isEmpty() ) continue;
+ String[] token = line.trim().split("\\s+");
String chainId = token[0];
Integer numberOfDomains = Integer.parseInt( token[1].substring(1) );
Integer numberOfFragments = Integer.parseInt( token[2].substring(1) );
@@ -637,27 +650,26 @@ private void parseCathDomall(BufferedReader bufferedReader) throws IOException{
}
protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOException{
-// System.out.println("downloading " + remoteURL + " to: " + localFile);
LOGGER.info("Downloading file {} to local file {}", remoteURL, localFile);
long timeS = System.currentTimeMillis();
- File tempFile = Files.createTempFile(FileDownloadUtils.getFilePrefix(localFile),"." + FileDownloadUtils.getFileExtension(localFile)).toFile();
- FileOutputStream out = new FileOutputStream(tempFile);
-
- InputStream in = remoteURL.openStream();
- byte[] buf = new byte[4 * 1024]; // 4K buffer
- int bytesRead;
- while ((bytesRead = in.read(buf)) != -1) {
- out.write(buf, 0, bytesRead);
+ File parent = localFile.getAbsoluteFile().getParentFile();
+ if (parent != null && !parent.isDirectory() && !parent.mkdirs()) {
+ throw new IOException("Could not create directory " + parent);
}
- in.close();
- out.close();
- Files.copy(tempFile.toPath(), localFile.toPath(), StandardCopyOption.REPLACE_EXISTING);
+ // Previously this read the response with a bare remoteURL.openStream() and
+ // copied whatever came back. That silently accepted error and redirect
+ // responses: when download.cathdb.info began redirecting http to https, the
+ // body of the 301 was written here as though it were classification data,
+ // and the failure only surfaced much later as an unparseable file.
+ FileDownloadUtils.downloadFileWithValidation(remoteURL, localFile, null,
+ FileDownloadUtils.Hash.UNKNOWN, FileDownloadUtils.ETagPolicy.USE_IF_HEX_DIGEST);
- // delete the tmp file
- tempFile.delete();
+ if (!FileDownloadUtils.validateFile(localFile)) {
+ throw new IOException("Downloaded file invalid: " + localFile);
+ }
long size = localFile.length();
@@ -674,25 +686,25 @@ protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOEx
private boolean domainDescriptionFileAvailable(){
String fileName = getDomainDescriptionFileName();
File f = new File(fileName);
- return f.exists();
+ return f.exists() && FileDownloadUtils.validateFile(f);
}
private boolean domainListFileAvailable(){
String fileName = getDomainListFileName();
File f = new File(fileName);
- return f.exists();
+ return f.exists() && FileDownloadUtils.validateFile(f);
}
private boolean nodeListFileAvailable(){
String fileName = getNodeListFileName();
File f = new File(fileName);
- return f.exists();
+ return f.exists() && FileDownloadUtils.validateFile(f);
}
private boolean domallFileAvailable() {
String fileName = getDomallFileName();
File f= new File(fileName);
- return f.exists();
+ return f.exists() && FileDownloadUtils.validateFile(f);
}
protected void downloadDomainListFile() throws IOException{
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java
index 9eb9c7c6cf..e19535bce8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java
@@ -1,5 +1,6 @@
package org.biojava.nbio.structure.chem;
+import org.biojava.nbio.core.util.FileDownloadUtils;
import org.biojava.nbio.core.util.InputStreamProvider;
import org.biojava.nbio.structure.align.util.URLConnectionTools;
import org.biojava.nbio.structure.align.util.UserConfiguration;
@@ -396,6 +397,17 @@ private static boolean downloadChemCompRecord(String recordName) {
url = new URL(u);
URLConnection uconn = URLConnectionTools.openURLConnection(url);
+ // A 4xx or 5xx already fails safely, because getInputStream() throws for
+ // those. A redirect does not: if the server answers 3xx and the JDK
+ // declines to follow it - which it always does when the redirect changes
+ // http to https - getInputStream() hands back the body of the redirect
+ // instead. That body is short but not empty, so the "did we read any
+ // lines" check below accepts it, and it is gzipped and stored under the
+ // component's name. Every later lookup then reads it back and fails to
+ // parse, long after the request that caused it. This is exactly how the
+ // CATH downloader broke when download.cathdb.info moved to https.
+ FileDownloadUtils.checkHttpStatus(uconn);
+
try (PrintWriter pw = new PrintWriter(new GZIPOutputStream(new FileOutputStream(newFile)));
BufferedReader fileBuffer = new BufferedReader(new InputStreamReader(uconn.getInputStream()))) {
String line;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java
index 4fe19aca58..a68019efb7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java
@@ -120,7 +120,7 @@ public ChemComp getChemComp(String recordName) {
}
// If a null record or an empty chemcomp, return a default ChemComp and blacklist.
- if (cc == null || (null == cc.getName() && cc.getAtoms().size() == 0)) {
+ if (cc == null || (null == cc.getName() && cc.getAtoms().isEmpty())) {
s_logger.info("Unable to find or download {} - excluding from future searches.", recordName);
unavailable.add(recordName);
return getEmptyChemComp(recordName);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
index 9a87e92f88..87c3c06e3c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
@@ -331,7 +331,7 @@ public boolean mergeIdenticalByEntityId(SubunitCluster other) {
}
}
- if (thisAligned.size() == 0 && otherAligned.size() == 0) {
+ if (thisAligned.isEmpty() && otherAligned.isEmpty()) {
logger.warn("No equivalent aligned atoms found between SubunitClusters {}-{} via entity SEQRES alignment. Is FileParsingParameters.setAlignSeqRes() set?", thisName, otherName);
}
@@ -507,27 +507,24 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p
}
}
- AFPChain afp = aligner.align(this.subunits.get(this.representative)
- .getRepresentativeAtoms(),
- other.subunits.get(other.representative)
- .getRepresentativeAtoms());
+ AFPChain afp = aligner.align(this.subunits.get(this.representative).getRepresentativeAtoms(),
+ other.subunits.get(other.representative).getRepresentativeAtoms());
+ String pairName = this.subunits.get(this.representative).getName() + "-" + other.subunits.get(other.representative).getName();
if (afp.getOptLength() < 1) {
// alignment failed (eg if chains were too short)
throw new StructureException(
- String.format("Subunits failed to align using %s", params.getSuperpositionAlgorithm()));
+ String.format("Subunits %s failed to align using %s", pairName, params.getSuperpositionAlgorithm()));
}
// Convert AFPChain to MultipleAlignment for convenience
MultipleAlignment msa = new MultipleAlignmentEnsembleImpl(
afp,
this.subunits.get(this.representative).getRepresentativeAtoms(),
- other.subunits.get(other.representative)
- .getRepresentativeAtoms(), false)
- .getMultipleAlignment(0);
+ other.subunits.get(other.representative).getRepresentativeAtoms(),
+ false).getMultipleAlignment(0);
- double structureCoverage = Math.min(msa.getCoverages().get(0), msa
- .getCoverages().get(1));
+ double structureCoverage = Math.min(msa.getCoverages().get(0), msa.getCoverages().get(1));
if(params.isUseStructureCoverage() && structureCoverage < params.getStructureCoverageThreshold()) {
return false;
@@ -543,8 +540,7 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p
return false;
}
- logger.info(String.format("SubunitClusters are structurally similar with "
- + "%.2f RMSD %.2f coverage", rmsd, structureCoverage));
+ logger.info("SubunitClusters {} are structurally similar with [ {} ] RMSD and [ {} ] coverage", pairName, String.format("%.2f", rmsd), String.format("%.2f", structureCoverage));
// Merge clusters
List> alignedRes = msa.getBlock(0).getAlignRes();
@@ -565,13 +561,18 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p
// Only consider residues that are part of the SubunitCluster
if (this.subunitEQR.get(this.representative).contains(thisIndex)
- && other.subunitEQR.get(other.representative).contains(
- otherIndex)) {
+ && other.subunitEQR.get(other.representative).contains(otherIndex)) {
thisAligned.add(thisIndex);
otherAligned.add(otherIndex);
}
}
+ // this can happen in very rare cases, e.g. 9y9z when merging E_1 into the cluster D_1, OM_1, Y_1
+ if (thisAligned.isEmpty() && otherAligned.isEmpty()) {
+ logger.warn("No equivalent aligned atoms found between SubunitClusters {} via structure alignment. Will not merge the second one into the first.", pairName);
+ return false;
+ }
+
updateEquivResidues(other, thisAligned, otherAligned);
this.method = SubunitClustererMethod.STRUCTURE;
@@ -602,18 +603,12 @@ private void updateEquivResidues(SubunitCluster other, List thisAligned
Collections.sort(otherRemove);
Collections.reverse(otherRemove);
- for (int t = 0; t < thisRemove.size(); t++) {
- for (List eqr : this.subunitEQR) {
- int column = thisRemove.get(t);
- eqr.remove(column);
- }
+ for (int column : thisRemove) {
+ this.subunitEQR.forEach(eqr -> eqr.remove(column));
}
- for (int t = 0; t < otherRemove.size(); t++) {
- for (List eqr : other.subunitEQR) {
- int column = otherRemove.get(t);
- eqr.remove(column);
- }
+ for (int column : otherRemove) {
+ other.subunitEQR.forEach(eqr -> eqr.remove(column));
}
// The representative is the longest sequence
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
index 6295f8fdf0..fa63b96d96 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
@@ -58,7 +58,7 @@ public static Stoichiometry cluster(Structure structure,
public static Stoichiometry cluster(List subunits, SubunitClustererParameters params) {
List clusters = new ArrayList<>();
- if (subunits.size() == 0)
+ if (subunits.isEmpty())
return new Stoichiometry(clusters);
// First generate a new cluster for each Subunit
@@ -83,8 +83,7 @@ public static Stoichiometry cluster(List subunits, SubunitClustererPara
}
} catch (CompoundNotFoundException e) {
- logger.warn("Could not merge by Sequence. {}",
- e.getMessage());
+ logger.info("Could not merge by Sequence. {}", e.getMessage());
}
}
}
@@ -100,7 +99,7 @@ public static Stoichiometry cluster(List subunits, SubunitClustererPara
clusters.remove(c2);
}
} catch (StructureException e) {
- logger.warn("Could not merge by Structure. {}", e.getMessage());
+ logger.info("Could not merge by Structure. {}", e.getMessage());
}
}
}
@@ -112,8 +111,7 @@ public static Stoichiometry cluster(List subunits, SubunitClustererPara
try {
clusters.get(c).divideInternally(params);
} catch (StructureException e) {
- logger.warn("Error analyzing internal symmetry. {}",
- e.getMessage());
+ logger.info("Error analyzing internal symmetry. {}", e.getMessage());
}
}
@@ -125,8 +123,7 @@ public static Stoichiometry cluster(List subunits, SubunitClustererPara
if (clusters.get(c1).mergeStructure(clusters.get(c2), params))
clusters.remove(c2);
} catch (StructureException e) {
- logger.warn("Could not merge by Structure. {}",
- e.getMessage());
+ logger.info("Could not merge by Structure. {}", e.getMessage());
}
}
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java
index 07b163730d..245d4481f6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java
@@ -57,7 +57,7 @@ public void setPair(Pair pair) {
}
public double getMinDistance() {
- if (atomContacts.size()==0) return 0;
+ if (atomContacts.isEmpty()) return 0;
double minDistance = Double.MAX_VALUE;
for (AtomContact atomContact:atomContacts) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
index 60f7c3a91b..00cf7ef65c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
@@ -380,7 +380,7 @@ public List getClusters(double contactOverlapScoreClu
clusters = new ArrayList<>();
// nothing to do if we have no interfaces
- if (list.size()==0) return clusters;
+ if (list.isEmpty()) return clusters;
logger.debug("Calculating all-vs-all Jaccard scores for {} interfaces", list.size());
double[][] matrix = new double[list.size()][list.size()];
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
index f4be5cd4f5..027907ffa6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
@@ -137,9 +137,15 @@ public List getDomainsForPdb(String id) throws IOException {
// unlock to allow ensureDomainsFileInstalled to get the write lock
logger.trace("UNLOCK readlock");
domainsFileLock.readLock().unlock();
- indexDomains();
- domainsFileLock.readLock().lock();
- logger.trace("LOCK readlock");
+ try {
+ indexDomains();
+ } finally {
+ // re-acquire even if indexing failed, so the outer finally has a
+ // lock to release; otherwise IllegalMonitorStateException replaces
+ // the real cause and the failure becomes unreadable
+ domainsFileLock.readLock().lock();
+ logger.trace("LOCK readlock");
+ }
}
PdbId pdbId = null;
@@ -244,9 +250,15 @@ public List getAllDomains() throws IOException {
// unlock to allow ensureDomainsFileInstalled to get the write lock
logger.trace("UNLOCK readlock");
domainsFileLock.readLock().unlock();
- ensureDomainsFileInstalled();
- domainsFileLock.readLock().lock();
- logger.trace("LOCK readlock");
+ try {
+ ensureDomainsFileInstalled();
+ } finally {
+ // re-acquire even if the download failed, so the outer finally has a
+ // lock to release; otherwise IllegalMonitorStateException replaces
+ // the real cause and the failure becomes unreadable
+ domainsFileLock.readLock().lock();
+ logger.trace("LOCK readlock");
+ }
}
return allDomains;
} finally {
@@ -272,12 +284,41 @@ public void clear() {
*
* Note that this may differ from the version requested in the constructor
* for the special case of "latest"
+ *
+ * Since 7.3.0 this reads only the file's header rather than parsing the whole
+ * file, so it no longer has the side effect of loading every domain.
