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Merge branch 'JAL-1956_featureStyles' into features/JAL-653_JAL-1766_htslib_refseqsupport
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
532a11b
..
7b05649
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-21,6
+21,7
@@
package jalview.datamodel;
import jalview.analysis.AlignSeq;
package jalview.datamodel;
import jalview.analysis.AlignSeq;
+import jalview.api.DBRefEntryI;
import jalview.util.StringUtils;
import java.util.ArrayList;
import jalview.util.StringUtils;
import java.util.ArrayList;
@@
-55,6
+56,8
@@
public class Sequence extends ASequence implements SequenceI
String vamsasId;
String vamsasId;
+ DBRefEntryI sourceDBRef;
+
DBRefEntry[] dbrefs;
RNA rna;
DBRefEntry[] dbrefs;
RNA rna;
@@
-216,6
+219,7
@@
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();
if (seq.getSequenceFeatures() != null)
{
SequenceFeature[] sf = seq.getSequenceFeatures();
if (seq.getSequenceFeatures() != null)
{
SequenceFeature[] sf = seq.getSequenceFeatures();
@@
-225,10
+229,10
@@
public class Sequence extends ASequence implements SequenceI
}
}
setDatasetSequence(seq.getDatasetSequence());
}
}
setDatasetSequence(seq.getDatasetSequence());
- if (datasetSequence == null && seq.getDBRef() != null)
+ if (datasetSequence == null && seq.getDBRefs() != null)
{
// only copy DBRefs if we really are a dataset sequence
{
// only copy DBRefs if we really are a dataset sequence
- DBRefEntry[] dbr = seq.getDBRef();
+ DBRefEntry[] dbr = seq.getDBRefs();
for (int i = 0; i < dbr.length; i++)
{
addDBRef(new DBRefEntry(dbr[i]));
for (int i = 0; i < dbr.length; i++)
{
addDBRef(new DBRefEntry(dbr[i]));
@@
-284,6
+288,7
@@
public class Sequence extends ASequence implements SequenceI
@Override
public synchronized void addSequenceFeature(SequenceFeature sf)
{
@Override
public synchronized void addSequenceFeature(SequenceFeature sf)
{
+ // TODO add to dataset sequence instead if there is one?
if (sequenceFeatures == null)
{
sequenceFeatures = new SequenceFeature[0];
if (sequenceFeatures == null)
{
sequenceFeatures = new SequenceFeature[0];
@@
-907,18
+912,18
@@
public class Sequence extends ASequence implements SequenceI
}
@Override
}
@Override
- public void setDBRef(DBRefEntry[] dbref)
+ public void setDBRefs(DBRefEntry[] dbref)
{
dbrefs = dbref;
}
@Override
{
dbrefs = dbref;
}
@Override
- public DBRefEntry[] getDBRef()
+ public DBRefEntry[] getDBRefs()
{
if (dbrefs == null && datasetSequence != null
&& this != datasetSequence)
{
{
if (dbrefs == null && datasetSequence != null
&& this != datasetSequence)
{
- return datasetSequence.getDBRef();
+ return datasetSequence.getDBRefs();
}
return dbrefs;
}
}
return dbrefs;
}
@@
-926,6
+931,7
@@
public class Sequence extends ASequence implements SequenceI
@Override
public void addDBRef(DBRefEntry entry)
{
@Override
public void addDBRef(DBRefEntry entry)
{
+ // TODO add to dataset sequence instead if there is one?
if (dbrefs == null)
{
dbrefs = new DBRefEntry[0];
if (dbrefs == null)
{
dbrefs = new DBRefEntry[0];
@@
-1076,8
+1082,8
@@
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(getDBRef());
- setDBRef(null);
+ datasetSequence.setDBRefs(getDBRefs());
+ setDBRefs(null);
datasetSequence.setPDBId(getAllPDBEntries());
setPDBId(null);
datasetSequence.updatePDBIds();
datasetSequence.setPDBId(getAllPDBEntries());
setPDBId(null);
datasetSequence.updatePDBIds();
@@
-1252,7
+1258,7
@@
public class Sequence extends ASequence implements SequenceI
}
}
// transfer database references
}
}
// transfer database references
- DBRefEntry[] entryRefs = entry.getDBRef();
+ DBRefEntry[] entryRefs = entry.getDBRefs();
if (entryRefs != null)
{
for (int r = 0; r < entryRefs.length; r++)
if (entryRefs != null)
{
for (int r = 0; r < entryRefs.length; r++)
@@
-1352,4
+1358,16
@@
public class Sequence extends ASequence implements SequenceI
return null;
}
return null;
}
+ @Override
+ public void setSourceDBRef(DBRefEntryI dbRef)
+ {
+ this.sourceDBRef = dbRef;
+ }
+
+ @Override
+ public DBRefEntryI getSourceDBRef()
+ {
+ return this.sourceDBRef;
+ }
+
}
}