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Hidden representatives moved from sequence to viewport
[jalview.git]
/
src
/
jalview
/
gui
/
SeqPanel.java
diff --git
a/src/jalview/gui/SeqPanel.java
b/src/jalview/gui/SeqPanel.java
index
bc9adfe
..
675325a
100755
(executable)
--- a/
src/jalview/gui/SeqPanel.java
+++ b/
src/jalview/gui/SeqPanel.java
@@
-366,7
+366,7
@@
public class SeqPanel extends JPanel implements MouseListener,
SequenceGroup sg = av.selectionGroup;
\r
//Find the top and bottom of this group
\r
int min = av.alignment.getHeight(), max = 0;
\r
SequenceGroup sg = av.selectionGroup;
\r
//Find the top and bottom of this group
\r
int min = av.alignment.getHeight(), max = 0;
\r
- for(int i=0; i<sg.getSize(false); i++)
\r
+ for(int i=0; i<sg.getSize(); i++)
\r
{
\r
int index = av.alignment.findIndex( sg.getSequenceAt(i) );
\r
if(index > max)
\r
{
\r
int index = av.alignment.findIndex( sg.getSequenceAt(i) );
\r
if(index > max)
\r
@@
-402,7
+402,7
@@
public class SeqPanel extends JPanel implements MouseListener,
else
\r
{
\r
// Now add any sequences between min and max
\r
else
\r
{
\r
// Now add any sequences between min and max
\r
- sg.getSequences(false).clear();
\r
+ sg.getSequences(null).clear();
\r
for (int i = min; i < max; i++)
\r
{
\r
sg.addSequence(av.alignment.getSequenceAt(i), false);
\r
for (int i = min; i < max; i++)
\r
{
\r
sg.addSequence(av.alignment.getSequenceAt(i), false);
\r
@@
-809,24
+809,20
@@
public class SeqPanel extends JPanel implements MouseListener,
boolean fixedColumns = false;
\r
SequenceGroup sg = av.getSelectionGroup();
\r
\r
boolean fixedColumns = false;
\r
SequenceGroup sg = av.getSelectionGroup();
\r
\r
+ SequenceI seq = av.alignment.getSequenceAt(startseq);
\r
\r
\r
+ //No group, but the sequence may represent a group
\r
if (!groupEditing && av.hasHiddenRows)
\r
{
\r
if (!groupEditing && av.hasHiddenRows)
\r
{
\r
- if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
\r
+ if (av.hiddenRepSequences!=null
\r
+ && av.hiddenRepSequences.containsKey(seq))
\r
{
\r
{
\r
+ sg = (SequenceGroup)av.hiddenRepSequences.get(seq);
\r
groupEditing = true;
\r
}
\r
}
\r
\r
groupEditing = true;
\r
}
\r
}
\r
\r
- //No group, but the sequence may represent a group
\r
- if (groupEditing
\r
- && sg == null
\r
- && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)
\r
- {
\r
- groupEditing = false;
\r
- }
\r
\r
\r
- SequenceI seq = av.alignment.getSequenceAt(startseq);
\r
StringBuffer message = new StringBuffer();
\r
if (groupEditing)
\r
{
\r
StringBuffer message = new StringBuffer();
\r
if (groupEditing)
\r
{
\r
@@
-855,7
+851,7
@@
public class SeqPanel extends JPanel implements MouseListener,
\r
//Are we editing within a selection group?
\r
if (groupEditing
\r
\r
//Are we editing within a selection group?