* @return the ECOD version
* @throws IOException If an error occurs while downloading or parsing the file
*/
@Override
public String getVersion() throws IOException {
- ensureDomainsFileInstalled();
+ domainsFileLock.readLock().lock();
+ logger.trace("LOCK readlock");
+ try {
+ if( parsedVersion != null ) {
+ return parsedVersion;
+ }
+ } finally {
+ logger.trace("UNLOCK readlock");
+ domainsFileLock.readLock().unlock();
+ }
+
+ // The version is declared in the first few lines of the file, so read those rather
+ // than the millions of domain records behind them. The current release is 657 MB and
+ // holds nearly three million records; parsing it in full to answer this question
+ // costs over a gigabyte of heap and several seconds.
+ ensureDomainsFileDownloaded();
+
+ domainsFileLock.writeLock().lock();
+ logger.trace("LOCK writelock");
+ try {
+ if( parsedVersion == null ) {
+ parsedVersion = parseVersionOnly();
+ }
+ } finally {
+ logger.trace("UNLOCK writelock");
+ domainsFileLock.writeLock().unlock();
+ }
if( parsedVersion == null) {
return requestedVersion;
@@ -285,6 +326,30 @@ public String getVersion() throws IOException {
return parsedVersion;
}
+ /**
+ * Reads the version from the header of the local domains file without parsing the
+ * domains themselves.
+ * @return the version, or null if the header does not declare one
+ * @throws IOException if the file cannot be read
+ * @since 7.3.0
+ */
+ private String parseVersionOnly() throws IOException {
+ try( BufferedReader in = new BufferedReader(new FileReader(getDomainFile())) ) {
+ String line;
+ while( (line = in.readLine()) != null ) {
+ Matcher match = EcodParser.VERSION_RE.matcher(line);
+ if( match.matches() ) {
+ return match.group(1);
+ }
+ if( !line.startsWith("#") ) {
+ // past the header block; from v294.1 the column names are not commented
+ return null;
+ }
+ }
+ }
+ return null;
+ }
+
/**
* Get the top-level ECOD server URL. Defaults to "http://prodata.swmed.edu"
* @return the url to the ecod server
@@ -325,6 +390,24 @@ public void setCacheLocation(String cacheLocation) {
domainsFileLock.writeLock().unlock();
}
+ /**
+ * Ensures the domains file is present and current locally, without parsing it.
+ * @throws IOException in cases of file I/O, including failure to download a healthy file
+ * @since 7.3.0
+ */
+ private void ensureDomainsFileDownloaded() throws IOException {
+ domainsFileLock.writeLock().lock();
+ logger.trace("LOCK writelock");
+ try {
+ if( !domainsAvailable() ) {
+ downloadDomains();
+ }
+ } finally {
+ logger.trace("UNLOCK writelock");
+ domainsFileLock.writeLock().unlock();
+ }
+ }
+
/**
* Blocks until ECOD domains file has been downloaded and parsed.
*
@@ -549,6 +632,24 @@ Current version (1.4) contains the following columns:
v1.2 - added f-group identifiers to fasta file, domain description file. ECODf identifiers now used when available for F-group name.
Domain assemblies now represented by assembly uid in domain assembly status.
v1.4 - added seqid_range and headers (develop101)
+v1.6 - renamed column 4 from f_id to t_id and inserted unp_acc (UniProt accession) as
+ column 9, giving 16 columns (seen in develop291)
+
+From v294.1 the distribution was redesigned. The header comment changed from
+"#ECOD version develop291" to "# Version: v294.1", the column header row is no longer
+commented out, and the columns became:
+
+ uid ecod_domain_id manual_rep f_id pdb chain pdb_range seqid_range architecture_name
+ x_name h_name t_name f_name assembly_id domain_id_short range_count arch_manual
+ x_manual h_manual t_manual f_manual valid_structure ligand_binding
+
+v295 appends ligand_comp_ids and ligand_pdbnum, for 25 columns. Also note that
+manual_rep now holds True/False rather than MANUAL_REP/AUTO_NONREP, that assembly_id
+and domain_id_short are empty on every row, that f_name is empty rather than
+F_UNCLASSIFIED for unclassified domains, and that uid restarts from 0.
+
+Because the columns have been renamed, reordered and added to repeatedly, files that
+declare a column header are read by column name rather than by position.
*/
/** String for unclassified F-groups */
@@ -561,10 +662,28 @@ Current version (1.4) contains the following columns:
public static final String IS_REPRESENTATIVE = "MANUAL_REP";
/** Indicates not a manual representative */
public static final String NOT_REPRESENTATIVE = "AUTO_NONREP";
+ /**
+ * Matches the comment declaring the version, which has taken two forms:
+ * {@code #ECOD version develop291} up to develop292, and {@code # Version: v295}
+ * from v294.1 onwards.
+ * @since 7.3.0
+ */
+ static final Pattern VERSION_RE = Pattern.compile(
+ "^\\s*#\\s*(?:ECOD\\s+)?version\\s*:?\\s*(\\S+).*", Pattern.CASE_INSENSITIVE);
private List domains;
private String version;
+ // prevent too many warnings; negative numbers print all warnings
+ private int warnIsDomainAssembly = 1;
+ private int warnHierarchicalFormat = 5;
+ private int warnNumberOfFields = 10;
+ private int warnNumberFormat = 10;
+ /** Data lines that could not be turned into a domain, for the summary at the end */
+ private int skippedLines = 0;
+ /** Data lines describing a domain in a computed model rather than a PDB entry */
+ private int modelLines = 0;
+
public EcodParser(String filename) throws IOException {
this(new File(filename));
}
@@ -584,30 +703,55 @@ private void parse(BufferedReader in) throws IOException {
// Allocate plenty of space for ECOD as of 2015
ArrayList domainsList = new ArrayList<>(500000);
- Pattern versionRE = Pattern.compile("^\\s*#.*ECOD\\s*version\\s+(\\S+).*");
Pattern commentRE = Pattern.compile("^\\s*#.*");
- // prevent too many warnings; negative numbers print all warnings
- int warnIsDomainAssembly = 1;
- int warnHierarchicalFormat = 5;
- int warnNumberOfFields = 10;
+ ColumnLayout layout = null;
String line = in.readLine();
int lineNum = 1;
while( line != null ) {
// Check for requestedVersion string
- Matcher match = versionRE.matcher(line);
+ Matcher match = VERSION_RE.matcher(line);
if(match.matches()) {
// special requestedVersion comment
this.version = match.group(1);
+ } else if( ColumnLayout.isColumnHeader(line) ) {
+ // The column names. Since the columns have been renamed, reordered and
+ // added to several times, later lines are read by name rather than by
+ // position wherever this header is present (develop101 onwards).
+ layout = ColumnLayout.fromHeader(line);
+ logger.debug("Read ECOD column header at line {}: {} columns",lineNum,layout.size());
} else {
match = commentRE.matcher(line);
if(match.matches()) {
// ignore comments
} else {
- // data line
- String[] fields = line.split("\t");
- if( fields.length == 13 || fields.length == 14 || fields.length == 15) {
+ // data line. The last column is frequently empty, so keep trailing
+ // empty fields rather than letting split() discard them.
+ String[] fields = line.split("\t", -1);
+ if( layout != null ) {
+ String pdb = layout.get(fields, "pdb");
+ if( pdb != null && pdb.isEmpty() ) {
+ // From v294.1 the distribution also classifies domains
+ // found in computed (AlphaFold) models, which have no PDB
+ // entry and so cannot be represented by an EcodDomain.
+ modelLines++;
+ } else {
+ try {
+ EcodDomain domain = parseDomain(fields, layout, lineNum);
+ if(domain != null) {
+ domainsList.add(domain);
+ } else {
+ skippedLines++;
+ warnMissingColumns(lineNum);
+ }
+ } catch(IllegalArgumentException e) {
+ // includes NumberFormatException and an unusable PDB id
+ skippedLines++;
+ warnUnparseableLine(lineNum, e);
+ }
+ }
+ } else if( fields.length == 13 || fields.length == 14 || fields.length == 15) {
try {
int i = 0; // field number, to allow future insertion of fields
@@ -620,32 +764,16 @@ private void parse(BufferedReader in) throws IOException {
// Manual column may be missing in version 1.0 files
Boolean manual = null;
if( fields.length >= 14) {
- String manualString = fields[i++];
- if(manualString.equalsIgnoreCase(IS_REPRESENTATIVE)) {
- manual = true;
- } else if(manualString.equalsIgnoreCase(NOT_REPRESENTATIVE)) {
- manual = false;
- } else {
- logger.warn("Unexpected value for manual field: {} in line {}",manualString,lineNum);
- }
+ manual = parseManualRep(fields[i++], lineNum);
}
//Column 4: ECOD hierachy identifier - [X-group].[H-group].[T-group].[F-group]
// hierarchical field, e.g. "1.1.4.1"
- String[] xhtGroup = fields[i++].split("\\.");
- if(xhtGroup.length < 3 || 4 < xhtGroup.length) {
- if(warnHierarchicalFormat > 1) {
- logger.warn("Unexpected format for hierarchical field \"{}\" in line {}",fields[i-1],lineNum);
- warnHierarchicalFormat--;
- } else if(warnHierarchicalFormat != 0) {
- logger.warn("Unexpected format for hierarchical field \"{}\" in line {}. Not printing future similar warnings.",fields[i-1],lineNum);
- warnHierarchicalFormat--;
- }
- }
- Integer xGroup = xhtGroup.length>0 ? Integer.parseInt(xhtGroup[0]) : null;
- Integer hGroup = xhtGroup.length>1 ? Integer.parseInt(xhtGroup[1]) : null;
- Integer tGroup = xhtGroup.length>2 ? Integer.parseInt(xhtGroup[2]) : null;
- Integer fGroup = xhtGroup.length>3 ? Integer.parseInt(xhtGroup[3]) : null;
+ Integer[] xhtfGroup = parseHierarchy(fields[i++], lineNum);
+ Integer xGroup = xhtfGroup[0];
+ Integer hGroup = xhtfGroup[1];
+ Integer tGroup = xhtfGroup[2];
+ Integer fGroup = xhtfGroup[3];
//Column 5: PDB identifier
String pdbId = fields[i++];
@@ -699,32 +827,18 @@ private void parse(BufferedReader in) throws IOException {
assemblyId = Long.parseLong(assemblyStr);
}
- String ligandStr = fields[i++];
- Set ligands = null;
- if( "NO_LIGANDS_4A".equals(ligandStr) || ligandStr.isEmpty() ) {
- ligands = Collections.emptySet();
- } else {
- String[] ligSplit = ligandStr.split(",");
- ligands = new LinkedHashSet<>(ligSplit.length);
- for(String s : ligSplit) {
- ligands.add(s.intern());
- }
- }
+ Set ligands = parseLigands(fields[i++]);
EcodDomain domain = new EcodDomain(uid, domainId, manual, xGroup, hGroup, tGroup, fGroup,pdbId, chainId, range, seqId, architectureName, xGroupName, hGroupName, tGroupName, fGroupName, assemblyId, ligands);
domainsList.add(domain);
} catch(NumberFormatException e) {
- logger.warn("Error in ECOD parsing at line "+lineNum,e);
+ skippedLines++;
+ warnUnparseableLine(lineNum, e);
}
} else {
- if(warnNumberOfFields > 1) {
- logger.warn("Unexpected number of fields in line {}.",lineNum);
- warnNumberOfFields--;
- } else if(warnNumberOfFields == 0) {
- logger.warn("Unexpected number of fields in line {}. Not printing future similar warnings",lineNum);
- warnIsDomainAssembly--;
- }
+ skippedLines++;
+ warnMissingColumns(lineNum);
}
}
}
@@ -737,6 +851,23 @@ private void parse(BufferedReader in) throws IOException {
else
logger.info("Parsed {} ECOD domains from version {}",domainsList.size(),this.version);
+ if(modelLines > 0) {
+ logger.info("Ignored {} ECOD domains classified from computed models, "
+ + "which have no PDB entry", modelLines);
+ }
+
+ if(domainsList.isEmpty() && skippedLines > 0) {
+ // Returning an empty list quietly is how an upstream format change went
+ // unnoticed for eight months. Say so instead.
