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JAL-1421 use generics JAL-1551 @Override annotations added
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Mon, 30 Nov 2015 09:19:11 +0000
(09:19 +0000)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Mon, 30 Nov 2015 09:19:11 +0000
(09:19 +0000)
src/jalview/datamodel/Sequence.java
patch
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diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
c7581d8
..
532a11b
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-261,11
+261,10
@@
public class Sequence extends ASequence implements SequenceI
}
if (seq.getAllPDBEntries() != null)
{
}
if (seq.getAllPDBEntries() != null)
{
- Vector ids = seq.getAllPDBEntries();
- Enumeration e = ids.elements();
- while (e.hasMoreElements())
+ Vector<PDBEntry> ids = seq.getAllPDBEntries();
+ for (PDBEntry pdb : ids)
{
{
- this.addPDBId(new PDBEntry((PDBEntry) e.nextElement()));
+ this.addPDBId(new PDBEntry(pdb));
}
}
}
}
}
}
@@
-276,11
+275,13
@@
public class Sequence extends ASequence implements SequenceI
* @param v
* DOCUMENT ME!
*/
* @param v
* DOCUMENT ME!
*/
+ @Override
public void setSequenceFeatures(SequenceFeature[] features)
{
sequenceFeatures = features;
}
public void setSequenceFeatures(SequenceFeature[] features)
{
sequenceFeatures = features;
}
+ @Override
public synchronized void addSequenceFeature(SequenceFeature sf)
{
if (sequenceFeatures == null)
public synchronized void addSequenceFeature(SequenceFeature sf)
{
if (sequenceFeatures == null)
@@
-303,6
+304,7
@@
public class Sequence extends ASequence implements SequenceI
sequenceFeatures = temp;
}
sequenceFeatures = temp;
}
+ @Override
public void deleteFeature(SequenceFeature sf)
{
if (sequenceFeatures == null)
public void deleteFeature(SequenceFeature sf)
{
if (sequenceFeatures == null)
@@
-352,6
+354,7
@@
public class Sequence extends ASequence implements SequenceI
*
* @return
*/
*
* @return
*/
+ @Override
public SequenceFeature[] getSequenceFeatures()
{
SequenceFeature[] features = sequenceFeatures;
public SequenceFeature[] getSequenceFeatures()
{
SequenceFeature[] features = sequenceFeatures;
@@
-367,6
+370,7
@@
public class Sequence extends ASequence implements SequenceI
return features;
}
return features;
}
+ @Override
public void addPDBId(PDBEntry entry)
{
if (pdbIds == null)
public void addPDBId(PDBEntry entry)
{
if (pdbIds == null)
@@
-419,6
+423,7
@@
public class Sequence extends ASequence implements SequenceI
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
+ @Override
public String getDisplayId(boolean jvsuffix)
{
StringBuffer result = new StringBuffer(name);
public String getDisplayId(boolean jvsuffix)
{
StringBuffer result = new StringBuffer(name);
@@
-436,6
+441,7
@@
public class Sequence extends ASequence implements SequenceI
* @param name
* DOCUMENT ME!
*/
* @param name
* DOCUMENT ME!
*/
+ @Override
public void setName(String name)
{
this.name = name;
public void setName(String name)
{
this.name = name;
@@
-447,6
+453,7
@@
public class Sequence extends ASequence implements SequenceI
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
+ @Override
public String getName()
{
return this.name;
public String getName()
{
return this.name;
@@
-458,6
+465,7
@@
public class Sequence extends ASequence implements SequenceI
* @param start
* DOCUMENT ME!
*/
* @param start
* DOCUMENT ME!
*/
+ @Override
public void setStart(int start)
{
this.start = start;
public void setStart(int start)
{
this.start = start;
@@
-468,6
+476,7
@@
public class Sequence extends ASequence implements SequenceI
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
+ @Override
public int getStart()
{
return this.start;
public int getStart()
{
return this.start;
@@
-479,6
+488,7
@@
public class Sequence extends ASequence implements SequenceI
* @param end
* DOCUMENT ME!
*/
* @param end
* DOCUMENT ME!
*/
+ @Override
public void setEnd(int end)
{
this.end = end;
public void setEnd(int end)
{
this.end = end;
@@
-489,6
+499,7
@@
public class Sequence extends ASequence implements SequenceI
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
+ @Override
public int getEnd()
{
return this.end;
public int getEnd()
{
return this.end;
@@
-499,6
+510,7
@@
public class Sequence extends ASequence implements SequenceI
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
+ @Override
public int getLength()
{
return this.sequence.length;
public int getLength()
{
return this.sequence.length;
@@
-510,22
+522,26
@@
public class Sequence extends ASequence implements SequenceI
* @param seq
* DOCUMENT ME!
*/
* @param seq
* DOCUMENT ME!
