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JAL-1942 JAL-1479 refactored SequenceI.getDBRef/SequenceI.setDBRef to SequenceI.getDB...
author
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Thu, 5 Nov 2015 12:58:32 +0000
(12:58 +0000)
committer
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Thu, 5 Nov 2015 12:58:32 +0000
(12:58 +0000)
src/MCview/PDBfile.java
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src/jalview/datamodel/Sequence.java
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src/jalview/datamodel/SequenceGroup.java
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src/jalview/datamodel/SequenceI.java
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test/jalview/analysis/AlignmentUtilsTests.java
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diff --git
a/src/MCview/PDBfile.java
b/src/MCview/PDBfile.java
index
a7ecc52
..
58611e2
100755
(executable)
--- a/
src/MCview/PDBfile.java
+++ b/
src/MCview/PDBfile.java
@@
-25,6
+25,7
@@
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
@@
-312,7
+313,7
@@
public class PDBfile extends jalview.io.AlignFile
DBRefEntry sourceDBRef = new DBRefEntry();
sourceDBRef.setAccessionId(id);
DBRefEntry sourceDBRef = new DBRefEntry();
sourceDBRef.setAccessionId(id);
- sourceDBRef.setSource("PDB");
+ sourceDBRef.setSource(DBRefSource.PDB);
sourceDBRef.setStartRes(pdbSequence.getStart());
sourceDBRef.setEndRes(pdbSequence.getEnd());
pdbSequence.setSourceDBRef(sourceDBRef);
sourceDBRef.setStartRes(pdbSequence.getStart());
sourceDBRef.setEndRes(pdbSequence.getEnd());
pdbSequence.setSourceDBRef(sourceDBRef);
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
fd710bd
..
ac2f9c1
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-912,7
+912,7
@@
public class Sequence extends ASequence implements SequenceI
}
@Override
}
@Override
- public void setDBRef(DBRefEntry[] dbref)
+ public void setDBRefs(DBRefEntry[] dbref)
{
dbrefs = dbref;
}
{
dbrefs = dbref;
}
@@
-1080,8
+1080,8
@@
public class Sequence extends ASequence implements SequenceI
datasetSequence.setDescription(getDescription());
setSequenceFeatures(null);
// move database references onto dataset sequence
datasetSequence.setDescription(getDescription());
setSequenceFeatures(null);
// move database references onto dataset sequence
- datasetSequence.setDBRef(getDBRefs());
- setDBRef(null);
+ datasetSequence.setDBRefs(getDBRefs());
+ setDBRefs(null);
datasetSequence.setPDBId(getAllPDBEntries());
setPDBId(null);
datasetSequence.updatePDBIds();
datasetSequence.setPDBId(getAllPDBEntries());
setPDBId(null);
datasetSequence.updatePDBIds();
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
d79a5f7
..
0e8fa17
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-209,7
+209,7
@@
public class SequenceGroup implements AnnotatedCollectionI
if (seqs[ipos] != null)
{
seqs[ipos].setDescription(seq.getDescription());
if (seqs[ipos] != null)
{
seqs[ipos].setDescription(seq.getDescription());
- seqs[ipos].setDBRef(seq.getDBRefs());
+ seqs[ipos].setDBRefs(seq.getDBRefs());
seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
if (seq.getDatasetSequence() != null)
{
seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
if (seq.getDatasetSequence() != null)
{
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
50f88f3
..
f1cba43
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-298,7
+298,7
@@
public interface SequenceI extends ASequenceI
public void setVamsasId(String id);
public void setVamsasId(String id);
- public void setDBRef(DBRefEntry[] dbs);
+ public void setDBRefs(DBRefEntry[] dbs);
public DBRefEntry[] getDBRefs();
public DBRefEntry[] getDBRefs();
diff --git
a/test/jalview/analysis/AlignmentUtilsTests.java
b/test/jalview/analysis/AlignmentUtilsTests.java
index
9756849
..
74e4940
100644
(file)
--- a/
test/jalview/analysis/AlignmentUtilsTests.java
+++ b/
test/jalview/analysis/AlignmentUtilsTests.java
@@
-988,7
+988,7
@@
public class AlignmentUtilsTests
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
// now the other way round
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
// now the other way round
- seq1.setDBRef(null);
+ seq1.setDBRefs(null);
seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));