X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=445ee11e675f90e28f11df608866c9507070161d;hb=refs%2Fheads%2Ffeatures%2Fhmmer_statistics;hp=a5b07163b4fc50357c3b7470680a4845b20c35b4;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index a5b0716..445ee11 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,6 +1,6 @@
/*
- * 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.
*
@@ -20,19 +20,47 @@
*/
package jalview.gui;
-import java.util.*;
-import java.util.regex.Pattern;
+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.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.MediaTracker;
+import java.awt.RenderingHints;
+import java.awt.Toolkit;
+import java.awt.datatransfer.StringSelection;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
import java.awt.geom.AffineTransform;
-import java.awt.image.*;
-import javax.swing.*;
+import java.awt.image.BufferedImage;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import java.util.regex.Pattern;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.util.MessageManager;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
/**
* DOCUMENT ME!
@@ -43,21 +71,28 @@ import jalview.util.MessageManager;
public class AnnotationLabels extends JPanel implements MouseListener,
MouseMotionListener, ActionListener
{
- static String TOGGLE_LABELSCALE = "Scale Label to Column";
+ private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
+ .compile("<");
- static String ADDNEW = "Add New Row";
- static String EDITNAME = "Edit Label/Description";
+ String TOGGLE_LABELSCALE = MessageManager
+ .getString("label.scale_label_to_column");
- static String HIDE = "Hide This Row";
+ String ADDNEW = MessageManager.getString("label.add_new_row");
- static String DELETE = "Delete This Row";
+ String EDITNAME = MessageManager
+ .getString("label.edit_label_description");
- static String SHOWALL = "Show All Hidden Rows";
+ String HIDE = MessageManager.getString("label.hide_row");
- static String OUTPUT_TEXT = "Export Annotation";
+ String DELETE = MessageManager.getString("label.delete_row");
- static String COPYCONS_SEQ = "Copy Consensus Sequence";
+ String SHOWALL = MessageManager.getString("label.show_all_hidden_rows");
+
+ String OUTPUT_TEXT = MessageManager.getString("label.export_annotation");
+
+ String COPYCONS_SEQ = MessageManager
+ .getString("label.copy_consensus_sequence");
boolean resizePanel = false;
@@ -75,7 +110,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
int selectedRow;
- int scrollOffset = 0;
+ private int scrollOffset = 0;
Font font = new Font("Arial", Font.PLAIN, 11);
@@ -115,11 +150,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
Graphics2D g = (Graphics2D) bi.getGraphics();
g.rotate(Math.toRadians(90));
g.drawImage(temp, 0, -bi.getWidth(this), this);
- image = (Image) bi;
+ image = bi;
addMouseListener(this);
addMouseMotionListener(this);
- addMouseWheelListener(ap.annotationPanel);
+ addMouseWheelListener(ap.getAnnotationPanel());
}
public AnnotationLabels(AlignViewport av)
@@ -180,11 +215,13 @@ public class AnnotationLabels extends JPanel implements MouseListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void actionPerformed(ActionEvent evt)
{
AlignmentAnnotation[] aa = ap.av.getAlignment()
.getAlignmentAnnotation();
+ boolean fullRepaint = false;
if (evt.getActionCommand().equals(ADDNEW))
{
AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
@@ -197,11 +234,16 @@ public class AnnotationLabels extends JPanel implements MouseListener,
ap.av.getAlignment().addAnnotation(newAnnotation);
ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
+ fullRepaint = true;
}
else if (evt.getActionCommand().equals(EDITNAME))
{
+ String name = aa[selectedRow].label;
editLabelDescription(aa[selectedRow]);
- repaint();
+ if (!name.equalsIgnoreCase(aa[selectedRow].label))
+ {
+ fullRepaint = true;
+ }
}
else if (evt.getActionCommand().equals(HIDE))
{
@@ -210,6 +252,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
else if (evt.getActionCommand().equals(DELETE))
{
ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
+ ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
+ fullRepaint = true;
}
else if (evt.getActionCommand().equals(SHOWALL))
{
@@ -220,12 +264,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
aa[i].visible = true;
}
}
