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[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
ed21f60
..
693291f
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-92,12
+92,12
@@
public class SequenceGroup implements AnnotatedCollectionI
* consensus calculation property
*/
private boolean showSequenceLogo = false;
* consensus calculation property
*/
private boolean showSequenceLogo = false;
+
/**
* flag indicating if logo should be rendered normalised
*/
private boolean normaliseSequenceLogo;
/**
* flag indicating if logo should be rendered normalised
*/
private boolean normaliseSequenceLogo;
-
/**
* @return the includeAllConsSymbols
*/
/**
* @return the includeAllConsSymbols
*/
@@
-285,11
+285,14
@@
public class SequenceGroup implements AnnotatedCollectionI
return eres;
}
return eres;
}
+
public List<SequenceI> getSequences()
{
return sequences;
}
public List<SequenceI> getSequences()
{
return sequences;
}
- public List<SequenceI> getSequences(Map<SequenceI, SequenceCollectionI> hiddenReps)
+
+ public List<SequenceI> getSequences(
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
{
if (hiddenReps == null)
{
{
if (hiddenReps == null)
{
@@
-306,7
+309,7
@@
public class SequenceGroup implements AnnotatedCollectionI
if (hiddenReps.containsKey(seq))
{
SequenceCollectionI hsg = hiddenReps.get(seq);
if (hiddenReps.containsKey(seq))
{
SequenceCollectionI hsg = hiddenReps.get(seq);
- for (SequenceI seq2:hsg.getSequences())
+ for (SequenceI seq2 : hsg.getSequences())
{
if (seq2 != seq && !allSequences.contains(seq2))
{
{
if (seq2 != seq && !allSequences.contains(seq2))
{
@@
-320,10
+323,11
@@
public class SequenceGroup implements AnnotatedCollectionI
}
}
}
}
- public SequenceI[] getSequencesAsArray(Map<SequenceI, SequenceCollectionI> map)
+ public SequenceI[] getSequencesAsArray(
+ Map<SequenceI, SequenceCollectionI> map)
{
List<SequenceI> tmp = getSequences(map);
{
List<SequenceI> tmp = getSequences(map);
- if (tmp==null)
+ if (tmp == null)
{
return null;
}
{
return null;
}
@@
-479,9
+483,9
@@
public class SequenceGroup implements AnnotatedCollectionI
{
return;
}
{
return;
}
- if (cs!=null)
+ if (cs != null)
{
{
- cs.alignmentChanged(this,null);
+ cs.alignmentChanged(this, null);
}
try
{
}
try
{
@@
-494,7
+498,7
@@
public class SequenceGroup implements AnnotatedCollectionI
if (cs != null)
{
cs.setConsensus(cnsns);
if (cs != null)
{
cs.setConsensus(cnsns);
- cs.alignmentChanged(this,null);
+ cs.alignmentChanged(this, null);
}
if ((conservation != null)
}
if ((conservation != null)
@@
-514,7
+518,7
@@
public class SequenceGroup implements AnnotatedCollectionI
if (cs.conservationApplied())
{
cs.setConservation(c);
if (cs.conservationApplied())
{
cs.setConservation(c);
- cs.alignmentChanged(this,null);
+ cs.alignmentChanged(this, null);
}
}
}
}
}
}
@@
-948,7
+952,8
@@
public class SequenceGroup implements AnnotatedCollectionI
* (may be null)
* @return new group containing sequences common to this group and alignment
*/
* (may be null)
* @return new group containing sequences common to this group and alignment
*/
- public SequenceGroup intersect(AlignmentI alignment, Map<SequenceI, SequenceCollectionI> map)
+ public SequenceGroup intersect(AlignmentI alignment,
+ Map<SequenceI, SequenceCollectionI> map)
{
SequenceGroup sgroup = new SequenceGroup(this);
SequenceI[] insect = getSequencesInOrder(alignment);
{
SequenceGroup sgroup = new SequenceGroup(this);
SequenceI[] insect = getSequencesInOrder(alignment);
@@
-1166,51
+1171,56
@@
public class SequenceGroup implements AnnotatedCollectionI
/**
* set flag indicating if logo should be normalised when rendered
/**
* set flag indicating if logo should be normalised when rendered
+ *
* @param norm
*/
public void setNormaliseSequenceLogo(boolean norm)
{
* @param norm
*/
public void setNormaliseSequenceLogo(boolean norm)
{
- normaliseSequenceLogo=norm;
+ normaliseSequenceLogo = norm;
}
}
+
public boolean isNormaliseSequenceLogo()
{
return normaliseSequenceLogo;
}
public boolean isNormaliseSequenceLogo()
{
return normaliseSequenceLogo;
}
+
@Override
/**
* returns a new array with all annotation involving this group
*/
public AlignmentAnnotation[] getAlignmentAnnotation()
{
@Override
/**
* returns a new array with all annotation involving this group
*/
public AlignmentAnnotation[] getAlignmentAnnotation()
{
- // TODO add in other methods like 'getAlignmentAnnotation(String label), etc'
+ // TODO add in other methods like 'getAlignmentAnnotation(String label),
+ // etc'
ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
- for (SequenceI seq:(Vector<SequenceI>)sequences)
+ for (SequenceI seq : (Vector<SequenceI>) sequences)
{
{
- for (AlignmentAnnotation al: seq.getAnnotation())
+ for (AlignmentAnnotation al : seq.getAnnotation())
{
{
- if (al.groupRef==this)
+ if (al.groupRef == this)
{
annot.add(al);
}
}
}
{
annot.add(al);
}
}
}
- if (consensus!=null)
+ if (consensus != null)
{
annot.add(consensus);
}
{
annot.add(consensus);
}
- if (conservation!=null)
+ if (conservation != null)
{
annot.add(conservation);
}
return annot.toArray(new AlignmentAnnotation[0]);
}
{
annot.add(conservation);
}
return annot.toArray(new AlignmentAnnotation[0]);
}
+
@Override
public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
{
@Override
public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
{
- ArrayList<AlignmentAnnotation> aa=new ArrayList<AlignmentAnnotation>();
- for (AlignmentAnnotation a:getAlignmentAnnotation())
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation a : getAlignmentAnnotation())
{
{
- if (a.getCalcId()==calcId)
+ if (a.getCalcId() == calcId)
{
aa.add(a);
}
{
aa.add(a);
}