X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=4e625e14aede3537513b21ca3936654100209011;hb=c6c94d2adb0d156345065b1a7e18e26c7b8dd2b8;hp=07a9b034c905cabb8fda05a6ee56b75072199473;hpb=6b544d4a85673db44b7f75f40c22d9b7425d444e;p=jalview.git
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 07a9b03..4e625e1 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,32 +1,65 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
+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;
+
+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.BufferedImage;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import java.util.regex.Pattern;
+
+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!
@@ -37,21 +70,23 @@ import jalview.io.*;
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";
+ String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column");
- static String EDITNAME = "Edit Label/Description";
+ String ADDNEW = MessageManager.getString("label.add_new_row");
- static String HIDE = "Hide This Row";
+ String EDITNAME = MessageManager.getString("label.edit_label_description");
- static String DELETE = "Delete This Row";
+ String HIDE = MessageManager.getString("label.hide_row");
- static String SHOWALL = "Show All Hidden Rows";
+ String DELETE = MessageManager.getString("label.delete_row");
- static String OUTPUT_TEXT = "Export Annotation";
+ String SHOWALL = MessageManager.getString("label.show_all_hidden_rows");
- static String COPYCONS_SEQ = "Copy Consensus Sequence";
+ String OUTPUT_TEXT = MessageManager.getString("label.export_annotation");
+
+ String COPYCONS_SEQ = MessageManager.getString("label.copy_consensus_sequence");
boolean resizePanel = false;
@@ -69,7 +104,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
int selectedRow;
- int scrollOffset = 0;
+ private int scrollOffset = 0;
Font font = new Font("Arial", Font.PLAIN, 11);
@@ -104,15 +139,16 @@ public class AnnotationLabels extends JPanel implements MouseListener,
{
}
- BufferedImage bi = new BufferedImage(temp.getHeight(this), temp
- .getWidth(this), BufferedImage.TYPE_INT_RGB);
+ BufferedImage bi = new BufferedImage(temp.getHeight(this),
+ temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
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.getAnnotationPanel());
}
public AnnotationLabels(AlignViewport av)
@@ -142,7 +178,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
void getSelectedRow(int y)
{
int height = 0;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
selectedRow = -2;
if (aa != null)
{
@@ -174,20 +211,21 @@ public class AnnotationLabels extends JPanel implements MouseListener,
*/
public void actionPerformed(ActionEvent evt)
{
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
if (evt.getActionCommand().equals(ADDNEW))
{
AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
- null, new Annotation[ap.av.alignment.getWidth()]);
+ null, new Annotation[ap.av.getAlignment().getWidth()]);
if (!editLabelDescription(newAnnotation))
{
return;
}
- ap.av.alignment.addAnnotation(newAnnotation);
- ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+ ap.av.getAlignment().addAnnotation(newAnnotation);
+ ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
}
else if (evt.getActionCommand().equals(EDITNAME))
{
@@ -197,15 +235,10 @@ public class AnnotationLabels extends JPanel implements MouseListener,
else if (evt.getActionCommand().equals(HIDE))
{
aa[selectedRow].visible = false;
-
- if (aa[selectedRow].label.equals("Quality"))
- {
- ap.av.quality = null;
- }
}
else if (evt.getActionCommand().equals(DELETE))
{
- ap.av.alignment.deleteAnnotation(aa[selectedRow]);
+ ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
}
else if (evt.getActionCommand().equals(SHOWALL))
{
@@ -221,7 +254,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
{
new AnnotationExporter().exportAnnotations(ap,
new AlignmentAnnotation[]
- { aa[selectedRow] }, null, null);
+ { aa[selectedRow] });
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
@@ -245,9 +278,18 @@ public class AnnotationLabels extends JPanel implements MouseListener,
aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
}
- ap.annotationPanel.adjustPanelHeight();
- ap.annotationScroller.validate();
- ap.paintAlignment(true);
+ refresh();
+
+ }
+
+ /**
+ * Redraw sensibly.