+ fullRepaint = true;
}
else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
new AnnotationExporter().exportAnnotations(ap,
- new AlignmentAnnotation[]
- { aa[selectedRow] }, null, null);
+ new AlignmentAnnotation[] { aa[selectedRow] });
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
@@ -249,11 +293,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
}
- ap.validateAnnotationDimensions(false);
- ap.addNotify();
- ap.repaint();
- // validate();
- // ap.paintAlignment(true);
+ ap.refresh(fullRepaint);
+
}
/**
@@ -264,6 +305,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
*/
boolean editLabelDescription(AlignmentAnnotation annotation)
{
+ // TODO i18n
EditNameDialog dialog = new EditNameDialog(annotation.label,
annotation.description, " Annotation Name ",
"Annotation Description ", "Edit Annotation Name/Description",
@@ -286,255 +328,30 @@ public class AnnotationLabels extends JPanel implements MouseListener,
return true;
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
+ @Override
public void mousePressed(MouseEvent evt)
{
- getSelectedRow(evt.getY() - scrollOffset);
+ getSelectedRow(evt.getY() - getScrollOffset());
oldY = evt.getY();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- public void mouseReleased(MouseEvent evt)
- {
- int start = selectedRow;
- getSelectedRow(evt.getY() - scrollOffset);
- int end = selectedRow;
-
- if (start != end)
- {
- // Swap these annotations
- AlignmentAnnotation startAA = ap.av.getAlignment()
- .getAlignmentAnnotation()[start];
- if (end == -1)
- {
- end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
- }
- AlignmentAnnotation endAA = ap.av.getAlignment()
- .getAlignmentAnnotation()[end];
-
- ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
- ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
- }
-
- resizePanel = false;
- dragEvent = null;
- repaint();
- ap.annotationPanel.repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- public void mouseEntered(MouseEvent evt)
- {
- if (evt.getY() < 10)
- {
- resizePanel = true;
- repaint();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- public void mouseExited(MouseEvent evt)
- {
- if (dragEvent == null)
- {
- resizePanel = false;
- repaint();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- public void mouseDragged(MouseEvent evt)
- {
- dragEvent = evt;
-
- if (resizePanel)
- {
- Dimension d = ap.annotationScroller.getPreferredSize();
- int dif = evt.getY() - oldY;
-
- dif /= ap.av.charHeight;
- dif *= ap.av.charHeight;
-
- if ((d.height - dif) > 20)
- {
- ap.annotationScroller.setPreferredSize(new Dimension(d.width,
- d.height - dif));
- d = ap.annotationSpaceFillerHolder.getPreferredSize();
- ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
- d.width, d.height - dif));
- ap.paintAlignment(true);
- }
-
- ap.addNotify();
- }
- else
- {
- repaint();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- public void mouseMoved(MouseEvent evt)
- {
- resizePanel = evt.getY() < 10;
-
- getSelectedRow(evt.getY() - scrollOffset);
-
- if (selectedRow > -1
- && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
+ if (evt.isPopupTrigger())
{
- AlignmentAnnotation aa = ap.av.getAlignment()
- .getAlignmentAnnotation()[selectedRow];
-
- StringBuffer desc = new StringBuffer();
- if (aa.description != null
- && !aa.description.equals("New description"))
- {
- // TODO: we could refactor and merge this code with the code in
- // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
- // tooltips
- desc.append(aa.getDescription(true).trim());
- // check to see if the description is an html fragment.
- if (desc.length() < 6
- || (desc.substring(0, 6).toLowerCase().indexOf("") < 0))
- {
- // clean the description ready for embedding in html
- desc = new StringBuffer(Pattern.compile("<").matcher(desc)
- .replaceAll("<"));
- desc.insert(0, "");
- }
- else
- {
- // remove terminating html if any
- int i = desc.substring(desc.length() - 7).toLowerCase()
- .lastIndexOf("");
- if (i > -1)
- {
- desc.setLength(desc.length() - 7 + i);
- }
- }
- if (aa.hasScore())
- {
- desc.append("
");
- }
-
- }
- else
- {
- // begin the tooltip's html fragment
- desc.append("");
- }
- if (aa.hasScore())
- {
- // TODO: limit precision of score to avoid noise from imprecise doubles
- // (64.7 becomes 64.7+/some tiny value).
