X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=d07cae270ebb4f259e8a21a7427f889fb8e9695e;hb=6a144c3b2b7f5f04d908c065a017088453bb7fc7;hp=fdb3975704379fa3ce0b1aeece782ad0d08c8d83;hpb=7e8241cdc284ef2586e36a3abbe3bd385dad10dc;p=jalview.git
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index fdb3975..d07cae2 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 +20,46 @@
*/
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.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!
@@ -40,14 +67,19 @@ import jalview.util.MessageManager;
* @author $author$
* @version $Revision$
*/
-public class AnnotationLabels extends JPanel implements MouseListener,
- MouseMotionListener, ActionListener
+public class AnnotationLabels extends JPanel
+ implements MouseListener, MouseMotionListener, ActionListener
{
- String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column");
+ 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");
- String EDITNAME = MessageManager.getString("label.edit_label_description");
+ String EDITNAME = MessageManager
+ .getString("label.edit_label_description");
String HIDE = MessageManager.getString("label.hide_row");
@@ -57,7 +89,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
String OUTPUT_TEXT = MessageManager.getString("label.export_annotation");
- String COPYCONS_SEQ = MessageManager.getString("label.copy_consensus_sequence");
+ String COPYCONS_SEQ = MessageManager
+ .getString("label.copy_consensus_sequence");
boolean resizePanel = false;
@@ -75,7 +108,7 @@ 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 +148,11 @@ 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 +213,13 @@ 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 +232,16 @@ 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 +250,8 @@ 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 +262,13 @@ 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);
+ { aa[selectedRow] });
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
@@ -249,11 +292,8 @@ 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 +304,7 @@ 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",
@@ -286,16 +327,283 @@ public class AnnotationLabels extends JPanel implements MouseListener,
return true;
}
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ getSelectedRow(evt.getY() - getScrollOffset());
+ oldY = evt.getY();
+ if (evt.isPopupTrigger())
+ {
+ showPopupMenu(evt);
+ }
+ }
+
/**
- * DOCUMENT ME!
+ * Build and show the Pop-up menu at the right-click mouse position
*
* @param evt
- * DOCUMENT ME!
*/
- public void mousePressed(MouseEvent evt)
+ void showPopupMenu(MouseEvent evt)
{
- getSelectedRow(evt.getY() - scrollOffset);
- oldY = evt.getY();
+ evt.consume();
+ final AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.annotations"));
+ JMenuItem item = new JMenuItem(ADDNEW);
+ item.addActionListener(this);
+ pop.add(item);
+ if (selectedRow < 0)
+ {
+ if (hasHiddenRows)
+ { // let the user make everything visible again
+ item = new JMenuItem(SHOWALL);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ pop.show(this, evt.getX(), evt.getY());
+ return;
+ }
+ item = new JMenuItem(EDITNAME);
+ item.addActionListener(this);
+ pop.add(item);
+ 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);
+ if (hasHiddenRows)
+ {
+ item = new JMenuItem(SHOWALL);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ item = new JMenuItem(OUTPUT_TEXT);
+ item.addActionListener(this);
+ pop.add(item);
+ // TODO: annotation object should be typed for autocalculated/derived
+ // property methods
+ if (selectedRow < aa.length)
+ {
+ final String label = aa[selectedRow].label;
+ if (!aa[selectedRow].autoCalculated)
+ {
+ if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
+ {
+ // display formatting settings for this row.
+ pop.addSeparator();
+ // av and sequencegroup need to implement same interface for
+ item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
+ aa[selectedRow].scaleColLabel);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ }
+ else if (label.indexOf("Consensus") > -1)
+ {
+ pop.addSeparator();
+ // av and sequencegroup need to implement same interface for
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ MessageManager.getString("label.ignore_gaps_consensus"),
+ (aa[selectedRow].groupRef != null)
+ ? aa[selectedRow].groupRef.getIgnoreGapsConsensus()
+ : ap.av.isIgnoreGapsConsensus());
+ final AlignmentAnnotation aaa = aa[selectedRow];
+ 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.getAnnotationPanel()
+ .paint(ap.getAnnotationPanel().getGraphics());
+ }
+ else
+ {
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+ }
+ ap.alignmentChanged();
+ }
+ });
+ pop.add(cbmi);
+ // av and sequencegroup need to implement same interface for
+ if (aaa.groupRef != null)
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_histogram"),
+ aa[selectedRow].groupRef.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setShowConsensusHistogram(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.isShowSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setshowSequenceLogo(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.isNormaliseSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ aaa.groupRef.setshowSequenceLogo(true);
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cproflnorm);
+ }
+ else
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_histogram"),
+ av.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowConsensusHistogram(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.isShowSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(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.isNormaliseSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(true);
+ av.setNormaliseSequenceLogo(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());
}
/**
@@ -304,10 +612,17 @@ public class AnnotationLabels extends JPanel implements MouseListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseReleased(MouseEvent evt)
{
+ if (evt.isPopupTrigger())
+ {
+ showPopupMenu(evt);
+ return;
+ }
+
int start = selectedRow;
- getSelectedRow(evt.getY() - scrollOffset);
+ getSelectedRow(evt.getY() - getScrollOffset());
int end = selectedRow;
if (start != end)
@@ -329,7 +644,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
resizePanel = false;
dragEvent = null;
repaint();
- ap.annotationPanel.repaint();
+ ap.getAnnotationPanel().repaint();
}
/**
@@ -338,6 +653,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseEntered(MouseEvent evt)
{
if (evt.getY() < 10)
@@ -353,6 +669,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseExited(MouseEvent evt)
{
if (dragEvent == null)
@@ -368,6 +685,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseDragged(MouseEvent evt)
{
dragEvent = evt;
@@ -377,16 +695,16 @@ public class AnnotationLabels extends JPanel implements MouseListener,
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)
{
- ap.annotationScroller.setPreferredSize(new Dimension(d.width,
- d.height - dif));
+ 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.annotationSpaceFillerHolder
+ .setPreferredSize(new Dimension(d.width, d.height - dif));
ap.paintAlignment(true);
}
@@ -404,14 +722,15 @@ public class AnnotationLabels extends JPanel implements MouseListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseMoved(MouseEvent evt)
{
resizePanel = evt.getY() < 10;
- getSelectedRow(evt.getY() - scrollOffset);
+ getSelectedRow(evt.getY() - getScrollOffset());
- if (selectedRow > -1
- && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
+ if (selectedRow > -1 && ap.av.getAlignment()
+ .getAlignmentAnnotation().length > selectedRow)
{
AlignmentAnnotation aa = ap.av.getAlignment()
.getAlignmentAnnotation()[selectedRow];
@@ -425,11 +744,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
// 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))
+ 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)
+ desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
.replaceAll("<"));
desc.insert(0, "");
}
@@ -447,42 +766,47 @@ public class AnnotationLabels extends JPanel implements MouseListener,
{
desc.append("
");
}
-
+ // if (aa.hasProperties())
+ // {
+ // desc.append("
" + prop + " | " + // + aa.getProperty(prop) + " |