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
apply jalview code style
[jalview.git]
/
src
/
jalview
/
appletgui
/
APopupMenu.java
diff --git
a/src/jalview/appletgui/APopupMenu.java
b/src/jalview/appletgui/APopupMenu.java
index
4d58689
..
5288fe4
100755
(executable)
--- a/
src/jalview/appletgui/APopupMenu.java
+++ b/
src/jalview/appletgui/APopupMenu.java
@@
-1,5
+1,5
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
@@
-151,7
+151,7
@@
public class APopupMenu extends java.awt.PopupMenu implements
showText.setState(sg.getDisplayText());
showColourText.setState(sg.getColourText());
showBoxes.setState(sg.getDisplayBoxes());
showText.setState(sg.getDisplayText());
showColourText.setState(sg.getColourText());
showBoxes.setState(sg.getDisplayBoxes());
- displayNonconserved.setState(sg.getShowunconserved());
+ displayNonconserved.setState(sg.getShowNonconserved());
if (!ap.av.alignment.getGroups().contains(sg))
{
groupMenu.remove(unGroupMenuItem);
if (!ap.av.alignment.getGroups().contains(sg))
{
groupMenu.remove(unGroupMenuItem);
@@
-184,9
+184,9
@@
public class APopupMenu extends java.awt.PopupMenu implements
{
// collect matching db-refs
{
// collect matching db-refs
- DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
- .getDBRef(), new String[]
- { target });
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+ seq.getDBRef(), new String[]
+ { target });
// collect id string too
String id = seq.getName();
String descr = seq.getDescription();
// collect id string too
String id = seq.getName();
String descr = seq.getDescription();
@@
-492,8
+492,8
@@
public class APopupMenu extends java.awt.PopupMenu implements
{
EditCommand editCommand = new EditCommand("Edit Sequences",
EditCommand.REPLACE, dialog.getName().replace(' ',
{
EditCommand editCommand = new EditCommand("Edit Sequences",
EditCommand.REPLACE, dialog.getName().replace(' ',
- ap.av.getGapCharacter()), sg
- .getSequencesAsArray(ap.av.hiddenRepSequences),
+ ap.av.getGapCharacter()),
+ sg.getSequencesAsArray(ap.av.hiddenRepSequences),
sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
ap.alignFrame.addHistoryItem(editCommand);
sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
ap.alignFrame.addHistoryItem(editCommand);
@@
-630,19
+630,20
@@
public class APopupMenu extends java.awt.PopupMenu implements
Frame frame = new Frame();
frame.add(cap);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Selection output - "
- + e.getActionCommand(), 600, 500);
+ jalview.bin.JalviewLite.addFrame(frame,
+ "Selection output - " + e.getActionCommand(), 600, 500);
- cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(e
- .getActionCommand(), new Alignment(ap.av
- .getSelectionAsNewSequence()), ap.av.showJVSuffix));
+ cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
+ e.getActionCommand(),
+ new Alignment(ap.av.getSelectionAsNewSequence()),
+ ap.av.showJVSuffix));
}
void editName()
{
}
void editName()
{
- EditNameDialog dialog = new EditNameDialog(seq.getName(), seq
- .getDescription(), " Sequence Name",
+ EditNameDialog dialog = new EditNameDialog(seq.getName(),
+ seq.getDescription(), " Sequence Name",
"Sequence Description", ap.alignFrame,
"Edit Sequence Name / Description", 500, 100, true);
"Sequence Description", ap.alignFrame,
"Edit Sequence Name / Description", 500, 100, true);
@@
-805,9
+806,9
@@
public class APopupMenu extends java.awt.PopupMenu implements
protected void clustalColour_actionPerformed()
{
SequenceGroup sg = getGroup();
protected void clustalColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg
- .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
- .getWidth());
+ sg.cs = new ClustalxColourScheme(
+ sg.getSequences(ap.av.hiddenRepSequences),
+ ap.av.alignment.getWidth());
refresh();
}
refresh();
}
@@
-869,9
+870,9
@@
public class APopupMenu extends java.awt.PopupMenu implements
if (abovePIDColour.getState())
{
if (abovePIDColour.getState())
{
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
- .getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.hiddenRepSequences), 0,
+ ap.av.alignment.getWidth()));
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
.getName());
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
.getName());
@@
-899,9
+900,9
@@
public class APopupMenu extends java.awt.PopupMenu implements
{
SequenceGroup sg = getGroup();
sg.cs = new PIDColourScheme();
{
SequenceGroup sg = getGroup();
sg.cs = new PIDColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
- .getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.hiddenRepSequences), 0,
+ ap.av.alignment.getWidth()));
refresh();
}
refresh();
}
@@
-911,9
+912,9
@@
public class APopupMenu extends java.awt.PopupMenu implements
sg.cs = new Blosum62ColourScheme();
sg.cs = new Blosum62ColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
- .getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.hiddenRepSequences), 0,
+ ap.av.alignment.getWidth()));
refresh();
}
refresh();
}
@@
-936,8
+937,8
@@
public class APopupMenu extends java.awt.PopupMenu implements
{
Conservation c = new Conservation("Group",
{
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg
- .getSequences(ap.av.hiddenRepSequences), 0,
+ ResidueProperties.propHash, 3,
+ sg.getSequences(ap.av.hiddenRepSequences), 0,
ap.av.alignment.getWidth());
c.calculate();
ap.av.alignment.getWidth());
c.calculate();
@@
-992,7
+993,7
@@
public class APopupMenu extends java.awt.PopupMenu implements
public void showNonconserved_itemStateChanged()
{
public void showNonconserved_itemStateChanged()
{
- getGroup().setShowunconserved(this.displayNonconserved.getState());
+ getGroup().setShowNonconserved(this.displayNonconserved.getState());
refresh();
}
refresh();
}