- desc.append(" Score: " + aa.score);
- }
-
- if (desc.length() > 6)
- {
- desc.append("");
- this.setToolTipText(desc.toString());
- }
- else
- this.setToolTipText(null);
+ showPopupMenu(evt);
}
-
}
/**
- * DOCUMENT ME!
+ * Build and show the Pop-up menu at the right-click mouse position
*
* @param evt
- * DOCUMENT ME!
*/
- public void mouseClicked(MouseEvent evt)
+ void showPopupMenu(MouseEvent evt)
{
- AlignmentAnnotation[] aa = ap.av.getAlignment()
+ evt.consume();
+ final AlignmentAnnotation[] aa = ap.av.getAlignment()
.getAlignmentAnnotation();
- if (SwingUtilities.isLeftMouseButton(evt))
- {
- if (selectedRow > -1 && selectedRow < aa.length)
- {
- if (aa[selectedRow].groupRef != null)
- {
- if (evt.getClickCount() >= 2)
- {
- // todo: make the ap scroll to the selection - not necessary, first
- // click highlights/scrolls, second selects
- ap.seqPanel.ap.idPanel.highlightSearchResults(null);
- ap.av.setSelectionGroup(// new SequenceGroup(
- aa[selectedRow].groupRef); // );
- ap.paintAlignment(false);
- PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
- ap.av.sendSelection();
- }
- else
- {
- ap.seqPanel.ap.idPanel
- .highlightSearchResults(aa[selectedRow].groupRef
- .getSequences(null));
- }
- return;
- }
- else if (aa[selectedRow].sequenceRef != null)
- {
- Vector sr = new Vector();
- sr.addElement(aa[selectedRow].sequenceRef);
- if (evt.getClickCount() == 1)
- {
- ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
- }
- else if (evt.getClickCount() >= 2)
- {
- ap.seqPanel.ap.idPanel.highlightSearchResults(null);
- SequenceGroup sg = new SequenceGroup();
- sg.addSequence(aa[selectedRow].sequenceRef, false);
- ap.av.setSelectionGroup(sg);
- ap.av.sendSelection();
- ap.paintAlignment(false);
- PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
- }
-
- }
- }
- }
- if (!SwingUtilities.isRightMouseButton(evt))
- {
- return;
- }
- JPopupMenu pop = new JPopupMenu(MessageManager.getString("label.annotations"));
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.annotations"));
JMenuItem item = new JMenuItem(ADDNEW);
item.addActionListener(this);
pop.add(item);
@@ -555,6 +372,39 @@ public class AnnotationLabels extends JPanel implements MouseListener,
item = new JMenuItem(HIDE);
item.addActionListener(this);
pop.add(item);
+ // JAL-1264 hide all sequence-specific annotations of this type
+ 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);
+ hideType.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ 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;
+ // }
+ // }
+ ap.refresh(true);
+ }
+ });
+ pop.add(hideType);
+ }
+ }
item = new JMenuItem(DELETE);
item.addActionListener(this);
pop.add(item);
@@ -571,7 +421,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
// property methods
if (selectedRow < aa.length)
{
- if (!aa[selectedRow].autoCalculated)
+ final String label = aa[selectedRow].label;
+ if (!(aa[selectedRow].autoCalculated
+ || label.indexOf("Information Content") > -1))
{
if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
{
@@ -584,30 +436,37 @@ public class AnnotationLabels extends JPanel implements MouseListener,
pop.add(item);
}
}
- else if (aa[selectedRow].label.indexOf("Consensus") > -1)
+ else if (label.indexOf("Consensus") > -1)
{
+
+
pop.addSeparator();
// av and sequencegroup need to implement same interface for
+ final AlignmentAnnotation aaa = aa[selectedRow];
+
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- "Ignore Gaps In Consensus",
+ MessageManager.getString("label.ignore_gaps_consensus"),
(aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
.getIgnoreGapsConsensus() : ap.av
- .getIgnoreGapsConsensus());
- final AlignmentAnnotation aaa = aa[selectedRow];
+ .isIgnoreGapsConsensus());
+
cbmi.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
if (aaa.groupRef != null)
{
// TODO: pass on reference to ap so the view can be updated.
aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
- ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ ap.getAnnotationPanel().paint(
+ ap.getAnnotationPanel().getGraphics());
}
else
{
ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
}
+ ap.alignmentChanged();
}
});
pop.add(cbmi);
@@ -615,10 +474,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
if (aaa.groupRef != null)
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- "Show Group Histogram",
+ MessageManager.getString("label.show_group_histogram"),
aa[selectedRow].groupRef.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
@@ -634,10 +494,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
});
pop.add(chist);
final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
- "Show Group Logo",
+ MessageManager.getString("label.show_group_logo"),
aa[selectedRow].groupRef.isShowSequenceLogo());
cprofl.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
@@ -653,10 +514,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
});
pop.add(cprofl);
final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
- "Normalise Group Logo",
+ MessageManager.getString("label.normalise_group_logo"),
aa[selectedRow].groupRef.isNormaliseSequenceLogo());
cproflnorm.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
@@ -678,9 +540,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
else
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- "Show Histogram", av.isShowConsensusHistogram());
+ MessageManager.getString("label.show_histogram"),
+ av.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
@@ -697,9 +561,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
});
pop.add(chist);
final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
- "Show Logo", av.isShowSequenceLogo());
+ MessageManager.getString("label.show_logo"),
+ av.isShowSequenceLogo());
cprof.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
@@ -716,9 +582,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
});
pop.add(cprof);
final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
- "Normalise Logo", av.isNormaliseSequenceLogo());
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseSequenceLogo());
cprofnorm.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: pass on reference
@@ -740,60 +608,557 @@ public class AnnotationLabels extends JPanel implements MouseListener,
consclipbrd.addActionListener(this);
pop.add(consclipbrd);
}
- }
- pop.show(this, evt.getX(), evt.getY());
- }
+ else if (label.indexOf("Information Content") > -1) // TODO create labels
+ // in message resource
+ // for these
+ {
+ pop.addSeparator();
+ final AlignmentAnnotation aaa = aa[selectedRow];
- /**
- * do a single sequence copy to jalview and the system clipboard
- *
- * @param sq
- * sequence to be copied to clipboard
- */
- protected void copy_annotseqtoclipboard(SequenceI sq)
- {
- SequenceI[] seqs = new SequenceI[]
- { sq };
- String[] omitHidden = null;
- SequenceI[] dseqs = new SequenceI[]
- { sq.getDatasetSequence() };
- if (dseqs[0] == null)
- {
- dseqs[0] = new Sequence(sq);
- dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, sq.getSequenceAsString()));
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ "Ignore Below Background Frequency",
+ (aa[selectedRow].groupRef != null)
+ ? aa[selectedRow].groupRef
+ .getIgnoreBelowBackground()
+ : ap.av.isIgnoreBelowBackground());
+
+ cbmi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (aaa.groupRef != null)
+ {
+ // TODO: pass on reference to ap so the view can be updated.