+ logger.error("Parsed no ECOD domains from {} data lines of version {}. "
+ + "The file format has probably changed; please report this at "
+ + "https://github.com/biojava/biojava/issues", skippedLines,
+ this.version == null ? "unknown" : this.version);
+ } else if(skippedLines > 0) {
+ logger.warn("Skipped {} of {} ECOD data lines that could not be parsed",
+ skippedLines, skippedLines + domainsList.size());
+ }
+
this.domains = Collections.unmodifiableList( domainsList );
@@ -747,6 +878,169 @@ private void parse(BufferedReader in) throws IOException {
}
}
+ /**
+ * Builds a domain from a data line using the column names the file declares in its
+ * header, rather than fixed offsets. This is what allows one parser to read the
+ * 15-column develop101 layout, the 16-column develop291 layout (which inserts
+ * {@code unp_acc}) and the 23- and 25-column v294.1 and v295 layouts.
+ * @param fields the tab-separated values of one data line
+ * @param layout the column names read from the file's header
+ * @param lineNum the line number, for warnings
+ * @return the domain, or null if the line does not carry every required column
+ * @throws NumberFormatException if a numeric column does not hold a number
+ * @since 7.3.0
+ */
+ private EcodDomain parseDomain(String[] fields, ColumnLayout layout, int lineNum) {
+ String uidStr = layout.get(fields, "uid");
+ String domainId = layout.get(fields, "ecod_domain_id");
+ // renamed from t_id to f_id when the hierarchy gained a fourth level
+ String hierarchy = layout.get(fields, "f_id", "t_id");
+ String pdbId = layout.get(fields, "pdb");
+ String chainId = layout.get(fields, "chain");
+ String range = layout.get(fields, "pdb_range");
+ if( uidStr == null || domainId == null || hierarchy == null
+ || pdbId == null || chainId == null || range == null ) {
+ return null;
+ }
+
+ Long uid = Long.parseLong(uidStr);
+ Boolean manual = parseManualRep(layout.get(fields, "manual_rep"), lineNum);
+ Integer[] xhtfGroup = parseHierarchy(hierarchy, lineNum);
+ // absent before version 1.4
+ String seqId = layout.get(fields, "seqid_range");
+
+ String architectureName = internName(layout.get(fields, "architecture_name", "arch_name"));
+ String xGroupName = internName(layout.get(fields, "x_name"));
+ String hGroupName = internName(layout.get(fields, "h_name"));
+ String tGroupName = internName(layout.get(fields, "t_name"));
+ // Up to develop292 an unclassified domain carried F_UNCLASSIFIED here. From
+ // v294.1 the name is simply empty, while f_id still classifies the domain to
+ // four levels, so the two are no longer equivalent and the empty value is
+ // deliberately left as it is rather than translated.
+ String fGroupName = internName(layout.get(fields, "f_name"));
+
+ // v294.1 and later declare assembly_id but leave it empty on every row, which
+ // means the same as the NOT_DOMAIN_ASSEMBLY of earlier versions.
+ Long assemblyId = null;
+ String assemblyStr = layout.get(fields, "assembly_id", "asm_status");
+ if( assemblyStr == null || assemblyStr.isEmpty() || NOT_DOMAIN_ASSEMBLY.equals(assemblyStr) ) {
+ assemblyId = uid;
+ } else if( IS_DOMAIN_ASSEMBLY.equals(assemblyStr) ) {
+ warnDomainAssembly(lineNum);
+ } else {
+ assemblyId = Long.parseLong(assemblyStr);
+ }
+
+ // the ligand list moved from the last column to ligand_comp_ids in v295
+ Set ligands = parseLigands(layout.get(fields, "ligand_comp_ids", "ligand"));
+
+ return new EcodDomain(uid, domainId, manual, xhtfGroup[0], xhtfGroup[1], xhtfGroup[2],
+ xhtfGroup[3], pdbId, chainId, range, seqId, architectureName, xGroupName,
+ hGroupName, tGroupName, fGroupName, assemblyId, ligands);
+ }
+
+ /**
+ * Reads the representative-status column, which held MANUAL_REP or AUTO_NONREP up to
+ * develop292 and True or False from v294.1 onwards.
+ * @return true, false, or null if the column is absent or unrecognised
+ * @since 7.3.0
+ */
+ private Boolean parseManualRep(String manualString, int lineNum) {
+ if(manualString == null) {
+ return null;
+ }
+ if(manualString.equalsIgnoreCase(IS_REPRESENTATIVE) || manualString.equalsIgnoreCase("true")) {
+ return true;
+ }
+ if(manualString.equalsIgnoreCase(NOT_REPRESENTATIVE) || manualString.equalsIgnoreCase("false")) {
+ return false;
+ }
+ logger.warn("Unexpected value for manual field: {} in line {}",manualString,lineNum);
+ return null;
+ }
+
+ /**
+ * Splits the hierarchical identifier, e.g. "1.1.4.1".
+ * @return the X, H, T and F group numbers, any of which may be null if absent
+ * @since 7.3.0
+ */
+ private Integer[] parseHierarchy(String hierarchy, int lineNum) {
+ String[] xhtGroup = hierarchy.split("\\.");
+ if(xhtGroup.length < 3 || 4 < xhtGroup.length) {
+ if(warnHierarchicalFormat > 1) {
+ logger.warn("Unexpected format for hierarchical field \"{}\" in line {}",hierarchy,lineNum);
+ warnHierarchicalFormat--;
+ } else if(warnHierarchicalFormat != 0) {
+ logger.warn("Unexpected format for hierarchical field \"{}\" in line {}. Not printing future similar warnings.",hierarchy,lineNum);
+ warnHierarchicalFormat--;
+ }
+ }
+ Integer[] groups = new Integer[4];
+ for(int j = 0; j < groups.length && j < xhtGroup.length; j++) {
+ groups[j] = Integer.parseInt(xhtGroup[j]);
+ }
+ return groups;
+ }
+
+ /**
+ * Reads a comma-separated list of non-polymer entities close to the domain.
+ * @return the ligands, or an empty set for NO_LIGANDS_4A, an empty value or no column
+ * @since 7.3.0
+ */
+ private Set parseLigands(String ligandStr) {
+ if( ligandStr == null || ligandStr.isEmpty() || "NO_LIGANDS_4A".equals(ligandStr) ) {
+ return Collections.emptySet();
+ }
+ String[] ligSplit = ligandStr.split(",");
+ Set ligands = new LinkedHashSet<>(ligSplit.length);
+ for(String s : ligSplit) {
+ ligands.add(s.intern());
+ }
+ return ligands;
+ }
+
+ /**
+ * Interns a name likely to be shared by many domains, stripping the quotes that
+ * versions up to develop292 wrapped some of them in.
+ * @since 7.3.0
+ */
+ private String internName(String name) {
+ if(name == null) {
+ return null;
+ }
+ return clearStringQuotes(name).intern();
+ }
+
+ private void warnDomainAssembly(int lineNum) {
+ if(warnIsDomainAssembly > 1) {
+ logger.info("Deprecated 'IS_DOMAIN_ASSEMBLY' value ignored in line {}.",lineNum);
+ warnIsDomainAssembly--;
+ } else if(warnIsDomainAssembly == 0) {
+ logger.info("Deprecated 'IS_DOMAIN_ASSEMBLY' value ignored in line {}. Not printing future similar warnings.",lineNum);
+ warnIsDomainAssembly--;
+ }
+ }
+
+ private void warnMissingColumns(int lineNum) {
+ if(warnNumberOfFields > 1) {
+ logger.warn("Unexpected number of fields in line {}.",lineNum);
+ warnNumberOfFields--;
+ } else if(warnNumberOfFields == 1) {
+ logger.warn("Unexpected number of fields in line {}. Not printing future similar warnings",lineNum);
+ warnNumberOfFields--;
+ }
+ }
+
+ private void warnUnparseableLine(int lineNum, IllegalArgumentException e) {
+ if(warnNumberFormat > 1) {
+ logger.warn("Error in ECOD parsing at line {}: {}", lineNum, e.getMessage());
+ warnNumberFormat--;
+ } else if(warnNumberFormat == 1) {
+ logger.warn("Error in ECOD parsing at line {}: {}. Not printing future similar warnings", lineNum, e.getMessage());
+ warnNumberFormat--;
+ }
+ }
+
private String clearStringQuotes(String name) {
if ( name.startsWith("\""))
name = name.substring(1);
@@ -770,6 +1064,77 @@ public List getDomains() {
public String getVersion() {
return version;
}
+
+ /**
+ * Maps the column names an ECOD domain file declares in its header onto their
+ * positions, so a data line can be read by name rather than by offset.
+ *
+ * Every distribution since develop101 carries such a header. It is commented
+ * (#uid<tab>ecod_domain_id<tab>...) up to develop292 and
+ * uncommented (uid<tab>ecod_domain_id<tab>...) from v294.1
+ * onwards. Because names have also been changed between versions, lookups accept
+ * aliases and any name the file does not declare simply reads as absent.