+ */
+ protected void refresh()
+ {
+ ap.validateAnnotationDimensions(false);
+ ap.addNotify();
+ ap.repaint();
}
/**
@@ -288,7 +330,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
*/
public void mousePressed(MouseEvent evt)
{
- getSelectedRow(evt.getY() - scrollOffset);
+ getSelectedRow(evt.getY() - getScrollOffset());
oldY = evt.getY();
}
@@ -301,28 +343,29 @@ public class AnnotationLabels extends JPanel implements MouseListener,
public void mouseReleased(MouseEvent evt)
{
int start = selectedRow;
- getSelectedRow(evt.getY() - scrollOffset);
+ getSelectedRow(evt.getY() - getScrollOffset());
int end = selectedRow;
if (start != end)
{
// Swap these annotations
- AlignmentAnnotation startAA = ap.av.alignment
+ AlignmentAnnotation startAA = ap.av.getAlignment()
.getAlignmentAnnotation()[start];
if (end == -1)
{
- end = ap.av.alignment.getAlignmentAnnotation().length - 1;
+ end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
}
- AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
+ AlignmentAnnotation endAA = ap.av.getAlignment()
+ .getAlignmentAnnotation()[end];
- ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
- ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
+ ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
+ ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
}
resizePanel = false;
dragEvent = null;
repaint();
- ap.annotationPanel.repaint();
+ ap.getAnnotationPanel().repaint();
}
/**
@@ -370,8 +413,8 @@ 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)
{
@@ -401,36 +444,78 @@ public class AnnotationLabels extends JPanel implements MouseListener,
{
resizePanel = evt.getY() < 10;
- getSelectedRow(evt.getY() - scrollOffset);
+ getSelectedRow(evt.getY() - getScrollOffset());
if (selectedRow > -1
- && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
+ && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
{
- AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow];
-
- StringBuffer desc = new StringBuffer("");
+ AlignmentAnnotation aa = ap.av.getAlignment()
+ .getAlignmentAnnotation()[selectedRow];
+ StringBuffer desc = new StringBuffer();
if (aa.description != null
&& !aa.description.equals("New description"))
{
- desc.append(aa.getDescription(true));
- if (aa.hasScore)
- desc.append("
");
+ // 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("
");
+ // for (String prop : aa.getProperties())
+ // {
+ // desc.append("" + prop + " | "
+ // + aa.getProperty(prop) + " |
");
+ // }
+ // desc.append("
");
+ // }
}
- if (aa.hasScore())
+ else
{
- desc.append("Score: " + aa.score);
+ // 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)
+ if (desc.length() > 6)
{
desc.append("");
this.setToolTipText(desc.toString());
}
else
+ {
this.setToolTipText(null);
+ }
}
-
}
/**
@@ -441,7 +526,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
*/
public void mouseClicked(MouseEvent evt)
{
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ final AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
if (SwingUtilities.isLeftMouseButton(evt))
{
if (selectedRow > -1 && selectedRow < aa.length)
@@ -450,17 +536,18 @@ public class AnnotationLabels extends JPanel implements MouseListener,
{
if (evt.getClickCount() >= 2)
{
- // todo: make the ap scroll to the selection
- ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+ // todo: make the ap scroll to the selection - not necessary, first
+ // click highlights/scrolls, second selects
+ ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
ap.av.setSelectionGroup(// new SequenceGroup(
- aa[selectedRow].groupRef); // );
- ap.av.sendSelection();
+ aa[selectedRow].groupRef); // );
ap.paintAlignment(false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
}
else
{
- ap.seqPanel.ap.idPanel
+ ap.getSeqPanel().ap.getIdPanel()
.highlightSearchResults(aa[selectedRow].groupRef
.getSequences(null));
}
@@ -468,17 +555,40 @@ public class AnnotationLabels extends JPanel implements MouseListener,
}
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);
+ ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(Arrays
+ .asList(new SequenceI[]
+ { aa[selectedRow].sequenceRef }));
}
else if (evt.getClickCount() >= 2)
{
- ap.seqPanel.ap.idPanel.highlightSearchResults(null);
- SequenceGroup sg = new SequenceGroup();
- sg.addSequence(aa[selectedRow].sequenceRef, false);
+ ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg!=null)
+ {
+ // 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 {
+ if (evt.isControlDown())
+ {
+ sg.addOrRemove(aa[selectedRow].sequenceRef, true);
+ } else {
+ // notionally, we should also add intermediate sequences from last added sequence ?
