/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
-import jalview.util.MessageManager;
-
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.image.BufferedImage;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collections;
import java.util.regex.Pattern;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
+
/**
* DOCUMENT ME!
*
public class AnnotationLabels extends JPanel implements MouseListener,
MouseMotionListener, ActionListener
{
+ private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern.compile("<");
+
String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column");
String ADDNEW = MessageManager.getString("label.add_new_row");
Dimension d = ap.annotationScroller.getPreferredSize();
int dif = evt.getY() - oldY;
- dif /= ap.av.charHeight;
- dif *= ap.av.charHeight;
+ dif /= ap.av.getCharHeight();
+ dif *= ap.av.getCharHeight();
if ((d.height - dif) > 20)
{
|| (desc.substring(0, 6).toLowerCase().indexOf("<html>") < 0))
{
// clean the description ready for embedding in html
- desc = new StringBuffer(Pattern.compile("<").matcher(desc)
+ desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
.replaceAll("<"));
desc.insert(0, "<html>");
}
item.addActionListener(this);
pop.add(item);
// JAL-1264 hide all sequence-specific annotations of this type
- final String label = aa[selectedRow].label;
if (selectedRow < aa.length)
{
if (aa[selectedRow].sequenceRef != null)
{
+ final String label = aa[selectedRow].label;
JMenuItem hideType = new JMenuItem();
String text = MessageManager.getString("label.hide_all") + " " + label;
hideType.setText(text);
@Override
public void actionPerformed(ActionEvent e)
{
- for (AlignmentAnnotation ann : ap.av.getAlignment()
- .getAlignmentAnnotation())
- {
- if (ann.sequenceRef != null && ann.label != null
- && ann.label.equals(label))
- {
- ann.visible = false;
- }
- }
+ AlignmentUtils.showOrHideSequenceAnnotations(
+ ap.av.getAlignment(), Collections.singleton(label),
+ null, false, false);
+ // for (AlignmentAnnotation ann : ap.av.getAlignment()
+ // .getAlignmentAnnotation())
+ // {
+ // if (ann.sequenceRef != null && ann.label != null
+ // && ann.label.equals(label))
+ // {
+ // ann.visible = false;
+ // }
+ // }
refresh();
}
});
// property methods
if (selectedRow < aa.length)
{
+ final String label = aa[selectedRow].label;
if (!aa[selectedRow].autoCalculated)
{
if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
pop.addSeparator();
// av and sequencegroup need to implement same interface for
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- MessageManager.getString("label.ignore_gaps_consensus"),
+ MessageManager.getString("label.ignore_gaps_consensus"),
(aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
.getIgnoreGapsConsensus() : ap.av
- .getIgnoreGapsConsensus());
+ .isIgnoreGapsConsensus());
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addActionListener(new ActionListener()
{
if (aaa.groupRef != null)
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_histogram"),
+ MessageManager.getString("label.show_group_histogram"),
aa[selectedRow].groupRef.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
});
pop.add(chist);
final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_logo"),
+ MessageManager.getString("label.show_group_logo"),
aa[selectedRow].groupRef.isShowSequenceLogo());
cprofl.addActionListener(new ActionListener()
{
});
pop.add(cprofl);
final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_group_logo"),
+ MessageManager.getString("label.normalise_group_logo"),
aa[selectedRow].groupRef.isNormaliseSequenceLogo());
cproflnorm.addActionListener(new ActionListener()
{
else
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
+ MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
pop.add(chist);
final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
+ MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
cprof.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
pop.add(cprof);
final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
+ MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
cprofnorm.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
String output = new FormatAdapter().formatSequences("Fasta", seqs,
- omitHidden);
+ omitHidden, null);
Toolkit.getDefaultToolkit().getSystemClipboard()
.setContents(new StringSelection(output), Desktop.instance);
dragEvent.getY() - getScrollOffset());
}
- if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
+ if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
{
g.drawString(MessageManager.getString("label.right_click"), 2, 8);
g.drawString(MessageManager.getString("label.to_add_annotation"), 2,