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pdb stuff moved to popupmenu
[jalview.git]
/
src
/
jalview
/
appletgui
/
APopupMenu.java
diff --git
a/src/jalview/appletgui/APopupMenu.java
b/src/jalview/appletgui/APopupMenu.java
index
1c9b3cd
..
3401cc4
100755
(executable)
--- a/
src/jalview/appletgui/APopupMenu.java
+++ b/
src/jalview/appletgui/APopupMenu.java
@@
-82,7
+82,7
@@
public class APopupMenu
\r
SequenceGroup sg = ap.av.getSelectionGroup();
\r
\r
\r
SequenceGroup sg = ap.av.getSelectionGroup();
\r
\r
- if (sg != null && sg.getSize()>0)
\r
+ if (sg != null && sg.getSize(false)>0)
\r
{
\r
showText.setState(sg.getDisplayText());
\r
showColourText.setState(sg.getColourText());
\r
{
\r
showText.setState(sg.getDisplayText());
\r
showColourText.setState(sg.getColourText());
\r
@@
-209,12
+209,14
@@
public class APopupMenu
SequenceGroup sg = ap.av.getSelectionGroup();
\r
if (sg != null)
\r
{
\r
SequenceGroup sg = ap.av.getSelectionGroup();
\r
if (sg != null)
\r
{
\r
- for (int g = 0; g < sg.getSize(); g++)
\r
+ for (int g = 0; g < sg.getSize(true); g++)
\r
{
\r
if (source == toggleCase)
\r
{
\r
if (source == toggleCase)
\r
- sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
\r
+ ((SequenceI) sg.getSequences(true).elementAt(g))
\r
+ .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
\r
else
\r
else
\r
- sg.getSequenceAt(g).changeCase(source == toUpper, sg.getStartRes(),
\r
+ ((SequenceI) sg.getSequences(true).elementAt(g))
\r
+ .changeCase(source == toUpper, sg.getStartRes(),
\r
sg.getEndRes() + 1);
\r
}
\r
ap.seqPanel.seqCanvas.repaint();
\r
sg.getEndRes() + 1);
\r
}
\r
ap.seqPanel.seqCanvas.repaint();
\r
@@
-333,7
+335,7
@@
public class APopupMenu
protected void clustalColour_actionPerformed()
\r
{
\r
SequenceGroup sg = getGroup();
\r
protected void clustalColour_actionPerformed()
\r
{
\r
SequenceGroup sg = getGroup();
\r
- sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
\r
+ sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());
\r
refresh();
\r
}
\r
\r
refresh();
\r
}
\r
\r
@@
-393,7
+395,7
@@
public class APopupMenu
\r
if (abovePIDColour.getState())
\r
{
\r
\r
if (abovePIDColour.getState())
\r
{
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
\r
ap.av.alignment.getWidth()));
\r
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
\r
getGroup().getName());
\r
ap.av.alignment.getWidth()));
\r
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
\r
getGroup().getName());
\r
@@
-421,7
+423,7
@@
public class APopupMenu
{
\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.sequences, 0,
\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
\r
ap.av.alignment.getWidth()));
\r
refresh();
\r
}
\r
ap.av.alignment.getWidth()));
\r
refresh();
\r
}
\r
@@
-432,7
+434,7
@@
public class APopupMenu
\r
sg.cs = new Blosum62ColourScheme();
\r
\r
\r
sg.cs = new Blosum62ColourScheme();
\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
\r
ap.av.alignment.getWidth()));
\r
\r
refresh();
\r
ap.av.alignment.getWidth()));
\r
\r
refresh();
\r
@@
-455,7
+457,7
@@
public class APopupMenu
\r
Conservation c = new Conservation("Group",
\r
ResidueProperties.propHash, 3,
\r
\r
Conservation c = new Conservation("Group",
\r
ResidueProperties.propHash, 3,
\r
- sg.sequences, 0,
\r
+ sg.getSequences(true), 0,
\r
ap.av.alignment.getWidth());
\r
\r
c.calculate();
\r
ap.av.alignment.getWidth());
\r
\r
c.calculate();
\r