\r
if (groupEditing
\r
- || (sg != null && sg.getSequences(true).contains(seq)))
\r
+ || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
\r
{
\r
fixedColumns = true;
\r
\r
{
\r
fixedColumns = true;
\r
\r
@@
-863,9
+859,7
@@
public class SeqPanel extends JPanel implements MouseListener,
//but the sequence represents a group
\r
if (sg == null)
\r
{
\r
//but the sequence represents a group
\r
if (sg == null)
\r
{
\r
- sg = new SequenceGroup(null, null, false, false, false, 0,
\r
- av.alignment.getWidth()-1);
\r
- sg.addSequence(av.alignment.getSequenceAt(startseq), false);
\r
+ sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
\r
}
\r
\r
fixedLeft = sg.getStartRes();
\r
}
\r
\r
fixedLeft = sg.getStartRes();
\r
@@
-924,7
+918,7
@@
public class SeqPanel extends JPanel implements MouseListener,
\r
if (groupEditing)
\r
{
\r
\r
if (groupEditing)
\r
{
\r
- Vector vseqs = sg.getSequences(true);
\r
+ Vector vseqs = sg.getSequences(av.hiddenRepSequences);
\r
int g, groupSize = vseqs.size();
\r
SequenceI[] groupSeqs = new SequenceI[groupSize];
\r
for (g = 0; g < groupSeqs.length; g++)
\r
int g, groupSize = vseqs.size();
\r
SequenceI[] groupSeqs = new SequenceI[groupSize];
\r
for (g = 0; g < groupSeqs.length; g++)
\r
@@
-972,7
+966,7
@@
public class SeqPanel extends JPanel implements MouseListener,
\r
if (!blank)
\r
{
\r
\r
if (!blank)
\r
{
\r
- if(sg.getSize(false) == av.alignment.getHeight() )
\r
+ if(sg.getSize() == av.alignment.getHeight() )
\r
{
\r
if((av.hasHiddenColumns
\r
&& startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
\r
{
\r
if((av.hasHiddenColumns
\r
&& startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
\r
@@
-1221,7
+1215,7
@@
public class SeqPanel extends JPanel implements MouseListener,
SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) );
\r
if(evt.getClickCount()>1)
\r
{
\r
SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) );
\r
if(evt.getClickCount()>1)
\r
{
\r
- if (av.getSelectionGroup().getSize(false) == 1
\r
+ if (av.getSelectionGroup().getSize() == 1
\r
&& av.getSelectionGroup().getEndRes()
\r
- av.getSelectionGroup().getStartRes() < 2)
\r
av.setSelectionGroup(null);
\r
&& av.getSelectionGroup().getEndRes()
\r
- av.getSelectionGroup().getStartRes() < 2)
\r
av.setSelectionGroup(null);
\r
@@
-1327,7
+1321,7
@@
public class SeqPanel extends JPanel implements MouseListener,
stretchGroup = null;
\r
}
\r
}
\r
stretchGroup = null;
\r
}
\r
}
\r
- else if (!stretchGroup.getSequences(false).contains(sequence) ||
\r
+ else if (!stretchGroup.getSequences(null).contains(sequence) ||
\r
(stretchGroup.getStartRes() > res) ||
\r
(stretchGroup.getEndRes() < res))
\r
{
\r
(stretchGroup.getStartRes() > res) ||
\r
(stretchGroup.getEndRes() < res))
\r
{
\r
@@
-1442,7
+1436,7
@@
public class SeqPanel extends JPanel implements MouseListener,
if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
{
\r
( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
\r
if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
{
\r
( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
\r
- stretchGroup.getSequences(true),
\r
+ stretchGroup.getSequences(av.hiddenRepSequences),
\r
stretchGroup.getWidth());
\r
}
\r
\r
stretchGroup.getWidth());
\r
}
\r
\r
@@
-1549,7
+1543,7
@@
public class SeqPanel extends JPanel implements MouseListener,
\r
Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
\r
\r
Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
\r
- if (stretchGroup.getSequences(false).contains(nextSeq))
\r
+ if (stretchGroup.getSequences(null).contains(nextSeq))
\r
{
\r
stretchGroup.deleteSequence(seq, false);
\r
}
\r
{
\r
stretchGroup.deleteSequence(seq, false);
\r
}
\r