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JAL-1919 fixed bug causing PDBfile test failure
author
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Thu, 3 Mar 2016 14:46:00 +0000
(14:46 +0000)
committer
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Thu, 3 Mar 2016 14:46:00 +0000
(14:46 +0000)
src/jalview/api/DBRefEntryI.java
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src/jalview/datamodel/DBRefEntry.java
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src/jalview/datamodel/Sequence.java
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src/jalview/io/StructureFile.java
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test/MCview/PDBfileTest.java
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diff --git
a/src/jalview/api/DBRefEntryI.java
b/src/jalview/api/DBRefEntryI.java
index
b927fa5
..
9415745
100644
(file)
--- a/
src/jalview/api/DBRefEntryI.java
+++ b/
src/jalview/api/DBRefEntryI.java
@@
-1,5
+1,7
@@
package jalview.api;
package jalview.api;
+import jalview.datamodel.Mapping;
+
public interface DBRefEntryI
{
public interface DBRefEntryI
{
@@
-69,4
+71,6
@@
public interface DBRefEntryI
* @return index of end residue in the source DB
*/
public int getEndRes();
* @return index of end residue in the source DB
*/
public int getEndRes();
+
+ public Mapping getMap();
}
}
diff --git
a/src/jalview/datamodel/DBRefEntry.java
b/src/jalview/datamodel/DBRefEntry.java
index
0b1fb6d
..
53642b5
100755
(executable)
--- a/
src/jalview/datamodel/DBRefEntry.java
+++ b/
src/jalview/datamodel/DBRefEntry.java
@@
-37,6
+37,7
@@
public class DBRefEntry implements DBRefEntryI
}
}
+
public DBRefEntry(String source, String version, String accessionId)
{
this(source, version, accessionId, null);
public DBRefEntry(String source, String version, String accessionId)
{
this(source, version, accessionId, null);
@@
-63,13
+64,14
@@
public class DBRefEntry implements DBRefEntryI
this.map = map;
}
this.map = map;
}
- public DBRefEntry(DBRefEntry entry)
+ public DBRefEntry(DBRefEntryI entry)
{
{
- this(
- (entry.source == null ? "" : new String(entry.source)),
- (entry.version == null ? "" : new String(entry.version)),
- (entry.accessionId == null ? "" : new String(entry.accessionId)),
- (entry.map == null ? null : new Mapping(entry.map)));
+ this((entry.getSource() == null ? "" : new String(entry.getSource())),
+ (entry.getVersion() == null ? "" : new String(
+ entry.getVersion())),
+ (entry.getAccessionId() == null ? "" : new String(
+ entry.getAccessionId())),
+ (entry.getMap() == null ? null : new Mapping(entry.getMap())));
}
@Override
}
@Override
@@
-165,6
+167,7
@@
public class DBRefEntry implements DBRefEntryI
}
}
+ @Override
public Mapping getMap()
{
return map;
public Mapping getMap()
{
return map;
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
d73b283
..
a2513ba
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-219,7
+219,8
@@
public class Sequence extends ASequence implements SequenceI
initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
seq.getEnd());
description = seq.getDescription();
initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
seq.getEnd());
description = seq.getDescription();
- sourceDBRef = seq.getSourceDBRef();
+ sourceDBRef = seq.getSourceDBRef() == null ? null : new DBRefEntry(
+ seq.getSourceDBRef());
if (seq.getSequenceFeatures() != null)
{
SequenceFeature[] sf = seq.getSequenceFeatures();
if (seq.getSequenceFeatures() != null)
{
SequenceFeature[] sf = seq.getSequenceFeatures();
diff --git
a/src/jalview/io/StructureFile.java
b/src/jalview/io/StructureFile.java
index
e2b73d1
..
4ba4c10
100644
(file)
--- a/
src/jalview/io/StructureFile.java
+++ b/
src/jalview/io/StructureFile.java
@@
-96,16
+96,11
@@
public abstract class StructureFile extends AlignFile
sourceDBRef.setStartRes(pdbSequence.getStart());
sourceDBRef.setEndRes(pdbSequence.getEnd());
sourceDBRef.setStartRes(pdbSequence.getStart());
sourceDBRef.setEndRes(pdbSequence.getEnd());
- // PDBChain objects maintain reference to dataset
-
- // SequenceI chainseq = pdbSequence.deriveSequence();
- // chainseq.setSourceDBRef(sourceDBRef);
- // chainseq.addPDBId(entry);
- // chainseq.addDBRef(sourceDBRef);
- SequenceI chainseq = chain.sequence;
- chainseq.addPDBId(entry);
+ SequenceI chainseq = pdbSequence.deriveSequence();
chainseq.setSourceDBRef(sourceDBRef);
chainseq.setSourceDBRef(sourceDBRef);
+ chainseq.addPDBId(entry);
chainseq.addDBRef(sourceDBRef);
chainseq.addDBRef(sourceDBRef);
+
seqs.addElement(chainseq);
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
seqs.addElement(chainseq);
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
diff --git
a/test/MCview/PDBfileTest.java
b/test/MCview/PDBfileTest.java
index
31c3beb
..
0fc7d1c
100644
(file)
--- a/
test/MCview/PDBfileTest.java
+++ b/
test/MCview/PDBfileTest.java
@@
-83,6
+83,8
@@
public class PDBfileTest
assertEquals("D", pf.getChains().get(3).id);
PDBChain chainA = pf.getChains().get(0);
assertEquals("D", pf.getChains().get(3).id);
PDBChain chainA = pf.getChains().get(0);
+ SequenceI seqA = pf.getSeqs().get(0);
+
assertEquals(0, chainA.seqstart); // not set
assertEquals(0, chainA.seqend); // not set
assertEquals(18, chainA.sequence.getStart());
assertEquals(0, chainA.seqstart); // not set
assertEquals(0, chainA.seqend); // not set
assertEquals(18, chainA.sequence.getStart());
@@
-91,8
+93,8
@@
public class PDBfileTest
assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
assertEquals("3W5V|A", chainA.sequence.getName());
assertNull(chainA.sequence.getAnnotation());
assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
assertEquals("3W5V|A", chainA.sequence.getName());
assertNull(chainA.sequence.getAnnotation());
- assertEquals(1, chainA.sequence.getAllPDBEntries().size());
- PDBEntry pdb = chainA.sequence.getAllPDBEntries().get(0);
+ assertEquals(1, seqA.getAllPDBEntries().size());
+ PDBEntry pdb = seqA.getAllPDBEntries().get(0);
assertEquals("A", pdb.getChainCode());
assertEquals("PDB", pdb.getType());
assertEquals("3W5V", pdb.getId());
assertEquals("A", pdb.getChainCode());
assertEquals("PDB", pdb.getType());
assertEquals("3W5V", pdb.getId());