*/
+ @Override
public void setSequence(String seq)
{
this.sequence = seq.toCharArray();
checkValidRange();
}
public void setSequence(String seq)
{
this.sequence = seq.toCharArray();
checkValidRange();
}
+ @Override
public String getSequenceAsString()
{
return new String(sequence);
}
public String getSequenceAsString()
{
return new String(sequence);
}
+ @Override
public String getSequenceAsString(int start, int end)
{
return new String(getSequence(start, end));
}
public String getSequenceAsString(int start, int end)
{
return new String(getSequence(start, end));
}
+ @Override
public char[] getSequence()
{
return sequence;
public char[] getSequence()
{
return sequence;
@@
-536,6
+552,7
@@
public class Sequence extends ASequence implements SequenceI
*
* @see jalview.datamodel.SequenceI#getSequence(int, int)
*/
*
* @see jalview.datamodel.SequenceI#getSequence(int, int)
*/
+ @Override
public char[] getSequence(int start, int end)
{
if (start < 0)
public char[] getSequence(int start, int end)
{
if (start < 0)
@@
-596,6
+613,7
@@
public class Sequence extends ASequence implements SequenceI
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
+ @Override
public char getCharAt(int i)
{
if (i < sequence.length)
public char getCharAt(int i)
{
if (i < sequence.length)
@@
-614,6
+632,7
@@
public class Sequence extends ASequence implements SequenceI
* @param desc
* DOCUMENT ME!
*/
* @param desc
* DOCUMENT ME!
*/
+ @Override
public void setDescription(String desc)
{
this.description = desc;
public void setDescription(String desc)
{
this.description = desc;
@@
-624,6
+643,7
@@
public class Sequence extends ASequence implements SequenceI
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
+ @Override
public String getDescription()
{
return this.description;
public String getDescription()
{
return this.description;
@@
-634,6
+654,7
@@
public class Sequence extends ASequence implements SequenceI
*
* @see jalview.datamodel.SequenceI#findIndex(int)
*/
*
* @see jalview.datamodel.SequenceI#findIndex(int)
*/
+ @Override
public int findIndex(int pos)
{
// returns the alignment position for a residue
public int findIndex(int pos)
{
// returns the alignment position for a residue
@@
-686,6
+707,7
@@
public class Sequence extends ASequence implements SequenceI
* @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
* residues in SequenceI object
*/
* @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
* residues in SequenceI object
*/
+ @Override
public int[] gapMap()
{
String seq = jalview.analysis.AlignSeq.extractGaps(
public int[] gapMap()
{
String seq = jalview.analysis.AlignSeq.extractGaps(
@@
-937,6
+959,7
@@
public class Sequence extends ASequence implements SequenceI
@Override
public void setDatasetSequence(SequenceI seq)
{
@Override
public void setDatasetSequence(SequenceI seq)
{
+ // TODO check for circular reference before setting?
datasetSequence = seq;
}
datasetSequence = seq;
}
@@
-973,6
+996,7
@@
public class Sequence extends ASequence implements SequenceI
annotation.setSequenceRef(this);
}
annotation.setSequenceRef(this);
}
+ @Override
public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
{
if (this.annotation != null)
public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
{
if (this.annotation != null)
@@
-1040,6
+1064,7
@@
public class Sequence extends ASequence implements SequenceI
*
* @see jalview.datamodel.SequenceI#createDatasetSequence()
*/
*
* @see jalview.datamodel.SequenceI#createDatasetSequence()
*/
+ @Override
public SequenceI createDatasetSequence()
{
if (datasetSequence == null)
public SequenceI createDatasetSequence()
{
if (datasetSequence == null)
@@
-1078,6
+1103,7
@@
public class Sequence extends ASequence implements SequenceI
* jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
* annotations)
*/
* jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
* annotations)
*/
+ @Override
public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
{
if (annotation != null)
public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
{
if (annotation != null)
@@
-1250,6
+1276,7
@@
public class Sequence extends ASequence implements SequenceI
* @return The index (zero-based) on this sequence in the MSA. It returns
* {@code -1} if this information is not available.
*/
* @return The index (zero-based) on this sequence in the MSA. It returns
* {@code -1} if this information is not available.
*/
+ @Override
public int getIndex()
{
return index;
public int getIndex()
{
return index;
@@
-1263,16
+1290,19
@@
public class Sequence extends ASequence implements SequenceI
* position for this sequence. This value is zero-based (zero for
* this first sequence)
*/
* position for this sequence. This value is zero-based (zero for
* this first sequence)
*/
+ @Override
public void setIndex(int value)
{
index = value;
}
public void setIndex(int value)
{
index = value;
}
+ @Override
public void setRNA(RNA r)
{
rna = r;
}
public void setRNA(RNA r)
{
rna = r;
}
+ @Override
public RNA getRNA()
{
return rna;
public RNA getRNA()
{
return rna;
@@
-1297,6
+1327,7
@@
public class Sequence extends ASequence implements SequenceI
return result;
}
return result;
}
+ @Override
public String toString()
{
return getDisplayId(false);
public String toString()
{
return getDisplayId(false);