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JAL-2034 moved ‘isDefinedGroup’ flag to a test method on AlignViewportI so controller...
[jalview.git]
/
src
/
jalview
/
gui
/
SeqPanel.java
diff --git
a/src/jalview/gui/SeqPanel.java
b/src/jalview/gui/SeqPanel.java
index
9006262
..
348c21c
100644
(file)
--- a/
src/jalview/gui/SeqPanel.java
+++ b/
src/jalview/gui/SeqPanel.java
@@
-836,7
+836,8
@@
public class SeqPanel extends JPanel implements MouseListener,
* set if av.getSelectionGroup() refers to a group that is defined on the
* alignment view, rather than a transient selection
*/
* set if av.getSelectionGroup() refers to a group that is defined on the
* alignment view, rather than a transient selection
*/
- private boolean editingDefinedGroup = false; // TODO: refactor to avcontroller or viewModel
+ // private boolean editingDefinedGroup = false; // TODO: refactor to
+ // avcontroller or viewModel
/**
* Set status message in alignment panel
/**
* Set status message in alignment panel
@@
-857,7
+858,8
@@
public class SeqPanel extends JPanel implements MouseListener,
* Sequence number (if known), and sequence name.
*/
String seqno = seq == -1 ? "" : " " + (seq + 1);
* Sequence number (if known), and sequence name.
*/
String seqno = seq == -1 ? "" : " " + (seq + 1);
- text.append("Sequence" + seqno + " ID: " + sequence.getName());
+ text.append("Sequence").append(seqno).append(" ID: ")
+ .append(sequence.getName());
String residue = null;
/*
String residue = null;
/*
@@
-1582,12
+1584,10
@@
public class SeqPanel extends JPanel implements MouseListener,
&& (res < stretchGroup.getEndRes()))
{
av.setSelectionGroup(stretchGroup);
&& (res < stretchGroup.getEndRes()))
{
av.setSelectionGroup(stretchGroup);
- editingDefinedGroup = true;
}
else
{
stretchGroup = null;
}
else
{
stretchGroup = null;
- editingDefinedGroup = false;
}
}
else if (!stretchGroup.getSequences(null).contains(sequence)
}
}
else if (!stretchGroup.getSequences(null).contains(sequence)
@@
-1606,7
+1606,6
@@
public class SeqPanel extends JPanel implements MouseListener,
&& (allGroups[i].getEndRes() >= res))
{
stretchGroup = allGroups[i];
&& (allGroups[i].getEndRes() >= res))
{
stretchGroup = allGroups[i];
- editingDefinedGroup = true;
break;
}
}
break;
}
}
@@
-1656,7
+1655,6
@@
public class SeqPanel extends JPanel implements MouseListener,
sg.setEndRes(res);
sg.addSequence(sequence, false);
av.setSelectionGroup(sg);
sg.setEndRes(res);
sg.addSequence(sequence, false);
av.setSelectionGroup(sg);
- editingDefinedGroup = false;
stretchGroup = sg;
if (av.getConservationSelected())
stretchGroup = sg;
if (av.getConservationSelected())
@@
-1702,7
+1700,7
@@
public class SeqPanel extends JPanel implements MouseListener,
// always do this - annotation has own state
// but defer colourscheme update until hidden sequences are passed in
boolean vischange = stretchGroup.recalcConservation(true);
// always do this - annotation has own state
// but defer colourscheme update until hidden sequences are passed in
boolean vischange = stretchGroup.recalcConservation(true);
- needOverviewUpdate |= vischange && editingDefinedGroup;
+ needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
if (stretchGroup.cs != null)
{
stretchGroup.cs.alignmentChanged(stretchGroup,
if (stretchGroup.cs != null)
{
stretchGroup.cs.alignmentChanged(stretchGroup,
@@
-1722,7
+1720,6
@@
public class SeqPanel extends JPanel implements MouseListener,
PaintRefresher.Refresh(this, av.getSequenceSetId());
ap.paintAlignment(needOverviewUpdate);
needOverviewUpdate =false;
PaintRefresher.Refresh(this, av.getSequenceSetId());
ap.paintAlignment(needOverviewUpdate);
needOverviewUpdate =false;
- editingDefinedGroup = false;
changeEndRes = false;
changeStartRes = false;
stretchGroup = null;
changeEndRes = false;
changeStartRes = false;
stretchGroup = null;
@@
-1776,7
+1773,7
@@
public class SeqPanel extends JPanel implements MouseListener,
if (res > (stretchGroup.getStartRes() - 1))
{
stretchGroup.setEndRes(res);
if (res > (stretchGroup.getStartRes() - 1))
{
stretchGroup.setEndRes(res);
- needOverviewUpdate |= editingDefinedGroup;
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
}
else if (changeStartRes)
}
}
else if (changeStartRes)
@@
-1784,7
+1781,7
@@
public class SeqPanel extends JPanel implements MouseListener,
if (res < (stretchGroup.getEndRes() + 1))
{
stretchGroup.setStartRes(res);
if (res < (stretchGroup.getEndRes() + 1))
{
stretchGroup.setStartRes(res);
- needOverviewUpdate |= editingDefinedGroup;
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
}
}
}
@@
-1818,7
+1815,7
@@
public class SeqPanel extends JPanel implements MouseListener,
if (stretchGroup.getSequences(null).contains(nextSeq))
{
stretchGroup.deleteSequence(seq, false);
if (stretchGroup.getSequences(null).contains(nextSeq))
{
stretchGroup.deleteSequence(seq, false);
- needOverviewUpdate |= editingDefinedGroup;
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
else
{
}
else
{
@@
-1828,7
+1825,7
@@
public class SeqPanel extends JPanel implements MouseListener,
}
stretchGroup.addSequence(nextSeq, false);
}
stretchGroup.addSequence(nextSeq, false);
- needOverviewUpdate |= editingDefinedGroup;
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
}
}
}
@@
-1970,10
+1967,12
@@
public class SeqPanel extends JPanel implements MouseListener,
// do we want to thread this ? (contention with seqsel and colsel locks, I
// suspect)
// do we want to thread this ? (contention with seqsel and colsel locks, I
// suspect)
- // rules are: colsel is copied if there is a real intersection between
- // sequence selection
+ /*
+ * only copy colsel if there is a real intersection between
+ * sequence selection and this panel's alignment
+ */
boolean repaint = false;
boolean repaint = false;
- boolean copycolsel = true;
+ boolean copycolsel = false;
SequenceGroup sgroup = null;
if (seqsel != null && seqsel.getSize() > 0)
SequenceGroup sgroup = null;
if (seqsel != null && seqsel.getSize() > 0)
@@
-1987,11
+1986,9
@@
public class SeqPanel extends JPanel implements MouseListener,
}
sgroup = seqsel.intersect(av.getAlignment(),
(av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
}
sgroup = seqsel.intersect(av.getAlignment(),
(av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
- if ((sgroup == null || sgroup.getSize() == 0)
- || (colsel == null || colsel.isEmpty()))
+ if ((sgroup != null && sgroup.getSize() > 0))
{
{
- // don't copy columns if the region didn't intersect.
- copycolsel = false;
+ copycolsel = true;
}
}
if (sgroup != null && sgroup.getSize() > 0)
}
}
if (sgroup != null && sgroup.getSize() > 0)