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JAL-2189 source formatting
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
68c8c50
..
c8b94ce
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-233,8
+233,7
@@
public class Sequence extends ASequence implements SequenceI
{
char[] oseq = seq.getSequence();
initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
{
char[] oseq = seq.getSequence();
initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
- seq.getStart(),
- seq.getEnd());
+ seq.getStart(), seq.getEnd());
}
description = seq.getDescription();
if (seq != datasetSequence)
}
description = seq.getDescription();
if (seq != datasetSequence)
@@
-293,7
+292,6
@@
public class Sequence extends ASequence implements SequenceI
}
}
}
}
-
@Override
public void setSequenceFeatures(SequenceFeature[] features)
{
@Override
public void setSequenceFeatures(SequenceFeature[] features)
{
@@
-318,7
+316,7
@@
public class Sequence extends ASequence implements SequenceI
@Override
public synchronized void addSequenceFeature(SequenceFeature sf)
{
@Override
public synchronized void addSequenceFeature(SequenceFeature sf)
{
- if (sequenceFeatures==null && datasetSequence != null)
+ if (sequenceFeatures == null && datasetSequence != null)
{
datasetSequence.addSequenceFeature(sf);
return;
{
datasetSequence.addSequenceFeature(sf);
return;
@@
-348,8
+346,9
@@
public class Sequence extends ASequence implements SequenceI
{
if (sequenceFeatures == null)
{
{
if (sequenceFeatures == null)
{
- if (datasetSequence!=null) {
- datasetSequence.deleteFeature(sf);
+ if (datasetSequence != null)
+ {
+ datasetSequence.deleteFeature(sf);
}
return;
}
}
return;
}
@@
-1094,7
+1093,7
@@
public class Sequence extends ASequence implements SequenceI
@Override
public SequenceI deriveSequence()
{
@Override
public SequenceI deriveSequence()
{
- Sequence seq=null;
+ Sequence seq = null;
if (datasetSequence == null)
{
if (isValidDatasetSequence())
if (datasetSequence == null)
{
if (isValidDatasetSequence())
@@
-1108,7
+1107,7
@@
public class Sequence extends ASequence implements SequenceI
else
{
// Create a new, valid dataset sequence
else
{
// Create a new, valid dataset sequence
- createDatasetSequence();
+ createDatasetSequence();
}
}
return new Sequence(this);
}
}
return new Sequence(this);
@@
-1156,9
+1155,9
@@
public class Sequence extends ASequence implements SequenceI
dsseq.setDescription(description);
// move features and database references onto dataset sequence
dsseq.sequenceFeatures = sequenceFeatures;
dsseq.setDescription(description);
// move features and database references onto dataset sequence
dsseq.sequenceFeatures = sequenceFeatures;
- sequenceFeatures=null;
+ sequenceFeatures = null;
dsseq.dbrefs = dbrefs;
dsseq.dbrefs = dbrefs;
- dbrefs=null;
+ dbrefs = null;
// TODO: search and replace any references to this sequence with
// references to the dataset sequence in Mappings on dbref
dsseq.pdbIds = pdbIds;
// TODO: search and replace any references to this sequence with
// references to the dataset sequence in Mappings on dbref
dsseq.pdbIds = pdbIds;
@@
-1416,15
+1415,14
@@
public class Sequence extends ASequence implements SequenceI
return null;
}
return null;
}
-
@Override
public List<DBRefEntry> getPrimaryDBRefs()
{
@Override
public List<DBRefEntry> getPrimaryDBRefs()
{
- if (datasetSequence!=null)
+ if (datasetSequence != null)
{
return datasetSequence.getPrimaryDBRefs();
}
{
return datasetSequence.getPrimaryDBRefs();
}
- if (dbrefs==null || dbrefs.length==0)
+ if (dbrefs == null || dbrefs.length == 0)
{
return Collections.emptyList();
}
{
return Collections.emptyList();
}