+ *
+ * @author Amr ALHOSSARY
+ * @since 7.3.0
+ */
+ private static class ColumnLayout {
+ private final Map columns;
+
+ private ColumnLayout(Map columns) {
+ this.columns = columns;
+ }
+
+ /**
+ * @return true if this line names the columns rather than holding domain data
+ */
+ public static boolean isColumnHeader(String line) {
+ int tab = line.indexOf('\t');
+ if(tab < 0) {
+ return false;
+ }
+ String first = line.substring(0, tab).trim();
+ if(first.startsWith("#")) {
+ first = first.substring(1).trim();
+ }
+ return first.equalsIgnoreCase("uid");
+ }
+
+ public static ColumnLayout fromHeader(String line) {
+ String[] names = line.split("\t", -1);
+ Map columns = new HashMap<>(names.length * 2);
+ for(int i = 0; i < names.length; i++) {
+ String name = names[i].trim();
+ if(i == 0 && name.startsWith("#")) {
+ name = name.substring(1).trim();
+ }
+ if(!name.isEmpty()) {
+ columns.put(name.toLowerCase(), i);
+ }
+ }
+ return new ColumnLayout(columns);
+ }
+
+ /**
+ * @param fields the values of one data line
+ * @param aliases the names this column has gone by, most recent first
+ * @return the value of the first alias the file declares, or null if it declares
+ * none of them or this line is too short to reach it
+ */
+ public String get(String[] fields, String... aliases) {
+ for(String alias : aliases) {
+ Integer i = columns.get(alias);
+ if(i != null) {
+ return i < fields.length ? fields[i] : null;
+ }
+ }
+ return null;
+ }
+
+ public int size() {
+ return columns.size();
+ }
+ }
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
index 8cfd032daa..5a6e69c4cf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
@@ -72,7 +72,7 @@ public void addPoint(Point3d point, double mass) {
public Point3d getCenterOfMass() {
- if (points.size() == 0) {
+ if (points.isEmpty()) {
throw new IllegalStateException(
"MomentsOfInertia: no points defined");
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
index e6b8548025..e81f7fb867 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
@@ -273,7 +273,7 @@ private void trimBondLists() {
for (Chain chain : structure.getChains(modelInd)) {
for (Group group : chain.getAtomGroups()) {
for (Atom atom : group.getAtoms()) {
- if (atom.getBonds()!=null && atom.getBonds().size() > 0) {
+ if (atom.getBonds()!=null && !atom.getBonds().isEmpty()) {
((ArrayList) atom.getBonds()).trimToSize();
}
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
index 4ec4577f59..2e6b09fe9a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
@@ -550,7 +550,7 @@ private File downloadStructure(PdbId pdbId, String pathOnServer, boolean obsolet
ftp = DEFAULT_BCIF_FILE_SERVER + filename;
} else {
ftp = String.format("%s%s/%s/%s",
- serverName, pathOnServer, id.substring(id.length()-3, id.length()-1), getFilename(id));
+ serverName, pathOnServer, getMiddleHash(id), getFilename(id));
}
URL url = new URL(ftp);
@@ -576,21 +576,45 @@ private File downloadStructure(PdbId pdbId, String pathOnServer, boolean obsolet
logger.info("Fetching {}", ftp);
logger.info("Writing to {}", realFile);
- FileDownloadUtils.createValidationFiles(url, realFile, null, FileDownloadUtils.Hash.UNKNOWN);
- FileDownloadUtils.downloadFile(url, realFile);
+ // A single connection, so the recorded size and checksum describe exactly the
+ // bytes that were written. The wwPDB servers return the content MD5 as the
+ // ETag, so this also gives the cached file a real integrity check.
+ FileDownloadUtils.downloadFileWithValidation(url, realFile, null, FileDownloadUtils.Hash.UNKNOWN,
+ FileDownloadUtils.ETagPolicy.USE_IF_HEX_DIGEST);
if(! FileDownloadUtils.validateFile(realFile))
throw new IOException("Downloaded file invalid: "+realFile);
return realFile;
}
+ /**
+ * Returns the two-character directory name under which an entry is filed in the
+ * PDB's divided layout, e.g. cb for 1cbs.
+ *
+ * The characters are taken relative to the end of the identifier rather
+ * than the start, so that both spellings of the same entry land in the same
+ * bucket: 1cbs and its extended form pdb_00001cbs both
+ * give cb. Taking them from the start would file the extended form
+ * under db instead. The extended PDB identifier format is expected
+ * to keep using this same hashing scheme.
+ *
+ * @param pdbId a PDB identifier, in either the short or the extended form
+ * @return the lowercase two-character directory name
+ * @since 7.3.0
+ */
+ public static String getMiddleHash(String pdbId) {
+ int offset = pdbId.length() - 3;
+ return pdbId.substring(offset, offset + 2).toLowerCase();
+ }
+
/**
* Get the last modified time of the file in given url by retrieveing the "Last-Modified" header.
* Note that this only works for http URLs
* @param url
* @return the last modified date or null if it couldn't be retrieved (in that case a warning will be logged)
+ * @since 7.3.0 made public so that other caching code can reuse it
*/
- private Date getLastModifiedTime(URL url) {
+ public static Date getLastModifiedTime(URL url) {
// see http://stackoverflow.com/questions/2416872/how-do-you-obtain-modified-date-from-a-remote-file-java
Date date = null;
@@ -629,14 +653,12 @@ private Date getLastModifiedTime(URL url) {
protected File getDir(String pdbId, boolean obsolete) {
File dir = null;
- int offset = pdbId.length() - 3;
+ String middle = getMiddleHash(pdbId);
if (obsolete) {
// obsolete is always split
- String middle = pdbId.substring(offset, offset + 2).toLowerCase();
dir = new File(obsoleteDirPath, middle);
} else {
- String middle = pdbId.substring(offset, offset + 2).toLowerCase();
dir = new File(splitDirPath, middle);
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
index 176459bbf2..b1d327599e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
@@ -1406,7 +1406,7 @@ public void handleResolutionLine(String line, Pattern pR) {
try {
float res = Float.parseFloat(resString);
final float resInHeader = pdbHeader.getResolution();
- if (resInHeader!=PDBHeader.DEFAULT_RESOLUTION && resInHeader != res) {
+ if (resInHeader!=PDBHeader.DEFAULT_RESOLUTION && Math.abs(resInHeader - res) > 0.001) {
logger.warn("More than 1 resolution value present, will use last one {} and discard previous {} "
,resString, String.format("%4.2f",resInHeader));
}
@@ -1943,7 +1943,7 @@ private Group getCorrectAltLocGroup( Character altLoc,
// see if we know this altLoc already;
List atoms = currentGroup.getAtoms();
- if ( atoms.size() > 0) {
+ if (!atoms.isEmpty()) {
Atom a1 = atoms.get(0);
// we are just adding atoms to the current group
// probably there is a second group following later...
@@ -1956,7 +1956,7 @@ private Group getCorrectAltLocGroup( Character altLoc,
List altLocs = currentGroup.getAltLocs();
for ( Group altLocG : altLocs ){
atoms = altLocG.getAtoms();
- if ( atoms.size() > 0) {
+ if (!atoms.isEmpty()) {
for ( Atom a1 : atoms) {
if (a1.getAltLoc().equals( altLoc)) {
@@ -1970,7 +1970,7 @@ private Group getCorrectAltLocGroup( Character altLoc,
// build it up.
if ( groupCode3.equals(currentGroup.getPDBName())) {
- if ( currentGroup.getAtoms().size() == 0) {
+ if ( currentGroup.getAtoms().isEmpty()) {
//System.out.println("current group is empty " + current_group + " " + altLoc);
return currentGroup;
}
@@ -2762,7 +2762,7 @@ private void makeCompounds(List compoundList,
}
// System.out.println("[makeCompounds] adding sources to compounds from sourceLines");
// since we're starting again from the first compound, reset it here
- if ( entities.size() == 0){
+ if ( entities.isEmpty()){
current_compound = new EntityInfo();
} else {
current_compound = entities.get(0);
@@ -2921,7 +2921,7 @@ private void triggerEndFileChecks(){
pdbHeader.setBioAssemblies(bioAssemblyParser.getTransformationMap());
}
- if (ncsOperators !=null && ncsOperators.size()>0) {
+ if (ncsOperators !=null && !ncsOperators.isEmpty()) {
crystallographicInfo.setNcsOperators(
ncsOperators.toArray(new Matrix4d[ncsOperators.size()]));
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java
index 7ee21de4b4..0652ad1809 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java
@@ -198,7 +198,7 @@ public void mapSeqresRecords(Chain atomRes, Chain seqRes) {
}
}
- if ( atomRes.getAtomGroups(GroupType.AMINOACID).size() < 1) {
+ if (atomRes.getAtomGroups(GroupType.AMINOACID).isEmpty()) {
logger.debug("ATOM chain {} does not contain amino acids, ignoring...", atomRes.getId());
return;
}
@@ -215,7 +215,7 @@ public void mapSeqresRecords(Chain atomRes, Chain seqRes) {
private void alignNucleotideChains(Chain seqRes, Chain atomRes) {
- if ( atomRes.getAtomGroups(GroupType.NUCLEOTIDE).size() < 1) {
+ if (atomRes.getAtomGroups(GroupType.NUCLEOTIDE).isEmpty()) {
logger.debug("ATOM chain {} does not contain nucleotides, ignoring...", atomRes.getId());
return;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java
index 826d9588ef..e43565c827 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java
@@ -40,8 +40,27 @@ protected CifFile getInternal(Structure structure, List wrappedAtom
// entity information
List entityInfos = structure.getEntityInfos();
+ PdbId pdbId = structure.getPdbId();
+
MmCifBlockBuilder blockBuilder = CifBuilder.enterFile(StandardSchemata.MMCIF)
- .enterBlock(structure.getPdbId() == null? "" : structure.getPdbId().getId());
+ .enterBlock(pdbId == null? "" : pdbId.getId());
+
+ if (pdbId != null) {
+ // The block header alone does not carry the identifier for consumers: readers pick it up from
+ // _entry.id (e.g. Jmol) or from _struct.entry_id (BioJava's own CifStructureConsumerImpl).
+ // Both are written so that the identifier survives a write-then-read round trip either way.
+ blockBuilder.enterEntry()
+ .enterId()
+ .add(pdbId.getId())
+ .leaveColumn()
+ .leaveCategory();
+
+ blockBuilder.enterStruct()
+ .enterEntryId()
+ .add(pdbId.getId())
+ .leaveColumn()
+ .leaveCategory();
+ }
blockBuilder.enterStructKeywords().enterText()
.add(String.join(", ", structure.getPDBHeader().getKeywords()))
@@ -308,7 +327,13 @@ public void accept(WrappedAtom wrappedAtom) {
}
}
labelEntityId.add(entityId);
- labelSeqId.add(seqId);
+ // see https://github.com/biojava/biojava/issues/1116
+ // note the first condition is to safeguard and to have a default that writes labelSeqId if there's no knowledge about what's the entity type
+ if (chain.getEntityInfo()==null || chain.getEntityInfo().getType() == EntityType.POLYMER) {
+ labelSeqId.add(seqId);
+ } else {
+ labelSeqId.markNextNotPresent();
+ }
String insCode = "";
if (group.getResidueNumber().getInsCode() != null) {
insCode = Character.toString(group.getResidueNumber().getInsCode());
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
index 67514edd84..f44eb44ab1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -372,7 +372,7 @@ public void consumeAtomSite(AtomSite atomSite) {
private Group getAltLocGroup(String recordName, Character altLoc, Character oneLetterCode, String threeLetterCode,
long seqId) {
List atoms = currentGroup.getAtoms();
- if (atoms.size() > 0) {
+ if (!atoms.isEmpty()) {
if (atoms.get(0).getAltLoc().equals(altLoc)) {
return currentGroup;
}
@@ -381,7 +381,7 @@ private Group getAltLocGroup(String recordName, Character altLoc, Character oneL
List altLocs = currentGroup.getAltLocs();
for (Group altLocGroup : altLocs) {
atoms = altLocGroup.getAtoms();
- if (atoms.size() > 0) {
+ if (!atoms.isEmpty()) {
for (Atom a1 : atoms) {
if (a1.getAltLoc().equals(altLoc)) {
return altLocGroup;
@@ -630,7 +630,8 @@ public void consumeDatabasePDBRev(DatabasePDBRev databasePDBrev) {
modDate = relDate;
} else {
String dbrev = databasePDBrev.getDate().get(rowIndex);
- modDate = convert(LocalDate.parse(dbrev, DATE_FORMAT));
+ if (dbrev != null && !dbrev.isBlank())
+ modDate = convert(LocalDate.parse(dbrev, DATE_FORMAT));
}
pdbHeader.setModDate(modDate);
}
@@ -855,7 +856,8 @@ public void consumeRefine(Refine refine) {
// we take the last one found so that behaviour is like in PDB file parsing
double lsDResHigh = refine.getLsDResHigh().get(rowIndex);
// TODO this could use a check to keep reasonable values - 1.5 may be overwritten by 0.0
- if (pdbHeader.getResolution() != PDBHeader.DEFAULT_RESOLUTION) {
+ if (pdbHeader.getResolution() != PDBHeader.DEFAULT_RESOLUTION &&
+ Math.abs(pdbHeader.getResolution() - lsDResHigh) > 0.001) {
logger.warn("More than 1 resolution value present, will use last one {} and discard previous {}",
lsDResHigh, String.format("%4.2f",pdbHeader.getResolution()));
}
@@ -1478,7 +1480,7 @@ private void setStructNcsOps() {
}
}
- if (ncsOperators.size() > 0) {
+ if (!ncsOperators.isEmpty()) {
structure.getCrystallographicInfo()
.setNcsOperators(ncsOperators.toArray(new Matrix4d[0]));
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
index c2830c1685..865c9e0da4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
@@ -372,7 +372,7 @@ public void setInterGroupBond(int indOne, int indTwo, int bondOrder) {
private Group getCorrectAltLocGroup(Character altLoc) {
// see if we know this altLoc already;
List atoms = group.getAtoms();
- if (atoms.size() > 0) {
+ if (!atoms.isEmpty()) {
Atom a1 = atoms.get(0);
// we are just adding atoms to the current group
// probably there is a second group following later...
