X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=68df498c3a5e0d7a582b0381c01677a02a0c1a19;hb=e879efcd79694e43a8081c9235a13740cb429076;hp=7483c4217d216bb27e141449c2e8c98025178c58;hpb=044474c2d4d044de3f4590f170db8d856cccc488;p=jalview.git
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 7483c42..68df498 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.
*
@@ -20,6 +20,7 @@
*/
package jalview.gui;
+import jalview.analysis.AlignmentUtils;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
@@ -47,8 +48,10 @@ 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.Vector;
+import java.util.Collections;
+import java.util.List;
import java.util.regex.Pattern;
import javax.swing.JCheckBoxMenuItem;
@@ -67,11 +70,16 @@ import javax.swing.ToolTipManager;
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");
@@ -81,7 +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;
@@ -99,7 +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);
@@ -143,7 +152,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
addMouseListener(this);
addMouseMotionListener(this);
- addMouseWheelListener(ap.annotationPanel);
+ addMouseWheelListener(ap.getAnnotationPanel());
}
public AnnotationLabels(AlignViewport av)
@@ -204,6 +213,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void actionPerformed(ActionEvent evt)
{
AlignmentAnnotation[] aa = ap.av.getAlignment()
@@ -248,8 +258,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
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))
{
@@ -317,278 +326,19 @@ 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)
+ if (!evt.isPopupTrigger())
{
- // 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)
- {
- 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);
- }
+ return;
}
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- public void mouseClicked(MouseEvent evt)
- {
+ evt.consume();
+ // handle popup menu event
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)
- {
- if (evt.getClickCount() == 1)
- {
- 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)
- {
- // 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);
- PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
- }
-
- }
- }
- }
- if (!SwingUtilities.isRightMouseButton(evt))
- {
- return;
- }
JPopupMenu pop = new JPopupMenu(
MessageManager.getString("label.annotations"));
@@ -613,28 +363,32 @@ public class AnnotationLabels extends JPanel implements MouseListener,
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;
+ String text = MessageManager.getString("label.hide_all") + " "
+ + label;
hideType.setText(text);
hideType.addActionListener(new ActionListener()
{
@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();
}
});
@@ -657,6 +411,7 @@ 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)
@@ -675,20 +430,22 @@ public class AnnotationLabels extends JPanel implements MouseListener,
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());
+ .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.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ ap.getAnnotationPanel().paint(
+ ap.getAnnotationPanel().getGraphics());
}
else
{
@@ -701,10 +458,11 @@ 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
@@ -720,10 +478,11 @@ 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
@@ -739,10 +498,11 @@ 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)
{
@@ -764,9 +524,11 @@ 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
@@ -783,9 +545,11 @@ 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
@@ -802,9 +566,11 @@ 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
@@ -828,6 +594,282 @@ public class AnnotationLabels extends JPanel implements MouseListener,
}
}
pop.show(this, evt.getX(), evt.getY());
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ 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) + " |