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JAL-2314 Tidy up
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
29d114d
..
b0faf21
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-22,6
+22,7
@@
package jalview.datamodel;
import jalview.analysis.AlignSeq;
import jalview.api.DBRefEntryI;
import jalview.analysis.AlignSeq;
import jalview.api.DBRefEntryI;
+import jalview.util.Comparison;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.StringUtils;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.StringUtils;
@@
-232,8
+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)
@@
-292,7
+292,6
@@
public class Sequence extends ASequence implements SequenceI
}
}
}
}
-
@Override
public void setSequenceFeatures(SequenceFeature[] features)
{
@Override
public void setSequenceFeatures(SequenceFeature[] features)
{
@@
-315,12
+314,11
@@
public class Sequence extends ASequence implements SequenceI
}
@Override
}
@Override
- public synchronized void addSequenceFeature(SequenceFeature sf)
+ public synchronized boolean addSequenceFeature(SequenceFeature sf)
{
{
- if (sequenceFeatures==null && datasetSequence != null)
+ if (sequenceFeatures == null && datasetSequence != null)
{
{
- datasetSequence.addSequenceFeature(sf);
- return;
+ return datasetSequence.addSequenceFeature(sf);
}
if (sequenceFeatures == null)
{
}
if (sequenceFeatures == null)
{
@@
-331,7
+329,7
@@
public class Sequence extends ASequence implements SequenceI
{
if (sequenceFeatures[i].equals(sf))
{
{
if (sequenceFeatures[i].equals(sf))
{
- return;
+ return false;
}
}
}
}
@@
-340,6
+338,7
@@
public class Sequence extends ASequence implements SequenceI
temp[sequenceFeatures.length] = sf;
sequenceFeatures = temp;
temp[sequenceFeatures.length] = sf;
sequenceFeatures = temp;
+ return true;
}
@Override
}
@Override
@@
-347,8
+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;
}
@@
-1013,12
+1013,12
@@
public class Sequence extends ASequence implements SequenceI
{
if (seq == this)
{
{
if (seq == this)
{
- throw new Error(
+ throw new IllegalArgumentException(
"Implementation Error: self reference passed to SequenceI.setDatasetSequence");
}
if (seq != null && seq.getDatasetSequence() != null)
{
"Implementation Error: self reference passed to SequenceI.setDatasetSequence");
}
if (seq != null && seq.getDatasetSequence() != null)
{
- throw new Error(
+ throw new IllegalArgumentException(
"Implementation error: cascading dataset sequences are not allowed.");
}
datasetSequence = seq;
"Implementation error: cascading dataset sequences are not allowed.");
}
datasetSequence = seq;
@@
-1093,7
+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())
@@
-1107,7
+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);
@@
-1117,6
+1117,10
@@
public class Sequence extends ASequence implements SequenceI
private long _seqhash = 0;
private long _seqhash = 0;
+ /**
+ * Answers false if the sequence is more than 85% nucleotide (ACGTU), else
+ * true
+ */
@Override
public boolean isProtein()
{
@Override
public boolean isProtein()
{
@@
-1127,7
+1131,7
@@
public class Sequence extends ASequence implements SequenceI
if (_seqhash != sequence.hashCode())
{
_seqhash = sequence.hashCode();
if (_seqhash != sequence.hashCode())
{
_seqhash = sequence.hashCode();
- _isNa=jalview.util.Comparison.isNucleotide(new SequenceI[] { this });
+ _isNa = Comparison.isNucleotide(this);
}
return !_isNa;
};
}
return !_isNa;
};
@@
-1151,9
+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;
@@
-1411,15
+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();
}