@@ -396,7 +396,7 @@ private Group getCorrectAltLocGroup(Character altLoc) {
}
// no matching altLoc group found.
// build it up.
- if (group.getAtoms().size() == 0) {
+ if (group.getAtoms().isEmpty()) {
return group;
}
Group altLocG = (Group) group.clone();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
index 7c359121de..8f76b2ae61 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
@@ -55,7 +55,7 @@ public static boolean isUnaryExpression(String expression) {
if (first < 0 || last < 0) {
return true;
}
- return ! (first == 0 && last > first);
+ return first != 0 || last <= first;
}
public static List parseUnaryOperatorExpression(String operatorExpression) {
@@ -279,7 +279,7 @@ public static double[] getBiologicalMoleculeCentroid( final Structure asymUnit,
return centroid;
}
- if ( transformations.size() == 0) {
+ if ( transformations.isEmpty()) {
return Calc.getCentroid(atoms).getCoords();
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
index c6ec6bc8ff..9edb8f404c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
@@ -205,7 +205,7 @@ private void addChainMultiModel(Structure s, Chain newChain, String transformId)
// multi-model bioassembly
- if ( modelIndex.size() == 0)
+ if (modelIndex.isEmpty())
modelIndex.add("PLACEHOLDER FOR ASYM UNIT");
int modelCount = modelIndex.indexOf(transformId);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java
index 36bccd7b39..ff1efd6e32 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyTransformation.java
@@ -226,7 +226,7 @@ public static BiologicalAssemblyTransformation fromXML(String xml)
List transformations = fromMultiXML(xml);
- if ( transformations.size() > 0)
+ if (!transformations.isEmpty())
return transformations.get(0);
else
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
index d092d5485e..4ac55cfa08 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
@@ -655,7 +655,7 @@ private List extractRanges(String range) {
}
protected void downloadClaFile() throws IOException{
- if(mirrors.size()<1) {
+ if(mirrors.isEmpty()) {
initScopURLs();
}
IOException exception = null;
@@ -676,7 +676,7 @@ protected void downloadClaFile() throws IOException{
}
protected void downloadDesFile() throws IOException{
- if(mirrors.size()<1) {
+ if(mirrors.isEmpty()) {
initScopURLs();
}
IOException exception = null;
@@ -697,7 +697,7 @@ protected void downloadDesFile() throws IOException{
}
protected void downloadHieFile() throws IOException{
- if(mirrors.size()<1) {
+ if(mirrors.isEmpty()) {
initScopURLs();
}
IOException exception = null;
@@ -719,7 +719,7 @@ protected void downloadHieFile() throws IOException{
}
protected void downloadComFile() throws IOException{
- if(mirrors.size()<1) {
+ if(mirrors.isEmpty()) {
initScopURLs();
}
IOException exception = null;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
index 7732c04b80..42191d682d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
@@ -57,7 +57,7 @@ public static List getSecStrucInfo(Structure s) {
Group g = iter.next();
if (g.hasAminoAtoms()) {
Object p = g.getProperty(Group.SEC_STRUC);
- if (!(p == null)) {
+ if (p != null) {
SecStrucInfo ss = (SecStrucInfo) p;
listSSI.add(ss);
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
index ff9c77cf13..cd16aa5f87 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
@@ -64,7 +64,7 @@ public Map getInteractingRepeatUnits() {
private void run() {
this.repeatUnitCenters = calcRepeatUnitCenters();
- if (this.repeatUnitCenters.size() == 0) {
+ if (this.repeatUnitCenters.isEmpty()) {
return;
}
this.repeatUnits = calcRepeatUnits();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
index e1f4792410..b3ac53f385 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
@@ -65,7 +65,7 @@ public void completeGroup() {
Set> known = new HashSet<>(permutations);
//breadth-first search through the map of all members
List> currentLevel = new ArrayList<>(permutations);
- while( currentLevel.size() > 0) {
+ while(!currentLevel.isEmpty()) {
List> nextLevel = new ArrayList<>();
for( List p : currentLevel) {
for(List gen : gens) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
index b0bef7f1e6..7f434cabaf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
@@ -211,7 +211,7 @@ public MomentsOfInertia getMomentsOfInertia() {
}
private void run() {
- if (centers.size() > 0) {
+ if (!centers.isEmpty()) {
return;
}
calcOriginalCenters();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
index 70b69afe14..002d046e52 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
@@ -83,7 +83,7 @@ public void removeRotation(int index) {
public void complete() {
if (modified) {
- if (rotations.size() > 0) {
+ if (!rotations.isEmpty()) {
findHighestOrderAxis();
setEAxis();
calcAxesDirections();
@@ -98,7 +98,7 @@ public void complete() {
public String getPointGroup() {
if (modified) {
- if (rotations.size() == 0) {
+ if (rotations.isEmpty()) {
return "C1";
}
complete();
@@ -344,7 +344,7 @@ private void calcPointGroup() {
// when a structure is symmetric, some subunits are below the rmsd threshold,
// and some are just above the rmsd threshold
int n = 0;
- if (rotations.size() > 0) {
+ if (!rotations.isEmpty()) {
n = rotations.get(0).getPermutation().size();
rotations.clear();
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
index 37a44be7ac..b1566a6d2f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
@@ -305,7 +305,7 @@ private boolean isSpherical() {
* @return null if invalid, or a rotation if valid
*/
private Rotation isValidPermutation(List permutation) {
- if (permutation.size() == 0) {
+ if (permutation.isEmpty()) {
return null;
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
index d13fa4db16..a449771b58 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
@@ -145,7 +145,7 @@ private void completeRotationGroup() {
}
private boolean isValidPermutation(List permutation) {
- if (permutation.size() == 0) {
+ if (permutation.isEmpty()) {
return false;
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java
index 2d9b1d6dca..25d37693fb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java
@@ -166,7 +166,7 @@ private List getBoxTwo(long location) {
}
// ensure that boxTwo has no empty element by copying from tempBox of defined size
List boxTwo = null;
- if (tempBox.size() == 0) {
+ if (tempBox.isEmpty()) {
boxTwo = Collections.emptyList();
} else if (tempBox.size() == 1) {
boxTwo = Collections.singletonList(tempBox.get(0));
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
index a6ad226698..0d52e92fef 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
@@ -79,7 +79,7 @@ public static AFPChain refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
// Refine the alignment Map
Map refined = refineSymmetry(alignment, k);
- if (refined.size() < 1)
+ if (refined.isEmpty())
throw new RefinerFailedException("Refiner returned empty alignment");
//Substitute and partition the alignment
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
index d03e90080f..627908ac8b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
@@ -392,10 +392,7 @@ private boolean checkGaps() {
length--;
}
- if (shrinkColumns.size() != 0)
- return true;
- else
- return false;
+ return !shrinkColumns.isEmpty();
}
/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java
index b2b3298157..5d1faa8754 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/BlastClustReader.java
@@ -140,7 +140,7 @@ public List> getChainIdsInEntry(String pdbId) {
private void loadClusters(int sequenceIdentity) {
// load clusters only once
- if (clusters.size() > 0) {
+ if (!clusters.isEmpty()) {
return;
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
index cff84c70f8..852d213bb9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
@@ -645,10 +645,10 @@ public List getTransfAlgebraic() {
public void setTransfAlgebraic(List transfAlgebraic) {
//System.out.println("setting transfAlgebraic " + transfAlgebraic);
- if ( transformations == null || transformations.size() == 0)
+ if ( transformations == null || transformations.isEmpty())
transformations = new ArrayList(transfAlgebraic.size());
- if ( this.transfAlgebraic == null || this.transfAlgebraic.size() == 0)
+ if ( this.transfAlgebraic == null || this.transfAlgebraic.isEmpty())
this.transfAlgebraic = new ArrayList<>(transfAlgebraic.size());
for ( String transf : transfAlgebraic){
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
index 073a679dbb..f2f06ed2f5 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
@@ -24,6 +24,7 @@
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.assertFalse;
import static org.junit.Assert.fail;
import java.io.File;
@@ -408,7 +409,7 @@ public void testEmptyChemComp() throws IOException, StructureException {
// should be unknown
ChemComp chem = g.getChemComp();
assertNotNull(chem);
- assertTrue(chem.getAtoms().size() > 0);
+ assertFalse(chem.getAtoms().isEmpty());
assertEquals("NON-POLYMER", chem.getType());
} finally {
FileDownloadUtils.deleteDirectory(tmpCache);
@@ -471,7 +472,7 @@ public void testEmptyGZChemComp() throws IOException, StructureException {
// should be unknown
ChemComp chem = g.getChemComp();
assertNotNull(chem);
- assertTrue(chem.getAtoms().size() > 0);
+ assertFalse(chem.getAtoms().isEmpty());
assertEquals("NON-POLYMER", chem.getType());
} finally {
FileDownloadUtils.deleteDirectory(tmpCache);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java
index 7be56be156..c6a268f1f5 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java
@@ -126,19 +126,19 @@ public void testNeighborIndicesFinding() throws StructureException, IOException
AsaCalculator.DEFAULT_PROBE_SIZE,
1000, 1, false);
- AsaCalculator.IndexAndDistance[][] allNbsSh = asaCalc.findNeighborIndicesSpatialHashing();
+ AsaCalculator.Neighbors[] allNbsSh = asaCalc.findNeighborIndicesSpatialHashing();
- AsaCalculator.IndexAndDistance[][] allNbs = asaCalc.findNeighborIndices();
+ AsaCalculator.Neighbors[] allNbs = asaCalc.findNeighborIndices();
for (int indexToTest =0; indexToTest < asaCalc.getAtomCoords().length; indexToTest++) {
//int indexToTest = 198;
- AsaCalculator.IndexAndDistance[] nbsSh = allNbsSh[indexToTest];
- AsaCalculator.IndexAndDistance[] nbs = allNbs[indexToTest];
+ int[] nbsSh = allNbsSh[indexToTest].indices;
+ int[] nbs = allNbs[indexToTest].indices;
List listOfMatchingIndices = new ArrayList<>();
for (int i = 0; i < nbsSh.length; i++) {
for (int j = 0; j < nbs.length; j++) {
- if (nbs[j].index == nbsSh[i].index) {
+ if (nbs[j] == nbsSh[i]) {
listOfMatchingIndices.add(j);
break;
}
@@ -229,21 +229,21 @@ public void testNoNeighborsIssue() {
AsaCalculator.DEFAULT_PROBE_SIZE,
1000, 1);
- AsaCalculator.IndexAndDistance[][] allNbsSh = asaCalc.findNeighborIndicesSpatialHashing();
+ AsaCalculator.Neighbors[] allNbsSh = asaCalc.findNeighborIndicesSpatialHashing();
- AsaCalculator.IndexAndDistance[][] allNbs = asaCalc.findNeighborIndices();
