return true;
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
@Override
public void mousePressed(MouseEvent evt)
{
getSelectedRow(evt.getY() - getScrollOffset());
oldY = 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)
+ if (!evt.isPopupTrigger())
{
- resizePanel = true;
- repaint();
+ return;
}
- }
+ evt.consume();
+ // handle popup menu event
+ final AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- @Override
- public void mouseExited(MouseEvent evt)
- {
- if (dragEvent == null)
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.annotations"));
+ JMenuItem item = new JMenuItem(ADDNEW);
+ item.addActionListener(this);
+ pop.add(item);
+ if (selectedRow < 0)
{
- resizePanel = false;
- repaint();
+ 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;
}
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- @Override
- public void mouseDragged(MouseEvent evt)
- {
- dragEvent = evt;
-
- if (resizePanel)
+ 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)
{
- Dimension d = ap.annotationScroller.getPreferredSize();
- int dif = evt.getY() - oldY;
-
- dif /= ap.av.getCharHeight();
- dif *= ap.av.getCharHeight();
-
- if ((d.height - dif) > 20)
+ if (aa[selectedRow].sequenceRef != null)
{
- 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);
+ 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);
}
-
- ap.addNotify();
}
- else
+ item = new JMenuItem(DELETE);
+ item.addActionListener(this);
+ pop.add(item);
+ if (hasHiddenRows)
{
- repaint();
+ item = new JMenuItem(SHOWALL);
+ item.addActionListener(this);
+ pop.add(item);
}
- }
-
- /**
- * 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)
+ 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)
{
- AlignmentAnnotation aa = ap.av.getAlignment()
- .getAlignmentAnnotation()[selectedRow];
-
- StringBuffer desc = new StringBuffer();
- if (aa.description != null
- && !aa.description.equals("New description"))
+ final String label = aa[selectedRow].label;
+ if (!aa[selectedRow].autoCalculated)
{
- // 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("<html>") < 0))
+ if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
{
- // clean the description ready for embedding in html
- desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
- .replaceAll("<"));
- desc.insert(0, "<html>");
+ // 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
+ }
+ 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()
{
- // remove terminating html if any
- int i = desc.substring(desc.length() - 7).toLowerCase()
- .lastIndexOf("</html>");
- if (i > -1)
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- desc.setLength(desc.length() - 7 + i);
+ 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);
+ }
}
- }
- if (aa.hasScore())
- {
- desc.append("<br/>");
- }
- // if (aa.hasProperties())
- // {
- // desc.append("<table>");
- // for (String prop : aa.getProperties())
- // {
- // desc.append("<tr><td>" + prop + "</td><td>"
- // + aa.getProperty(prop) + "</td><tr>");
- // }
- // desc.append("</table>");
- // }
- }
- else
- {
- // begin the tooltip's html fragment
- desc.append("<html>");
- 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("</html>");
- this.setToolTipText(desc.toString());
- }
- else
- {
- this.setToolTipText(null);
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- @Override
- public void mouseClicked(MouseEvent evt)
- {
- 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.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
- ap.av.setSelectionGroup(// new SequenceGroup(
- aa[selectedRow].groupRef); // );
- ap.paintAlignment(false);
- PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
- ap.av.sendSelection();
- }
- else
- {
- ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(
- aa[selectedRow].groupRef.getSequences(null));
- }
- return;
- }
- else if (aa[selectedRow].sequenceRef != null)
- {
- if (evt.getClickCount() == 1)
- {
- ap.getSeqPanel().ap
- .getIdPanel()
- .highlightSearchResults(
- Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
- }
- else if (evt.getClickCount() >= 2)
- {
- 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);
- PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
- }
-
- }
- }
- }
- if (!evt.isPopupTrigger())
- {
- return;
- }
-
- 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;
- // }
- // }
- refresh();
- }
- });
- 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);
- }
- }
- });
- pop.add(cbmi);
- // av and sequencegroup need to implement same interface for
- if (aaa.groupRef != null)
+ });
+ 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"),
}
}
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("<html>") < 0))
+ {
+ // clean the description ready for embedding in html
+ desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
+ .replaceAll("<"));
+ desc.insert(0, "<html>");
+ }
+ else
+ {
+ // remove terminating html if any
+ int i = desc.substring(desc.length() - 7).toLowerCase()
+ .lastIndexOf("</html>");
+ if (i > -1)
+ {
+ desc.setLength(desc.length() - 7 + i);
+ }
+ }
+ if (aa.hasScore())
+ {
+ desc.append("<br/>");
+ }
+ // if (aa.hasProperties())
+ // {
+ // desc.append("<table>");
+ // for (String prop : aa.getProperties())
+ // {
+ // desc.append("<tr><td>" + prop + "</td><td>"
+ // + aa.getProperty(prop) + "</td><tr>");
+ // }
+ // desc.append("</table>");
+ // }
+ }
+ else
+ {
+ // begin the tooltip's html fragment
+ desc.append("<html>");
+ 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("</html>");
+ this.setToolTipText(desc.toString());
+ }
+ else
+ {
+ this.setToolTipText(null);
+ }
+ }
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ final AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ if (!evt.isPopupTrigger() && 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.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
+ ap.av.setSelectionGroup(// new SequenceGroup(
+ aa[selectedRow].groupRef); // );
+ ap.paintAlignment(false);
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
+ }
+ else
+ {
+ ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(
+ aa[selectedRow].groupRef.getSequences(null));
+ }
+ return;
+ }
+ else if (aa[selectedRow].sequenceRef != null)
+ {
+ if (evt.getClickCount() == 1)
+ {
+ ap.getSeqPanel().ap
+ .getIdPanel()
+ .highlightSearchResults(
+ Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
+ }
+ else if (evt.getClickCount() >= 2)
+ {
+ 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);
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ }
+
+ }
+ }
+ return;
+ }
}
/**
git://source.jalview.org / jalview.git / commitdiff