/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.appletgui;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.util.ParseHtmlBodyAndLinks;
+
import java.awt.Checkbox;
import java.awt.CheckboxMenuItem;
import java.awt.Color;
import java.util.Collections;
import java.util.Vector;
-import jalview.analysis.AlignmentUtils;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-import jalview.util.ParseHtmlBodyAndLinks;
-
public class AnnotationLabels extends Panel implements ActionListener,
MouseListener, MouseMotionListener
{
if (aaa.groupRef != null)
{
final CheckboxMenuItem chist = new CheckboxMenuItem(
- MessageManager.getString("label.show_group_histogram"),
+ MessageManager
+ .getString("label.show_group_histogram"),
aa[selectedRow].groupRef.isShowConsensusHistogram());
chist.addItemListener(new ItemListener()
{
popup.add(cprofl);
final CheckboxMenuItem cprofn = new CheckboxMenuItem(
- MessageManager.getString("label.normalise_group_logo"),
+ MessageManager
+ .getString("label.normalise_group_logo"),
aa[selectedRow].groupRef.isNormaliseSequenceLogo());
cprofn.addItemListener(new ItemListener()
{
else
{
final CheckboxMenuItem chist = new CheckboxMenuItem(
- MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
+ MessageManager.getString("label.show_histogram"),
+ av.isShowConsensusHistogram());
chist.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
});
popup.add(chist);
final CheckboxMenuItem cprof = new CheckboxMenuItem(
- MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
+ MessageManager.getString("label.show_logo"),
+ av.isShowSequenceLogo());
cprof.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
});
popup.add(cprof);
final CheckboxMenuItem cprofn = new CheckboxMenuItem(
- MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseSequenceLogo());
cprofn.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
{
if (evt.getClickCount() == 1)
{
- ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays
- .asList(new SequenceI[]
- { aa[selectedRow].sequenceRef }));
+ ap.seqPanel.ap.idPanel
+ .highlightSearchResults(Arrays
+ .asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
}
else if (evt.getClickCount() >= 2)
{
ap.seqPanel.ap.idPanel.highlightSearchResults(null);
SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg!=null)
+ if (sg != null)
{
- // we make a copy rather than edit the current selection if no modifiers pressed
+ // we make a copy rather than edit the current selection if no
+ // modifiers pressed
// see Enhancement JAL-1557
if (!(evt.isControlDown() || evt.isShiftDown()))
{
sg = new SequenceGroup(sg);
sg.clear();
sg.addSequence(aa[selectedRow].sequenceRef, false);
- } else {
+ }
+ else
+ {
if (evt.isControlDown())
{
sg.addOrRemove(aa[selectedRow].sequenceRef, true);
- } else {
- // notionally, we should also add intermediate sequences from last added sequence ?
+ }
+ else
+ {
+ // notionally, we should also add intermediate sequences from
+ // last added sequence ?
sg.addSequence(aa[selectedRow].sequenceRef, true);
}
}
- } else {
+ }
+ else
+ {
sg = new SequenceGroup();
sg.setStartRes(0);
- sg.setEndRes(ap.av.getAlignment().getWidth()-1);
+ sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
sg.addSequence(aa[selectedRow].sequenceRef, false);
}
ap.av.setSelectionGroup(sg);
for (int[] region : av.getColumnSelection().getHiddenColumns())
{
jalview.appletgui.AlignFrame.copiedHiddenColumns
- .addElement(new int[]
- { region[0], region[1] });
+ .addElement(new int[] { region[0], region[1] });
}
}
}