+ AsaCalculator.Neighbors[] allNbs = asaCalc.findNeighborIndices();
assertEquals(3, allNbs.length);
assertEquals(3, allNbsSh.length);
for (int indexToTest =0; indexToTest < asaCalc.getAtomCoords().length; indexToTest++) {
- AsaCalculator.IndexAndDistance[] nbsSh = allNbsSh[indexToTest];
- AsaCalculator.IndexAndDistance[] nbs = allNbs[indexToTest];
+ int[] nbsSh = allNbsSh[indexToTest].indices;
+ int[] nbs = allNbs[indexToTest].indices;
List listOfMatchingIndices = new ArrayList<>();
for (int i = 0; i < nbsSh.length; i++) {
for (int j = 0; j < nbs.length; j++) {
- if (nbs[j].index == nbsSh[i].index) {
+ if (nbs[j] == nbsSh[i]) {
listOfMatchingIndices.add(j);
break;
}
@@ -256,7 +256,7 @@ public void testNoNeighborsIssue() {
}
// first atom should have no neighbors
- assertEquals(0, allNbsSh[0].length);
+ assertEquals(0, allNbsSh[0].indices.length);
}
private Atom getAtom(double x, double y, double z) {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/cath/CathInstallationTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/cath/CathInstallationTest.java
new file mode 100644
index 0000000000..69944cb51c
--- /dev/null
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/cath/CathInstallationTest.java
@@ -0,0 +1,87 @@
+/*
+ * BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence. This should
+ * be distributed with the code. If you do not have a copy,
+ * see:
+ *
+ * http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors. These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ * http://www.biojava.org/
+ */
+package org.biojava.nbio.structure.cath;
+
+import org.junit.jupiter.api.Test;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.StringReader;
+import java.util.concurrent.atomic.AtomicBoolean;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+
+public class CathInstallationTest {
+
+ @Test
+ public void testParseCathDomainListSuccess() throws IOException {
+ String data = "# CATH domain list\n"
+ + "\n"
+ + "1oaiA00 1 10 490 10 1 1 1 1 1 124 1.80\n"
+ + "1oaiA01 1 10 490 10 1 1 1 1 2 150 1.80\n";
+
+ CathInstallation installation = new CathInstallation("");
+ BufferedReader reader = new BufferedReader(new StringReader(data));
+ installation.parseCathDomainList(reader);
+ installation.setInstalledDomainList(new AtomicBoolean(true)); //1
+ installation.setInstalledDomall(new AtomicBoolean(true)); //2
+
+ CathDomain domain = installation.getDomainByCathId("1oaiA00");
+ assertNotNull(domain);
+ assertEquals("1oaiA00", domain.getDomainName());
+ assertEquals(1, domain.getClassId());
+ assertEquals(10, domain.getArchitectureId());
+ assertEquals(490, domain.getTopologyId());
+ assertEquals(10, domain.getHomologyId());
+ assertEquals(124, domain.getLength());
+ assertEquals(1.80, domain.getResolution(), 0.001);
+ }
+
+ @Test
+ public void testParseCathDomainListEmptyThrowsException() {
+ CathInstallation installation = new CathInstallation("");
+ BufferedReader reader = new BufferedReader(new StringReader(""));
+ assertThrows(IOException.class, () -> installation.parseCathDomainList(reader));
+ }
+
+ @Test
+ public void testParseCathDomainListOnlyCommentsAndWhitespaceThrowsException() {
+ String data = "# comment 1\n"
+ + "# comment 2\n"
+ + " \n"
+ + "\t\n";
+ CathInstallation installation = new CathInstallation("");
+ BufferedReader reader = new BufferedReader(new StringReader(data));
+ assertThrows(IOException.class, () -> installation.parseCathDomainList(reader));
+ }
+
+ @Test
+ public void testParseCathDomainListNoParsableLinesThrowsException() {
+ String data = "# comment\n"
+ + "invalid line with too few tokens\n"
+ + "another bad line\n";
+ CathInstallation installation = new CathInstallation("");
+ BufferedReader reader = new BufferedReader(new StringReader(data));
+ IOException exception = assertThrows(IOException.class, () -> installation.parseCathDomainList(reader));
+ assertNotNull(exception.getMessage());
+ }
+}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/chem/TestChemCompRedirectNotCached.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/chem/TestChemCompRedirectNotCached.java
new file mode 100644
index 0000000000..b948e9fbfb
--- /dev/null
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/chem/TestChemCompRedirectNotCached.java
@@ -0,0 +1,154 @@
+/**
+ * BioJava development code
+ *
+ * This code may be freely distributed and modified under the terms of the GNU
+ * Lesser General Public Licence. This should be distributed with the code. If
+ * you do not have a copy, see:
+ *
+ * http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual authors. These
+ * should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims, or to join the
+ * biojava-l mailing list, visit the home page at:
+ *
+ * http://www.biojava.org/
+ */
+package org.biojava.nbio.structure.chem;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.net.InetSocketAddress;
+import java.nio.charset.StandardCharsets;
+
+import com.sun.net.httpserver.HttpServer;
+
+import org.biojava.nbio.core.util.FlatFileCache;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * A server that redirects, or errors, must not have its response body cached as
+ * though it were a chemical component definition.
+ *
+ * This is the failure that took the CATH downloader out when
+ * download.cathdb.info moved to https, and the chem comp download had
+ * the same shape. A 4xx already failed safely, because
+ * getInputStream() throws for those; a redirect did not, because when
+ * the JDK declines to follow a 3xx it hands back the redirect's body instead, and
+ * that body is short but not empty.
+ *
+ * The test serves the responses from a local {@link HttpServer} rather than a real
+ * service. Pointing it at a third-party server that happens to redirect today would
+ * make the test fail on the day they stop, which is precisely the coupling that made
+ * the build unreliable in the first place.
+ *
+ * @author Amr ALHOSSARY
+ * @since 7.3.0
+ */
+public class TestChemCompRedirectNotCached {
+
+ private HttpServer server;
+ private String originalServerUrl;
+
+ @Before
+ public void setUp() {
+ originalServerUrl = DownloadChemCompProvider.serverBaseUrl;
+ }
+
+ @After
+ public void tearDown() {
+ if (server != null) {
+ server.stop(0);
+ }
+ // Static state: leaving either of these set would corrupt unrelated tests.
+ DownloadChemCompProvider.serverBaseUrl = originalServerUrl;
+ FlatFileCache.clear();
+ }
+
+ /**
+ * Starts a local server that answers every request with the given status and body.
+ *
+ * @return the base URL to point the provider at
+ */
+ private String startServer(int status, String location, String body) throws IOException {
+ server = HttpServer.create(new InetSocketAddress("127.0.0.1", 0), 0);
+ server.createContext("/", exchange -> {
+ byte[] bytes = body.getBytes(StandardCharsets.UTF_8);
+ if (location != null) {
+ exchange.getResponseHeaders().add("Location", location);
+ }
+ exchange.sendResponseHeaders(status, bytes.length);
+ try (OutputStream out = exchange.getResponseBody()) {
+ out.write(bytes);
+ }
+ });
+ server.start();
+ return "http://127.0.0.1:" + server.getAddress().getPort() + "/";
+ }
+
+ private File cacheFileFor(String id) {
+ File file = new File(DownloadChemCompProvider.getLocalFileName(id));
+ file.delete();
+ FlatFileCache.clear();
+ return file;
+ }
+
+ /**
+ * The case that broke CATH: a redirect the JDK will not follow because it
+ * changes protocol. Its body must not end up on disk under the component's name.
+ */
+ @Test
+ public void redirectBodyIsNotCached() throws IOException {
+ File cached = cacheFileFor("ATP");
+ DownloadChemCompProvider.serverBaseUrl =
+ startServer(301, "https://example.invalid/ATP.cif", "Moved Permanently");
+
+ ChemComp cc = new DownloadChemCompProvider().getChemComp("ATP");
+
+ assertFalse("the body of a redirect must never be cached as a definition", cached.exists());
+ assertNull("nothing parseable was returned, so the component must be empty", cc.getName());
+ }
+
+ /**
+ * A 200 is still cached, so the guard has not simply disabled downloading.
+ *
+ * What is under test is the download path, not the CIF parser: the response is
+ * written to the cache before anything tries to parse it, so a parse failure on
+ * this deliberately minimal body says nothing about whether the guard behaved.
+ */
+ @Test
+ public void aValidResponseIsStillCached() throws IOException {
+ File cached = cacheFileFor("ATP");
+ DownloadChemCompProvider.serverBaseUrl = startServer(200, null,
+ "data_ATP\n#\n_chem_comp.id ATP\n_chem_comp.name \"ADENOSINE-5'-TRIPHOSPHATE\"\n#\n");
+
+ try {
+ new DownloadChemCompProvider().getChemComp("ATP");
+ } catch (RuntimeException parseFailure) {
+ // see the note above
+ }
+
+ assertTrue("a 200 response should still be cached", cached.exists());
+ cached.delete();
+ }
+
+ /** A server error must not be cached either. */
+ @Test
+ public void serverErrorBodyIsNotCached() throws IOException {
+ File cached = cacheFileFor("ATP");
+ DownloadChemCompProvider.serverBaseUrl =
+ startServer(503, null, "Service Unavailable");
+
+ new DownloadChemCompProvider().getChemComp("ATP");
+
+ assertFalse("the body of a 5xx must never be cached as a definition", cached.exists());
+ }
+}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/ecod/EcodParserTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/ecod/EcodParserTest.java
new file mode 100644
index 0000000000..295806e915
--- /dev/null
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/ecod/EcodParserTest.java
@@ -0,0 +1,323 @@
+/*
+ * BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence. This should
+ * be distributed with the code. If you do not have a copy,
+ * see:
+ *
+ * http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors. These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ * http://www.biojava.org/
+ */
+package org.biojava.nbio.structure.ecod;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.io.IOException;
+import java.io.StringReader;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.LinkedHashSet;
+import java.util.List;
+
+import org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser;
+import org.junit.jupiter.api.Nested;
+import org.junit.jupiter.api.Test;
+
+/**
+ * Checks that {@link EcodParser} reads every layout ECOD has distributed.
+ *
+ * The columns have been renamed, reordered and added to several times, and the version
+ * comment itself changed form at v294.1. Because the full distribution is 657 MB, none of
+ * that was covered by a test that could run in reasonable time, and a format change went
+ * unnoticed for months. These fixtures are taken verbatim from the real files, so the
+ * contract is pinned in milliseconds rather than by a download.