+ sg.addSequence(aa[selectedRow].sequenceRef, true);
+ }
+ }
+ } else {
+ sg = new SequenceGroup();
+ sg.setStartRes(0);
+ sg.setEndRes(ap.av.getAlignment().getWidth()-1);
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ }
ap.av.setSelectionGroup(sg);
ap.av.sendSelection();
ap.paintAlignment(false);
@@ -493,7 +603,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
return;
}
- JPopupMenu pop = new JPopupMenu("Annotations");
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.annotations"));
JMenuItem item = new JMenuItem(ADDNEW);
item.addActionListener(this);
pop.add(item);
@@ -514,6 +625,38 @@ 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;
+ // }
+ // }
+ refresh();
+ }
+ });
+ pop.add(hideType);
+ }
+ }
item = new JMenuItem(DELETE);
item.addActionListener(this);
pop.add(item);
@@ -530,6 +673,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
// property methods
if (selectedRow < aa.length)
{
+ final String label = aa[selectedRow].label;
if (!aa[selectedRow].autoCalculated)
{
if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
@@ -543,15 +687,15 @@ 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 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());
+ .getIgnoreGapsConsensus() : ap.av
+ .isIgnoreGapsConsensus());
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addActionListener(new ActionListener()
{
@@ -561,7 +705,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
{
// 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
{
@@ -574,8 +718,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
if (aaa.groupRef != null)
{
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- "Show Group Histogram", aa[selectedRow].groupRef
- .isShowConsensusHistogram());
+ MessageManager.getString("label.show_group_histogram"),
+ aa[selectedRow].groupRef.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -593,8 +737,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
});
pop.add(chist);
final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
- "Show Group Logo", aa[selectedRow].groupRef
- .isShowSequenceLogo());
+ MessageManager.getString("label.show_group_logo"),
+ aa[selectedRow].groupRef.isShowSequenceLogo());
cprofl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -611,11 +755,33 @@ public class AnnotationLabels extends JPanel implements MouseListener,
}
});
pop.add(cprofl);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ 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(
- "Show Histogram", av.isShowConsensusHistogram());
+ MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -627,13 +793,14 @@ public class AnnotationLabels extends JPanel implements MouseListener,
// 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(
- "Show Logo", av.isShowSequenceLogo());
+ MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
cprof.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -645,11 +812,32 @@ public class AnnotationLabels extends JPanel implements MouseListener,
// 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()
+ {
+ 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);
@@ -681,28 +869,33 @@ public class AnnotationLabels extends JPanel implements MouseListener,
sq.setDatasetSequence(dseqs[0]);
}
Alignment ds = new Alignment(dseqs);
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
sq.getLength(), seqs);
}
+ int[] alignmentStartEnd = new int[]
+ { 0, ds.getWidth() - 1 };
+ List hiddenCols = av.getColumnSelection().getHiddenColumns();
+ if (hiddenCols != null)
+ {
+ alignmentStartEnd = AlignFrame.getStartEnd(alignmentStartEnd,
+ hiddenCols);
+ }
String output = new FormatAdapter().formatSequences("Fasta", seqs,
- omitHidden);
+ omitHidden, alignmentStartEnd);
- Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
- new StringSelection(output), Desktop.instance);
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(output), Desktop.instance);
- Vector hiddenColumns = null;
- if (av.hasHiddenColumns)
+ ArrayList hiddenColumns = null;
+ if (av.hasHiddenColumns())
{
- hiddenColumns = new Vector();
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+ hiddenColumns = new ArrayList();
+ for (int[] region : av.getColumnSelection().getHiddenColumns())
{
- int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
- .elementAt(i);
-
- hiddenColumns.addElement(new int[]
+ hiddenColumns.add(new int[]
{ region[0], region[1] });
}
}
@@ -735,18 +928,41 @@ public class AnnotationLabels extends JPanel implements MouseListener,
RenderingHints.VALUE_ANTIALIAS_ON);
}
- drawComponent(g2, width);
+ drawComponent(g2, true, width);
}
/**
- * DOCUMENT ME!
+ * Draw the full set of annotation Labels for the alignment at the given
+ * cursor
*
* @param g
- * DOCUMENT ME!
