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JAL-1372 JAL-1114 JAL-1628 tidy sequenceI/sequence
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
0652fb5
..
cf1c983
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-661,11
+661,7
@@
public class Sequence implements SequenceI
return map;
}
return map;
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#findPositionMap()
- */
+ @Override
public int[] findPositionMap()
{
int map[] = new int[sequence.length];
public int[] findPositionMap()
{
int map[] = new int[sequence.length];
@@
-685,11
+681,7
@@
public class Sequence implements SequenceI
return map;
}
return map;
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#deleteChars(int, int)
- */
+ @Override
public void deleteChars(int i, int j)
{
int newstart = start, newend = end;
public void deleteChars(int i, int j)
{
int newstart = start, newend = end;
@@
-768,16
+760,7
@@
public class Sequence implements SequenceI
sequence = tmp;
}
sequence = tmp;
}
- /**
- * DOCUMENT ME!
- *
- * @param i
- * DOCUMENT ME!
- * @param c
- * DOCUMENT ME!
- * @param chop
- * DOCUMENT ME!
- */
+ @Override
public void insertCharAt(int i, int length, char c)
{
char[] tmp = new char[sequence.length + length];
public void insertCharAt(int i, int length, char c)
{
char[] tmp = new char[sequence.length + length];
@@
-807,26
+790,31
@@
public class Sequence implements SequenceI
sequence = tmp;
}
sequence = tmp;
}
+ @Override
public void insertCharAt(int i, char c)
{
insertCharAt(i, 1, c);
}
public void insertCharAt(int i, char c)
{
insertCharAt(i, 1, c);
}
+ @Override
public String getVamsasId()
{
return vamsasId;
}
public String getVamsasId()
{
return vamsasId;
}
+ @Override
public void setVamsasId(String id)
{
vamsasId = id;
}
public void setVamsasId(String id)
{
vamsasId = id;
}
+ @Override
public void setDBRef(DBRefEntry[] dbref)
{
dbrefs = dbref;
}
public void setDBRef(DBRefEntry[] dbref)
{
dbrefs = dbref;
}
+ @Override
public DBRefEntry[] getDBRef()
{
if (dbrefs == null && datasetSequence != null
public DBRefEntry[] getDBRef()
{
if (dbrefs == null && datasetSequence != null
@@
-837,6
+825,7
@@
public class Sequence implements SequenceI
return dbrefs;
}
return dbrefs;
}
+ @Override
public void addDBRef(DBRefEntry entry)
{
if (dbrefs == null)
public void addDBRef(DBRefEntry entry)
{
if (dbrefs == null)
@@
-869,40
+858,33
@@
public class Sequence implements SequenceI
dbrefs = temp;
}
dbrefs = temp;
}
+ @Override
public void setDatasetSequence(SequenceI seq)
{
datasetSequence = seq;
}
public void setDatasetSequence(SequenceI seq)
{
datasetSequence = seq;
}
+ @Override
public SequenceI getDatasetSequence()
{
return datasetSequence;
}
public SequenceI getDatasetSequence()
{
return datasetSequence;
}
- /**
- * Returns a new array containing this sequence's annotations, or null.
- */
+ @Override
public AlignmentAnnotation[] getAnnotation()
{
return annotation == null ? null : annotation
.toArray(new AlignmentAnnotation[annotation.size()]);
}
public AlignmentAnnotation[] getAnnotation()
{
return annotation == null ? null : annotation
.toArray(new AlignmentAnnotation[annotation.size()]);
}
- /**
- * Returns true if this sequence has the given annotation (by object
- * identity).
- */
+
@Override
public boolean hasAnnotation(AlignmentAnnotation ann)
{
return annotation == null ? false : annotation.contains(ann);
}
@Override
public boolean hasAnnotation(AlignmentAnnotation ann)
{
return annotation == null ? false : annotation.contains(ann);
}
- /**
- * Add the given annotation, if not already added, and set its sequence ref to
- * be this sequence. Does nothing if this sequence's annotations already
- * include this annotation (by identical object reference).
- */
+ @Override
public void addAlignmentAnnotation(AlignmentAnnotation annotation)
{
if (this.annotation == null)
public void addAlignmentAnnotation(AlignmentAnnotation annotation)
{
if (this.annotation == null)
@@
-948,11
+930,7
@@
public class Sequence implements SequenceI
return true;
}
return true;
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#deriveSequence()
- */
+ @Override
public SequenceI deriveSequence()
{
SequenceI seq = new Sequence(this);
public SequenceI deriveSequence()
{
SequenceI seq = new Sequence(this);
@@
-1043,11
+1021,7
@@
public class Sequence implements SequenceI
}
}
}
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
- */
+ @Override
public AlignmentAnnotation[] getAnnotation(String label)
{
if (annotation == null || annotation.size() == 0)
public AlignmentAnnotation[] getAnnotation(String label)
{
if (annotation == null || annotation.size() == 0)
@@
-1080,6
+1054,7
@@
public class Sequence implements SequenceI
return anns;
}
return anns;
}
+ @Override
public boolean updatePDBIds()
{
if (datasetSequence != null)
public boolean updatePDBIds()
{
if (datasetSequence != null)
@@
-1133,13
+1108,7
@@
public class Sequence implements SequenceI
return false;
}
return false;
}
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
- * jalview.datamodel.Mapping)
- */
+ @Override
public void transferAnnotation(SequenceI entry, Mapping mp)
{
if (datasetSequence != null)
public void transferAnnotation(SequenceI entry, Mapping mp)
{
if (datasetSequence != null)
@@
-1235,13
+1204,6
@@
public class Sequence implements SequenceI
return rna;
}
return rna;
}
- /**
- * Returns a (possibly empty) list of any annotations that match on given
- * calcId (source) and label (type). Null values do not match.
- *
- * @param calcId
- * @param label
- */
@Override
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label)
@Override
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label)