+ *
+ * @author Amr ALHOSSARY
+ * @since 7.3.0
+ */
+class EcodParserTest {
+
+ /** develop204, list format 1.5: 15 columns, commented header, quoted names. */
+ private static final String DEVELOP204 = String.join("\n",
+ "#/data/ecod/database_versions/v204/ecod.develop204.domains.txt",
+ "#ECOD version develop204",
+ "#Domain list version 1.5",
+ "#Grishin lab (http://prodata.swmed.edu/ecod)",
+ "#uid\tecod_domain_id\tmanual_rep\tf_id\tpdb\tchain\tpdb_range\tseqid_range"
+ + "\tarch_name\tx_name\th_name\tt_name\tf_name\tasm_status\tligand",
+ "002137905\te6b4nA1\tAUTO_NONREP\t1.1.1\t6b4n\tA\tA:1-99\tA:1-99\tbeta barrels"
+ + "\t\"cradle loop barrel\"\t\"RIFT-related\"\t\"acid protease\""
+ + "\tF_UNCLASSIFIED\tNOT_DOMAIN_ASSEMBLY\tCL,G53,NA");
+
+ /** develop291, list format 1.6: 16 columns, f_id renamed t_id, unp_acc inserted at 9. */
+ private static final String DEVELOP291 = String.join("\n",
+ "#/data/ecod/database_versions/v291/ecod.develop291.domains.txt",
+ "#ECOD version develop291",
+ "#Domain list version 1.6",
+ "#Grishin lab (http://prodata.swmed.edu/ecod)",
+ "#uid\tecod_domain_id\tmanual_rep\tt_id\tpdb\tchain\tpdb_range\tseqid_range\tunp_acc"
+ + "\tarch_name\tx_name\th_name\tt_name\tf_name\tasm_status\tligand",
+ "000000267\te1udzA1\tMANUAL_REP\t1.1.1\t1udz\tA\tA:203-381\tA:4-182\tP12345"
+ + "\tbeta barrels\t\"cradle loop barrel\"\t\"RIFT-related\"\t\"acid protease\""
+ + "\tF_UNCLASSIFIED\tNOT_DOMAIN_ASSEMBLY\tNO_LIGANDS_4A");
+
+ private static final String V295_COLUMNS =
+ "uid\tecod_domain_id\tmanual_rep\tf_id\tpdb\tchain\tpdb_range\tseqid_range"
+ + "\tarchitecture_name\tx_name\th_name\tt_name\tf_name\tassembly_id\tdomain_id_short"
+ + "\trange_count\tarch_manual\tx_manual\th_manual\tt_manual\tf_manual"
+ + "\tvalid_structure\tligand_binding\tligand_comp_ids\tligand_pdbnum";
+
+ /** v295: 25 columns, uncommented header, True/False, empty assembly_id, moved ligands. */
+ private static final String V295 = String.join("\n",
+ "# ECOD Domain List",
+ "# Version: v295",
+ "# Generated: 2026-06-24 22:47:42",
+ "# Ligand cutoff: 4.0 A (NO_LIGANDS_4A = no contact within cutoff)",
+ "#",
+ V295_COLUMNS,
+ "0\te2nmzA1\tTrue\t1.1.1.3\t2nmz\tA\tA:1-99\tA:1-99\tbeta barrels\tcradle loop barrel"
+ + "\tRIFT-related\tacid protease\tRVP\t\t\t1\tFalse\tFalse\tFalse\tFalse\tTrue"
+ + "\tTrue\tTrue\tROC,SO4\tA:601,A:602,B:401",
+ // the last column is empty on four rows in five, so split() must keep it
+ "3\te2rspA1\tTrue\t1.1.1.3\t2rsp\tA\tA:1-124\tA:1-124\tbeta barrels\tcradle loop barrel"
+ + "\tRIFT-related\tacid protease\tRVP\t\t\t1\tFalse\tFalse\tFalse\tFalse\tTrue"
+ + "\tTrue\tFalse\tNO_LIGANDS_4A\t",
+ // a domain classified from an AlphaFold model: no PDB entry, so no EcodDomain
+ "3163557\tP44140_F1_nD2\tFalse\t2004.1.1.123\t\t\t131-315\t131-315\talpha bundles"
+ + "\tsomething\tsomething else\ta third thing\t\t\t\t1\tFalse\tFalse\tFalse"
+ + "\tFalse\tTrue\tTrue\tFalse\tNO_LIGANDS_4A\t");
+
+ private static List parse(String contents) throws IOException {
+ return new EcodParser(new StringReader(contents)).getDomains();
+ }
+
+ private static String version(String contents) throws IOException {
+ return new EcodParser(new StringReader(contents)).getVersion();
+ }
+
+ @Nested
+ class Version {
+ @Test
+ void oldHeaderForm() throws IOException {
+ assertEquals("develop204", version(DEVELOP204));
+ assertEquals("develop291", version(DEVELOP291));
+ }
+
+ @Test
+ void newHeaderForm() throws IOException {
+ assertEquals("v295", version(V295));
+ assertEquals("v294.1", version("# ECOD Domain List\n# Version: v294.1\n"));
+ }
+
+ @Test
+ void listFormatVersionIsNotTheEcodVersion() throws IOException {
+ // "#Domain list version 1.5" describes the columns, not the release
+ assertNull(version("#Grishin lab\n#Domain list version 1.5\n"));
+ }
+
+ @Test
+ void absentVersionIsNull() throws IOException {
+ assertNull(version("#Grishin lab (http://prodata.swmed.edu/ecod)\n"));
+ }
+ }
+
+ @Nested
+ class OldFormats {
+ @Test
+ void listFormat15() throws IOException {
+ List domains = parse(DEVELOP204);
+ assertEquals(1, domains.size());
+ EcodDomain d = domains.get(0);
+ assertEquals(Long.valueOf(2137905), d.getUid());
+ assertEquals("e6b4nA1", d.getDomainId());
+ assertEquals(Boolean.FALSE, d.getManual());
+ assertEquals(Integer.valueOf(1), d.getXGroup());
+ assertEquals(Integer.valueOf(1), d.getHGroup());
+ assertEquals(Integer.valueOf(1), d.getTGroup());
+ assertNull(d.getFGroup());
+ assertEquals("6B4N", d.getPdbId().getId());
+ assertEquals("A", d.getChainId());
+ assertEquals("A:1-99", d.getRange());
+ assertEquals("A:1-99", d.getSeqIdRange());
+ assertEquals("beta barrels", d.getArchitectureName());
+ // quotes were stripped up to develop292
+ assertEquals("cradle loop barrel", d.getXGroupName());
+ assertEquals("RIFT-related", d.getHGroupName());
+ assertEquals("acid protease", d.getTGroupName());
+ assertEquals("F_UNCLASSIFIED", d.getFGroupName());
+ assertEquals(Long.valueOf(2137905), d.getAssemblyId());
+ assertEquals(new LinkedHashSet<>(Arrays.asList("CL", "G53", "NA")), d.getLigands());
+ }
+
+ /**
+ * develop291 inserted unp_acc before arch_name. Read positionally, every field from
+ * there on shifts by one and the domain is silently mangled or dropped.
+ */
+ @Test
+ void listFormat16InsertsUnpAcc() throws IOException {
+ List domains = parse(DEVELOP291);
+ assertEquals(1, domains.size());
+ EcodDomain d = domains.get(0);
+ assertEquals(Boolean.TRUE, d.getManual());
+ assertEquals("1UDZ", d.getPdbId().getId());
+ assertEquals("A:4-182", d.getSeqIdRange());
+ assertEquals("beta barrels", d.getArchitectureName());
+ assertEquals("acid protease", d.getTGroupName());
+ assertEquals("F_UNCLASSIFIED", d.getFGroupName());
+ assertEquals(Long.valueOf(267), d.getAssemblyId());
+ assertEquals(Collections.emptySet(), d.getLigands());
+ }
+
+ /**
+ * Headers were only added in develop101. Older files are still read by position.
+ */
+ @Test
+ void thirteenColumnsWithoutAHeader() throws IOException {
+ List domains = parse(String.join("\n",
+ "#ECOD version develop45",
+ "000000001\te1udzA1\t1.1.1\t1udz\tA\tA:203-381\tbeta barrels"
+ + "\t\"cradle loop barrel\"\t\"RIFT-related\"\t\"acid protease\""
+ + "\tF_UNCLASSIFIED\tNOT_DOMAIN_ASSEMBLY\tNO_LIGANDS_4A"));
+ assertEquals(1, domains.size());
+ EcodDomain d = domains.get(0);
+ assertNull(d.getManual(), "no manual_rep column before list format 1.1");
+ assertNull(d.getSeqIdRange(), "no seqid_range column before list format 1.4");
+ assertEquals("1UDZ", d.getPdbId().getId());
+ assertEquals("acid protease", d.getTGroupName());
+ }
+ }
+
+ @Nested
+ class NewFormat {
+ @Test
+ void twentyFiveColumns() throws IOException {
+ List domains = parse(V295);
+ // two PDB domains; the AlphaFold-derived row cannot be an EcodDomain
+ assertEquals(2, domains.size());
+
+ EcodDomain d = domains.get(0);
+ assertEquals(Long.valueOf(0), d.getUid());
+ assertEquals("e2nmzA1", d.getDomainId());
+ assertEquals(Boolean.TRUE, d.getManual(), "manual_rep is now True/False");
+ assertEquals(Integer.valueOf(1), d.getXGroup());
+ assertEquals(Integer.valueOf(1), d.getHGroup());
+ assertEquals(Integer.valueOf(1), d.getTGroup());
+ assertEquals(Integer.valueOf(3), d.getFGroup(), "f_id now carries a fourth level");
+ assertEquals("2NMZ", d.getPdbId().getId());
+ assertEquals("A", d.getChainId());
+ assertEquals("A:1-99", d.getRange());
+ assertEquals("A:1-99", d.getSeqIdRange());
+ assertEquals("beta barrels", d.getArchitectureName());
+ assertEquals("cradle loop barrel", d.getXGroupName());
+ assertEquals("RIFT-related", d.getHGroupName());
+ assertEquals("acid protease", d.getTGroupName());
+ assertEquals("RVP", d.getFGroupName());
+ // assembly_id is empty on every row of v294.1 and later, which means the same
+ // as the NOT_DOMAIN_ASSEMBLY of earlier versions
+ assertEquals(Long.valueOf(0), d.getAssemblyId());
+ assertEquals(new LinkedHashSet<>(Arrays.asList("ROC", "SO4")), d.getLigands(),
+ "the ligand list moved to ligand_comp_ids");
+ }
+
+ /**
+ * ligand_pdbnum, the last column, is empty on four rows in five. String.split
+ * discards trailing empty fields unless asked not to, which would make those rows
+ * look one column short.
+ */
+ @Test
+ void rowEndingInAnEmptyColumn() throws IOException {
+ EcodDomain d = parse(V295).get(1);
+ assertEquals("e2rspA1", d.getDomainId());
+ assertEquals("2RSP", d.getPdbId().getId());
+ assertEquals(Collections.emptySet(), d.getLigands());
+ }
+
+ @Test
+ void twentyThreeColumnsOfV2941() throws IOException {
+ List domains = parse(String.join("\n",
+ "# ECOD Domain List",
+ "# Version: v294.1",
+ "#",
+ "uid\tecod_domain_id\tmanual_rep\tf_id\tpdb\tchain\tpdb_range\tseqid_range"
+ + "\tarchitecture_name\tx_name\th_name\tt_name\tf_name\tassembly_id"
+ + "\tdomain_id_short\trange_count\tarch_manual\tx_manual\th_manual"
+ + "\tt_manual\tf_manual\tvalid_structure\tligand_binding",
+ "1\te1hvcA1\tFalse\t1.1.1.3\t1hvc\tA\tA:1B-99A\tA:1-203\tbeta barrels"
+ + "\tcradle loop barrel\tRIFT-related\tacid protease\tRVP\t\t\t\tFalse"
+ + "\tFalse\tFalse\tFalse\tFalse\tTrue\tFalse"));
+ assertEquals(1, domains.size());
+ EcodDomain d = domains.get(0);
+ assertEquals("1HVC", d.getPdbId().getId());
+ assertEquals("A:1B-99A", d.getRange());
+ assertEquals("RVP", d.getFGroupName());
+ // there is no ligand column at all in v294.1
+ assertEquals(Collections.emptySet(), d.getLigands());
+ }
+
+ @Test
+ void columnHeaderIsNotADomain() throws IOException {
+ // v294.1 stopped commenting the column names out, so they arrive looking like data
+ for (EcodDomain d : parse(V295)) {
+ assertFalse("uid".equals(d.getDomainId()));
+ }
+ }
+
+ /**
+ * An empty f_name is not the same as F_UNCLASSIFIED: f_id still classifies the
+ * domain to four levels, so the empty value is left as it is rather than translated.
