X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=68df498c3a5e0d7a582b0381c01677a02a0c1a19;hb=e879efcd79694e43a8081c9235a13740cb429076;hp=1577477d78d94a203cfeb18658bd56cb8a78343d;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 1577477..68df498 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,34 +1,65 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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
");
- }
-
- }
- 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);
- }
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
- public void mouseClicked(MouseEvent evt)
- {
- 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))
+ if (!evt.isPopupTrigger())
{
return;
}
+ evt.consume();
+ // handle popup menu event
+ final AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
- JPopupMenu pop = new JPopupMenu("Annotations");
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.annotations"));
JMenuItem item = new JMenuItem(ADDNEW);
item.addActionListener(this);
pop.add(item);
@@ -551,6 +362,39 @@ 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;
+ // }
+ // }
+ refresh();
+ }
+ });
+ pop.add(hideType);
+ }
+ }
item = new JMenuItem(DELETE);
item.addActionListener(this);
pop.add(item);
@@ -567,6 +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)
@@ -580,25 +425,27 @@ 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());
+ .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
{
@@ -611,10 +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
@@ -630,10 +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
@@ -649,10 +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)
{
@@ -674,9 +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
@@ -693,9 +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
@@ -712,9 +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
@@ -738,6 +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) + " |