git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into...
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
6b797d7
..
861595c
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-88,7
+88,7
@@
public class SequenceGroup implements AnnotatedCollectionI
/**
* group members
*/
/**
* group members
*/
- private List<SequenceI> sequences = new ArrayList<>();
+ private List<SequenceI> sequences;
/**
* representative sequence for this group (if any)
/**
* representative sequence for this group (if any)
@@
-102,11
+102,15
@@
public class SequenceGroup implements AnnotatedCollectionI
*/
public ResidueShaderI cs;
*/
public ResidueShaderI cs;
- // start column (base 0)
- int startRes = 0;
+ /**
+ * start column (base 0)
+ */
+ private int startRes = 0;
- // end column (base 0)
- int endRes = 0;
+ /**
+ * end column (base 0)
+ */
+ private int endRes = 0;
public Color outlineColour = Color.black;
public Color outlineColour = Color.black;
@@
-158,6
+162,7
@@
public class SequenceGroup implements AnnotatedCollectionI
{
groupName = "JGroup:" + this.hashCode();
cs = new ResidueShader();
{
groupName = "JGroup:" + this.hashCode();
cs = new ResidueShader();
+ sequences = new ArrayList<>();
}
/**
}
/**
@@
-209,6
+214,7
@@
public class SequenceGroup implements AnnotatedCollectionI
displayBoxes = seqsel.displayBoxes;
displayText = seqsel.displayText;
colourText = seqsel.colourText;
displayBoxes = seqsel.displayBoxes;
displayText = seqsel.displayText;
colourText = seqsel.colourText;
+
startRes = seqsel.startRes;
endRes = seqsel.endRes;
cs = new ResidueShader((ResidueShader) seqsel.cs);
startRes = seqsel.startRes;
endRes = seqsel.endRes;
cs = new ResidueShader((ResidueShader) seqsel.cs);
@@
-238,6
+244,17
@@
public class SequenceGroup implements AnnotatedCollectionI
}
}
}
}
+ /**
+ * Constructor that copies the given list of sequences
+ *
+ * @param seqs
+ */
+ public SequenceGroup(List<SequenceI> seqs)
+ {
+ this();
+ this.sequences.addAll(seqs);
+ }
+
public boolean isShowSequenceLogo()
{
return showSequenceLogo;
public boolean isShowSequenceLogo()
{
return showSequenceLogo;
@@
-252,16
+269,15
@@
public class SequenceGroup implements AnnotatedCollectionI
for (int i = 0, ipos = 0; i < inorder.length; i++)
{
SequenceI seq = inorder[i];
for (int i = 0, ipos = 0; i < inorder.length; i++)
{
SequenceI seq = inorder[i];
-
- seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
- if (seqs[ipos] != null)
+ SequenceI seqipos = seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
+ if (seqipos != null)
{
{
- seqs[ipos].setDescription(seq.getDescription());
- seqs[ipos].setDBRefs(seq.getDBRefs());
- seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
+ seqipos.setDescription(seq.getDescription());
+ seqipos.setDBRefs(seq.getDBRefs());
+ seqipos.setSequenceFeatures(seq.getSequenceFeatures());
if (seq.getDatasetSequence() != null)
{
if (seq.getDatasetSequence() != null)
{
- seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
+ seqipos.setDatasetSequence(seq.getDatasetSequence());
}
if (seq.getAnnotation() != null)
}
if (seq.getAnnotation() != null)
@@
-275,7
+291,7
@@
public class SequenceGroup implements AnnotatedCollectionI
if (alann != null)
{
boolean found = false;
if (alann != null)
{
boolean found = false;
- for (int pos = 0; pos < alann.length; pos++)
+ for (int pos = 0, np = alann.length; pos < np; pos++)
{
if (alann[pos] == tocopy)
{
{
if (alann[pos] == tocopy)
{
@@
-293,7
+309,7
@@
public class SequenceGroup implements AnnotatedCollectionI
newannot.restrict(startRes, endRes);
newannot.setSequenceRef(seqs[ipos]);
newannot.adjustForAlignment();
newannot.restrict(startRes, endRes);
newannot.setSequenceRef(seqs[ipos]);
newannot.adjustForAlignment();
- seqs[ipos].addAlignmentAnnotation(newannot);
+ seqipos.addAlignmentAnnotation(newannot);
}
}
ipos++;
}
}
ipos++;
@@
-752,13
+768,16
@@
public class SequenceGroup implements AnnotatedCollectionI
/**
* Set the first column selected by this group. Runs from 0<=i<N_cols
*
/**
* Set the first column selected by this group. Runs from 0<=i<N_cols
*
- * @param i
+ * @param newStart
*/
*/
- public void setStartRes(int i)
+ public void setStartRes(int newStart)
{
int before = startRes;
{
int before = startRes;
- startRes = i;
- changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+ startRes= Math.max(0,newStart); // sanity check for negative start column positions
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+
+
+
}
/**
}
/**
@@
-1189,9
+1208,10
@@
public class SequenceGroup implements AnnotatedCollectionI
{
if (consensus.annotations[i] != null)
{
{
if (consensus.annotations[i] != null)
{
- if (consensus.annotations[i].description.charAt(0) == '[')
+ String desc = consensus.annotations[i].description;
+ if (desc.length() > 1 && desc.charAt(0) == '[')
{
{
- seqs.append(consensus.annotations[i].description.charAt(1));
+ seqs.append(desc.charAt(1));
}
else
{
}
else
{