+ */
+ @Test
+ void emptyFGroupNameIsLeftAlone() throws IOException {
+ List domains = parse(String.join("\n",
+ "# Version: v295",
+ V295_COLUMNS,
+ "7\te4fivA1\tTrue\t1.1.1.3\t4fiv\tA\tA:4-116\tA:1-113\tbeta barrels"
+ + "\tcradle loop barrel\tRIFT-related\tacid protease\t\t\t\t1\tFalse"
+ + "\tFalse\tFalse\tFalse\tTrue\tTrue\tTrue\tLP1\tA:201"));
+ assertEquals(1, domains.size());
+ assertEquals("", domains.get(0).getFGroupName());
+ }
+ }
+
+ @Nested
+ class Robustness {
+ @Test
+ void unparseableLinesAreSkippedNotFatal() throws IOException {
+ List domains = parse(String.join("\n",
+ "# Version: v295",
+ V295_COLUMNS,
+ "not-a-number\tefoo\tTrue\t1.1.1.3\tfoo1\tA\tA:1-9\tA:1-9\ta\tb\tc\td\te"
+ + "\t\t\t1\tFalse\tFalse\tFalse\tFalse\tTrue\tTrue\tFalse\t\t",
+ "0\te2nmzA1\tTrue\t1.1.1.3\t2nmz\tA\tA:1-99\tA:1-99\tbeta barrels"
+ + "\tcradle loop barrel\tRIFT-related\tacid protease\tRVP\t\t\t1"
+ + "\tFalse\tFalse\tFalse\tFalse\tTrue\tTrue\tTrue\tROC,SO4\tA:601"));
+ assertEquals(1, domains.size(), "the good line is still read");
+ assertEquals("e2nmzA1", domains.get(0).getDomainId());
+ }
+
+ @Test
+ void shortLineIsSkipped() throws IOException {
+ assertTrue(parse(String.join("\n",
+ "# Version: v295",
+ V295_COLUMNS,
+ "0\te2nmzA1\tTrue")).isEmpty());
+ }
+
+ @Test
+ void emptyFileYieldsNoDomains() throws IOException {
+ assertTrue(parse("").isEmpty());
+ }
+ }
+}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java
index d3c9568240..f579752d4c 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java
@@ -205,8 +205,7 @@ public boolean doSeqResHaveAtoms(Structure s) {
* @return true if has any Atom(s)
*/
public boolean hasAtoms(Group g) {
- if (g.getAtoms().size() > 0) return true;
- return false;
+ return !g.getAtoms().isEmpty();
}
/**
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java
index 8d018f6c0a..2cbdbca679 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java
@@ -37,7 +37,7 @@
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.assertFalse;
public class TestMMcifOrganismParsing {
@@ -90,7 +90,7 @@ private void checkPDB(String pdbId, String organismTaxId) throws IOException, St
Structure s = StructureIO.getStructure(pdbId);
assertNotNull(s.getEntityInfos());
- assertTrue(s.getEntityInfos().size() > 0);
+ assertFalse(s.getEntityInfos().isEmpty());
for ( EntityInfo c : s.getEntityInfos()) {
if(EntityType.POLYMER.equals(c.getType())) {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java
index 6a9f6ae93c..2b99d660d8 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java
@@ -47,9 +47,9 @@ public void test4DIA() throws Exception {
for (SiftsEntity e : entities) {
//System.out.println(e.getEntityId() + " " +e.getType());
- Assert.assertTrue(e.getSegments().size() > 0);
+ Assert.assertFalse(e.getSegments().isEmpty());
for (SiftsSegment seg : e.getSegments()) {
- Assert.assertTrue(seg.getResidues().size() > 0);
+ Assert.assertFalse(seg.getResidues().isEmpty());
for (SiftsResidue res : seg.getResidues()) {
@@ -78,9 +78,9 @@ public void test4jn3() throws Exception {
for (SiftsEntity e : entities) {
//System.out.println(e.getEntityId() + " " +e.getType());
- Assert.assertTrue(e.getSegments().size() > 0);
+ Assert.assertFalse(e.getSegments().isEmpty());
for (SiftsSegment seg : e.getSegments()) {
- Assert.assertTrue(seg.getResidues().size() > 0);
+ Assert.assertFalse(seg.getResidues().isEmpty());
//System.out.println(seg.getResidues().size());
//System.out.println(" Segment: " + seg.getSegId() + " " + seg.getStart() + " " + seg.getEnd()) ;
@@ -125,7 +125,7 @@ public void test4DOU() throws Exception {
//assertTrue(seg1.getResidues().size() == 17);
for (SiftsSegment seg : e.getSegments()) {
- Assert.assertTrue(seg.getResidues().size() > 0);
+ Assert.assertFalse(seg.getResidues().isEmpty());
//System.out.println(" Segment: " + seg.getSegId() + " " + seg.getStart() + " " + seg.getEnd() + " res. size: " + seg.getResidues().size()) ;
@@ -175,7 +175,7 @@ public void test4O6W() throws Exception {
//System.out.println(" Segment: " + seg1.getSegId() + " " + seg1.getStart() + " " + seg1.getEnd() + " res. size: " + seg1.getResidues().size());
//assertTrue(seg1.getResidues().size() == 17);
- Assert.assertTrue(seg.getResidues().size() > 0);
+ Assert.assertFalse(seg.getResidues().isEmpty());
for (SiftsResidue res : seg.getResidues()) {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImplTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImplTest.java
index a8925afa88..8fbd1060b0 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImplTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImplTest.java
@@ -147,7 +147,7 @@ public void testWaterOnlyChainCif() throws IOException {
Chain c = s2.getWaterChainByPDB("F");
assertNotNull("Got null when looking for water-only chain with author id F", c);
- assertTrue(c.getAtomGroups().size() > 0);
+ assertFalse(c.getAtomGroups().isEmpty());
// checking that compounds are linked
assertNotNull(c.getEntityInfo());
@@ -157,7 +157,7 @@ public void testWaterOnlyChainCif() throws IOException {
Chain cAsymId = s2.getWaterChain("E");
assertNotNull("Got null when looking for water-only chain with asym id E", cAsymId);
- assertTrue(cAsymId.getAtomGroups().size() > 0);
+ assertFalse(cAsymId.getAtomGroups().isEmpty());
assertSame(c, cAsymId);
}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileSupplierImplTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileSupplierImplTest.java
index df227a8669..1d5f496ff5 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileSupplierImplTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileSupplierImplTest.java
@@ -1,5 +1,6 @@
package org.biojava.nbio.structure.io.cif;
+import org.biojava.nbio.structure.PdbId;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.io.PDBFileParser;
@@ -41,4 +42,43 @@ public void shouldReadRawPdbOutputtingCifWithEntity() throws IOException {
}
}
+
+ /**
+ * The identifier must be written as a data item and not only as the name of the data block: consumers read it
+ * from _entry.id or from _struct.entry_id, so writing the block header alone loses it. See issue #1143.
+ */
+ @Test
+ public void shouldWriteEntryIdAndSurviveRoundTrip() throws IOException {
+ Structure s;
+ try (InputStream inStream = new GZIPInputStream(this.getClass().getResourceAsStream("/4hhb.cif.gz"))) {
+ s = CifStructureConverter.fromInputStream(inStream);
+ }
+ assertEquals(new PdbId("4HHB"), s.getPdbId());
+
+ String cifText = CifStructureConverter.toText(s);
+ assertTrue("_entry.id must be written", cifText.contains("_entry.id"));
+ assertTrue("_struct.entry_id must be written", cifText.contains("_struct.entry_id"));
+
+ Structure readStruct = CifStructureConverter.fromInputStream(
+ new ByteArrayInputStream(cifText.getBytes()));
+
+ assertEquals(s.getPdbId(), readStruct.getPdbId());
+ assertEquals(s.getPdbId(), readStruct.getPDBHeader().getPdbId());
+ }
+
+ /**
+ * Structures without an identifier must not gain empty entry categories.
+ */
+ @Test
+ public void shouldNotWriteEntryIdWhenPdbIdIsAbsent() throws IOException {
+ Structure s;
+ try (InputStream inStream = new GZIPInputStream(this.getClass().getResourceAsStream("/4hhb.cif.gz"))) {
+ s = CifStructureConverter.fromInputStream(inStream);
+ }
+ s.setPdbId(null);
+
+ String cifText = CifStructureConverter.toText(s);
+ assertFalse(cifText.contains("_entry.id"));
+ assertFalse(cifText.contains("_struct.entry_id"));
+ }
}
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 4f3e00f56b..570a2dd99b 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
org.biojava
biojava
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
biojava-survival
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
index c9f4f18056..eebdaf86ba 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
@@ -32,7 +32,7 @@
/**
* Holds the results of a cox analysis where calling dump(), toString() will give an output similar to R
- * @author Scooter Willis
+ * @author Scooter Willis
*/
public class CoxInfo {
@@ -505,7 +505,7 @@ public String toString(String beginLine, String del, String endLine) {
o = o + beginLine + endLine;
- if (baselineSurvivorFunction.size() > 0) {
+ if (!baselineSurvivorFunction.isEmpty()) {
o = o + beginLine + "Baseline Survivor Function (at predictor means)" + endLine;
for (Double time : baselineSurvivorFunction.keySet()) {
Double mean = baselineSurvivorFunction.get(time);
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java
index 42b34905cc..955a7c1f6d 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java
@@ -29,7 +29,7 @@
/**
*
- * @author Scooter Willis
+ * @author Scooter Willis
*/
public class ResidualsCoxph {
@@ -108,7 +108,7 @@ public static double[][] process(CoxInfo ci, Type type, boolean useWeighted, Arr
double[] weighted = ci.getWeighted();
rr = Matrix.scale(rr, weighted);
}
- if (cluster != null && cluster.size() > 0) {
+ if (cluster != null && !cluster.isEmpty()) {
rr = rowsum(rr, cluster);
}
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
index 542085942e..17ed18419a 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
@@ -27,7 +27,7 @@
* Need to handle very large spreadsheets of expression data so keep memory
* footprint low
*
- * @author Scooter Willis
+ * @author Scooter Willis
*/
public class WorkSheet {
@@ -1391,7 +1391,7 @@ static public WorkSheet unionWorkSheetsRowJoin(WorkSheet w1, WorkSheet w2, boole
ArrayList joinedColumns = new ArrayList<>();
joinedColumns.addAll(w1DataColumns);
joinedColumns.addAll(w2DataColumns);
- if (!joinedColumns.contains("META_DATA") && (w1MetaDataColumns.size() > 0 || w2MetaDataColumns.size() > 0)) {
+ if (!joinedColumns.contains("META_DATA") && (!w1MetaDataColumns.isEmpty() || !w2MetaDataColumns.isEmpty())) {
joinedColumns.add("META_DATA");
}
for (String column : w1MetaDataColumns) {
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
index c4578f1c8b..144942a809 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
@@ -76,7 +76,7 @@ private void paintTable(Graphics g) {
sfiHashMap = sfi.getStrataInfoHashMap();
}
- if(sfiHashMap.size() == 0)
+ if(sfiHashMap.isEmpty())
return;
//int height = this.getHeight();
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 7a4fa63589..c3fe2a9513 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
biojava
org.biojava
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
biojava-ws
biojava-ws
@@ -19,7 +19,7 @@
org.biojava
biojava-core
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
compile
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
index 3304e78d4f..373b78cd0a 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
@@ -140,7 +140,7 @@ public int compareTo(HmmerResult o) {
return(me.getSqFrom().compareTo(other.getSqFrom()));
}
private boolean emptyDomains(HmmerResult o) {
- if ( o.getDomains() == null || o.getDomains().size() == 0)
+ if ( o.getDomains() == null || o.getDomains().isEmpty())
return true;
return false;
}
diff --git a/pom.xml b/pom.xml
index f17d3c2d67..79db94ee26 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
org.biojava
biojava
pom
- 7.2.3-SNAPSHOT
+ 7.2.7-SNAPSHOT
biojava
BioJava is an open-source project dedicated to providing a Java framework for processing biological
data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -41,7 +41,7 @@
512M
1.0.11
2.0.12
- 2.23.1
+ 2.25.5
5.10.1
ciftools-java
7.0.1
@@ -217,7 +217,8 @@
3.1.1
true
- clean install
+ -DskipTests
+ clean verify -DskipTests
true
@@ -325,12 +326,6 @@
3.1.3
-
- org.apache.maven.plugins
- maven-javadoc-plugin
- 3.11.2
-
-
org.apache.maven.plugins
maven-site-plugin
@@ -486,7 +481,7 @@
com.google.guava
guava
- 33.4.0-jre
+ 33.6.0-jre
@@ -580,17 +575,20 @@
release
-
-
+
- org.sonatype.plugins
- nexus-staging-maven-plugin
- 1.6.13
+ org.sonatype.central
+ central-publishing-maven-plugin
+ 0.8.0
true
- ossrh
- https://oss.sonatype.org/
- true
+
+ central
+
+
+ true
+
+ published
-[](https://github.com/biojava/biojava/releases/tag/biojava-7.2.2) [](https://github.com/biojava/biojava/blob/master/LICENSE) [](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[](https://github.com/biojava/biojava/releases/tag/biojava-7.2.5) [](https://github.com/biojava/biojava/blob/master/LICENSE) [](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
BioJava is an open-source project dedicated to providing a Java framework for **processing biological data**. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
@@ -29,7 +29,7 @@ If you are using Maven you can add the BioJava repository by adding the followin