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Dont set the dataset name and description
[jalview.git]
/
src
/
jalview
/
gui
/
PopupMenu.java
diff --git
a/src/jalview/gui/PopupMenu.java
b/src/jalview/gui/PopupMenu.java
index
d099944
..
6d3f073
100755
(executable)
--- a/
src/jalview/gui/PopupMenu.java
+++ b/
src/jalview/gui/PopupMenu.java
@@
-142,8
+142,7
@@
public class PopupMenu extends JPopupMenu
\r
if (seq != null)
\r
{
\r
\r
if (seq != null)
\r
{
\r
- int start = Math.max(sequence.getName().length()-15, 0);
\r
- sequenceMenu.setText(sequence.getName().substring(start));
\r
+ sequenceMenu.setText(sequence.getName());
\r
\r
JMenuItem menuItem;
\r
if( seq.getDatasetSequence().getPDBId() != null)
\r
\r
JMenuItem menuItem;
\r
if( seq.getDatasetSequence().getPDBId() != null)
\r
@@
-814,9
+813,9
@@
public class PopupMenu extends JPopupMenu
\r
if (abovePIDColour.isSelected())
\r
{
\r
\r
if (abovePIDColour.isSelected())
\r
{
\r
- sg.cs.setConsensus(AAFrequency.calculate(
\r
- sg.getSequences(true), 0,
\r
- ap.av.alignment.getWidth()));
\r
+ sg.cs.setConsensus(AAFrequency.calculate(
\r
+ sg.getSequences(true), sg.getStartRes(),
\r
+ sg.getEndRes() + 1));
\r
\r
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
\r
getGroup().getName());
\r
\r
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
\r
getGroup().getName());
\r
@@
-862,8
+861,9
@@
public class PopupMenu extends JPopupMenu
{
\r
SequenceGroup sg = getGroup();
\r
sg.cs = new PIDColourScheme();
\r
{
\r
SequenceGroup sg = getGroup();
\r
sg.cs = new PIDColourScheme();
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
\r
- ap.av.alignment.getWidth()));
\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
\r
+ sg.getStartRes(),
\r
+ sg.getEndRes() + 1));
\r
refresh();
\r
}
\r
\r
refresh();
\r
}
\r
\r
@@
-878,8
+878,9
@@
public class PopupMenu extends JPopupMenu
\r
sg.cs = new Blosum62ColourScheme();
\r
\r
\r
sg.cs = new Blosum62ColourScheme();
\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
\r
- ap.av.alignment.getWidth()));
\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
\r
+ sg.getStartRes(),
\r
+ sg.getEndRes() + 1));
\r
\r
refresh();
\r
}
\r
\r
refresh();
\r
}
\r
@@
-910,8
+911,9
@@
public class PopupMenu extends JPopupMenu
{
\r
Conservation c = new Conservation("Group",
\r
ResidueProperties.propHash, 3,
\r
{
\r
Conservation c = new Conservation("Group",
\r
ResidueProperties.propHash, 3,
\r
- sg.getSequences(true), 0,
\r
- ap.av.alignment.getWidth());
\r
+ sg.getSequences(true),
\r
+ sg.getStartRes(),
\r
+ sg.getEndRes() + 1);
\r
\r
c.calculate();
\r
c.verdict(false, ap.av.ConsPercGaps);
\r
\r
c.calculate();
\r
c.verdict(false, ap.av.ConsPercGaps);
\r
@@
-1038,13
+1040,15
@@
public class PopupMenu extends JPopupMenu
}
\r
\r
s = s.replace(' ', '_');
\r
}
\r
\r
s = s.replace(' ', '_');
\r
- sequence.getDatasetSequence().setName(s);
\r
sequence.setName(s);
\r
ap.repaint();
\r
}
\r
\r
sequence.setName(s);
\r
ap.repaint();
\r
}
\r
\r
- sequence.getDatasetSequence().setDescription(description.getText());
\r
sequence.setDescription(description.getText());
\r
sequence.setDescription(description.getText());
\r
+
\r
+ ap.av.firePropertyChange("alignment", null,
\r
+ ap.av.getAlignment().getSequences());
\r
+
\r
}
\r
\r
/**
\r
}
\r
\r
/**
\r
@@
-1242,7
+1246,9
@@
public class PopupMenu extends JPopupMenu
ap.alignFrame.addHistoryItem(caseCommand);
\r
\r
\r
ap.alignFrame.addHistoryItem(caseCommand);
\r
\r
\r
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
\r
+ ap.av.firePropertyChange("alignment", null,
\r
+ ap.av.getAlignment().getSequences());
\r
+
\r
}
\r
}
\r
\r
}
\r
}
\r
\r