+ aaa.groupRef.setIgnoreBelowBackground(cbmi.getState());
+ ap.getAnnotationPanel()
+ .paint(ap.getAnnotationPanel().getGraphics());
+ }
+ else
+ {
+ ap.av.setIgnoreBelowBackground(cbmi.getState(), ap);
+ }
+ ap.alignmentChanged();
+ }
+ });
+ pop.add(cbmi);
+ if (aaa.groupRef != null)
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_histogram"),
+ aa[selectedRow].groupRef.isShowInformationHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setShowInformationHistogram(chist.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_logo"),
+ aa[selectedRow].groupRef.isShowHMMSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setshowHMMSequenceLogo(cprofl.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprofl);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ aa[selectedRow].groupRef.isNormaliseHMMSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef
+ .setNormaliseHMMSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ aaa.groupRef.setshowHMMSequenceLogo(true);
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cproflnorm);
+ }
+ else
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_histogram"),
+ av.isShowInformationHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowInformationHistogram(chist.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_logo"),
+ av.isShowHMMSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowHMMSequenceLogo(cprof.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprof);
+ final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseHMMSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowHMMSequenceLogo(true);
+ av.setNormaliseHMMSequenceLogo(cprofnorm.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprofnorm);
+ }
+ final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+ consclipbrd.addActionListener(this);
+ pop.add(consclipbrd);
+ }
+ }
+ pop.show(this, evt.getX(), evt.getY());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger())
+ {
+ showPopupMenu(evt);
+ return;
+ }
+
+ int start = selectedRow;
+ getSelectedRow(evt.getY() - getScrollOffset());
+ int end = selectedRow;
+
+ if (start != end)
+ {
+ // Swap these annotations
+ AlignmentAnnotation startAA = ap.av.getAlignment()
+ .getAlignmentAnnotation()[start];
+ if (end == -1)
+ {
+ end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
+ }
+ AlignmentAnnotation endAA = ap.av.getAlignment()
+ .getAlignmentAnnotation()[end];
+
+ ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
+ ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
+ }
+
+ resizePanel = false;
+ dragEvent = null;
+ repaint();
+ ap.getAnnotationPanel().repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseEntered(MouseEvent evt)
+ {
+ if (evt.getY() < 10)
+ {
+ resizePanel = true;
+ repaint();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseExited(MouseEvent evt)
+ {
+ if (dragEvent == null)
+ {
+ resizePanel = false;
+ repaint();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ dragEvent = evt;
+
+ if (resizePanel)
+ {
+ Dimension d = ap.annotationScroller.getPreferredSize();
+ int dif = evt.getY() - oldY;
+
+ dif /= ap.av.getCharHeight();
+ dif *= ap.av.getCharHeight();
+
+ if ((d.height - dif) > 20)
+ {
+ ap.annotationScroller.setPreferredSize(new Dimension(d.width,
+ d.height - dif));
+ d = ap.annotationSpaceFillerHolder.getPreferredSize();
+ ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+ d.width, d.height - dif));
+ ap.paintAlignment(true);
+ }
+
+ ap.addNotify();
+ }
+ else
+ {
+ repaint();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ resizePanel = evt.getY() < 10;
+
+ getSelectedRow(evt.getY() - getScrollOffset());
+
+ if (selectedRow > -1
+ && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
+ {
+ AlignmentAnnotation aa = ap.av.getAlignment()
+ .getAlignmentAnnotation()[selectedRow];
+
+ StringBuffer desc = new StringBuffer();
+ if (aa.description != null
+ && !aa.description.equals("New description"))
+ {
+ // TODO: we could refactor and merge this code with the code in
+ // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
+ // tooltips
+ desc.append(aa.getDescription(true).trim());
+ // check to see if the description is an html fragment.
+ if (desc.length() < 6
+ || (desc.substring(0, 6).toLowerCase().indexOf("") < 0))
+ {
+ // clean the description ready for embedding in html
+ desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
+ .replaceAll("<"));
+ desc.insert(0, "");
+ }
+ else
+ {
+ // remove terminating html if any
+ int i = desc.substring(desc.length() - 7).toLowerCase()
+ .lastIndexOf("");
+ if (i > -1)
+ {
+ desc.setLength(desc.length() - 7 + i);
+ }
+ }
+ if (aa.hasScore())
+ {
+ desc.append("
");
+ }
+ // if (aa.hasProperties())
+ // {
+ // desc.append("
" + prop + " | " + // + aa.getProperty(prop) + " |