+ * Graphics2D instance (needed for font scaling)
+ * @param width
+ * Width for scaling labels
+ *
*/
public void drawComponent(Graphics g, int width)
{
+ drawComponent(g, false, width);
+ }
+
+ private final boolean debugRedraw = false;
+
+ /**
+ * Draw the full set of annotation Labels for the alignment at the given
+ * cursor
+ *
+ * @param g
+ * Graphics2D instance (needed for font scaling)
+ * @param clip
+ * - true indicates that only current visible area needs to be
+ * rendered
+ * @param width
+ * Width for scaling labels
+ */
+ public void drawComponent(Graphics g, boolean clip, int width)
+ {
if (av.getFont().getSize() < 10)
{
g.setFont(font);
@@ -760,30 +976,74 @@ public class AnnotationLabels extends JPanel implements MouseListener,
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
- g.translate(0, scrollOffset);
+ g.translate(0, getScrollOffset());
g.setColor(Color.black);
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
int fontHeight = g.getFont().getSize();
int y = 0;
int x = 0;
int graphExtras = 0;
int offset = 0;
-
+ Font baseFont = g.getFont();
+ FontMetrics baseMetrics = fm;
+ int ofontH = fontHeight;
+ int sOffset = 0;
+ int visHeight = 0;
+ int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap.getAnnotationPanel()
+ .getVisibleVRange() : null;
+ if (clip && visr != null)
+ {
+ sOffset = visr[0];
+ visHeight = visr[1];
+ }
+ boolean visible = true, before = false, after = false;
if (aa != null)
{
hasHiddenRows = false;
+ int olY = 0;
for (int i = 0; i < aa.length; i++)
{
- g.setColor(Color.black);
-
+ visible = true;
if (!aa[i].visible)
{
hasHiddenRows = true;
continue;
}
-
+ olY = y;
y += aa[i].height;
+ if (clip)
+ {
+ if (y < sOffset)
+ {
+ if (!before)
+ {
+ if (debugRedraw)
+ {
+ System.out.println("before vis: " + i);
+ }
+ before = true;
+ }
+ // don't draw what isn't visible
+ continue;
+ }
+ if (olY > visHeight)
+ {
+
+ if (!after)
+ {
+ if (debugRedraw)
+ {
+ System.out.println("Scroll offset: " + sOffset
+ + " after vis: " + i);
+ }
+ after = true;
+ }
+ // don't draw what isn't visible
+ continue;
+ }
+ }
+ g.setColor(Color.black);
offset = -aa[i].height / 2;
@@ -793,13 +1053,17 @@ public class AnnotationLabels extends JPanel implements MouseListener,
offset -= fm.getDescent();
}
else
+ {
offset += fm.getDescent();
+ }
x = width - fm.stringWidth(aa[i].label) - 3;
if (aa[i].graphGroup > -1)
{
int groupSize = 0;
+ // TODO: JAL-1291 revise rendering model so the graphGroup map is
+ // computed efficiently for all visible labels
for (int gg = 0; gg < aa.length; gg++)
{
if (aa[gg].graphGroup == aa[i].graphGroup)
@@ -807,30 +1071,55 @@ public class AnnotationLabels extends JPanel implements MouseListener,
groupSize++;
}
}
-
if (groupSize * (fontHeight + 8) < aa[i].height)
{
graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
}
-
- for (int gg = 0; gg < aa.length; gg++)
+ else
{
- if (aa[gg].graphGroup == aa[i].graphGroup)
+ // scale font to fit
+ float h = aa[i].height / (float) groupSize, s;
+ if (h < 9)
+ {
+ visible = false;
+ }
+ else
+ {
+ fontHeight = -8 + (int) h;
+ s = ((float) fontHeight) / (float) ofontH;
+ Font f = baseFont.deriveFont(AffineTransform
+ .getScaleInstance(s, s));
+ g.setFont(f);
+ fm = g.getFontMetrics();
+ graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+ }
+ }
+ if (visible)
+ {
+ for (int gg = 0; gg < aa.length; gg++)
{
- x = width - fm.stringWidth(aa[gg].label) - 3;
- g.drawString(aa[gg].label, x, y - graphExtras);
- if (aa[gg].annotations[0] != null)
+ if (aa[gg].graphGroup == aa[i].graphGroup)
{
- g.setColor(aa[gg].annotations[0].colour);
- }
+ x = width - fm.stringWidth(aa[gg].label) - 3;
+ g.drawString(aa[gg].label, x, y - graphExtras);
+
+ if (aa[gg]._linecolour != null)
+ {
- g.drawLine(x, y - graphExtras - 3, x
- + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
+ g.setColor(aa[gg]._linecolour);
+ g.drawLine(x, y - graphExtras + 3,
+ x + fm.stringWidth(aa[gg].label), y - graphExtras
+ + 3);
+ }
- g.setColor(Color.black);
- graphExtras += fontHeight + 8;
+ g.setColor(Color.black);
+ graphExtras += fontHeight + 8;
+ }
}
}
+ g.setFont(baseFont);
+ fm = baseMetrics;
+ fontHeight = ofontH;
}
else
{
@@ -841,20 +1130,25 @@ public class AnnotationLabels extends JPanel implements MouseListener,
if (resizePanel)
{
- g.drawImage(image, 2, 0 - scrollOffset, this);
+ g.drawImage(image, 2, 0 - getScrollOffset(), this);
}
else if (dragEvent != null && aa != null)
{
g.setColor(Color.lightGray);
- g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent
- .getY()
- - scrollOffset);
+ g.drawString(aa[selectedRow].label, dragEvent.getX(),
+ dragEvent.getY() - getScrollOffset());
}
- if ((aa == null) || (aa.length < 1))
+ if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
{
- g.drawString("Right click", 2, 8);
- g.drawString("to add annotation", 2, 18);
+ g.drawString(MessageManager.getString("label.right_click"), 2, 8);
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+ 18);
}
}
+
+ public int getScrollOffset()
+ {
+ return scrollOffset;
+ }
}