/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
Font font = new Font("Arial", Font.PLAIN, 11);
+ private boolean hasHiddenRows;
+
/**
* Creates a new AnnotationLabels object.
*
* @param ap
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public AnnotationLabels(AlignmentPanel ap)
{
* DOCUMENT ME!
*
* @param y
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setScrollOffset(int y)
{
repaint();
}
+ /**
+ * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at
+ * y
+ *
+ * @param y
+ * coordinate position to search for a row
+ */
void getSelectedRow(int y)
{
int height = 0;
AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
+ selectedRow = -2;
if (aa != null)
{
for (int i = 0; i < aa.length; i++)
{
+ selectedRow = -1;
if (!aa[i].visible)
{
continue;
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void actionPerformed(ActionEvent evt)
{
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
SequenceI cons = null;
- if (aa[selectedRow].groupRef!=null)
+ if (aa[selectedRow].groupRef != null)
{
cons = aa[selectedRow].groupRef.getConsensusSeq();
- } else {
+ }
+ else
+ {
cons = av.getConsensusSeq();
}
if (cons != null)
}
else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
{
- aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
+ aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
}
ap.annotationPanel.adjustPanelHeight();
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
boolean editLabelDescription(AlignmentAnnotation annotation)
{
EditNameDialog dialog = new EditNameDialog(annotation.label,
annotation.description, " Annotation Name ",
- "Annotation Description ", "Edit Annotation Name/Description");
+ "Annotation Description ", "Edit Annotation Name/Description",
+ ap.alignFrame);
if (!dialog.accept)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mousePressed(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseReleased(MouseEvent evt)
{
// Swap these annotations
AlignmentAnnotation startAA = ap.av.alignment
.getAlignmentAnnotation()[start];
+ if (end == -1)
+ {
+ end = ap.av.alignment.getAlignmentAnnotation().length - 1;
+ }
AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseEntered(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseExited(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseDragged(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseMoved(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseClicked(MouseEvent evt)
{
AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
if (SwingUtilities.isLeftMouseButton(evt))
{
- if (selectedRow < aa.length)
- {
- if (aa[selectedRow].groupRef!=null)
+ if (selectedRow > -1 && selectedRow < aa.length)
+ {
+ if (aa[selectedRow].groupRef != null)
{
- if (evt.getClickCount()>=2)
+ if (evt.getClickCount() >= 2)
{
// todo: make the ap scroll to the selection
ap.seqPanel.ap.idPanel.highlightSearchResults(null);
- ap.av.setSelectionGroup(//new SequenceGroup(
+ ap.av.setSelectionGroup(// new SequenceGroup(
aa[selectedRow].groupRef); // );
+ ap.av.sendSelection();
ap.paintAlignment(false);
- } else {
- ap.seqPanel.ap.idPanel.highlightSearchResults(aa[selectedRow].groupRef.getSequences(null));
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ }
+ else
+ {
+ ap.seqPanel.ap.idPanel
+ .highlightSearchResults(aa[selectedRow].groupRef
+ .getSequences(null));
}
return;
- } else
- if (aa[selectedRow].sequenceRef!=null){
+ }
+ else if (aa[selectedRow].sequenceRef != null)
+ {
Vector sr = new Vector();
sr.addElement(aa[selectedRow].sequenceRef);
- if (evt.getClickCount()==1)
+ if (evt.getClickCount() == 1)
{
- ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
- } else
- if (evt.getClickCount()>=2)
+ 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.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());
}
-
+
}
}
}
return;
}
-
JPopupMenu pop = new JPopupMenu("Annotations");
JMenuItem item = new JMenuItem(ADDNEW);
item.addActionListener(this);
-
- if ((aa == null) || (aa.length == 0))
+ pop.add(item);
+ if (selectedRow < 0)
{
- item = new JMenuItem(SHOWALL);
- item.addActionListener(this);
- pop.add(item);
+ 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;
}
-
- pop.add(item);
item = new JMenuItem(EDITNAME);
item.addActionListener(this);
pop.add(item);
item = new JMenuItem(DELETE);
item.addActionListener(this);
pop.add(item);
- item = new JMenuItem(SHOWALL);
- 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
+ // TODO: annotation object should be typed for autocalculated/derived
+ // property methods
if (selectedRow < aa.length)
{
- if (!aa[selectedRow].autoCalculated) {
- if (aa[selectedRow].graph==AlignmentAnnotation.NO_GRAPH)
+ 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);
+ aa[selectedRow].scaleColLabel);
item.addActionListener(this);
pop.add(item);
}
{
if (aaa.groupRef != null)
{
- // TODO: pass on reference to ap so the view can be updated.
- aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+ // TODO: pass on reference to ap so the view can be updated.
+ aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
else
}
});
pop.add(chist);
- final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
"Show Group Logo", aa[selectedRow].groupRef
- .isIncludeAllConsSymbols());
- cprof.addActionListener(new ActionListener()
+ .isShowSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
// view
// can be
// updated.
- aaa.groupRef.setIncludeAllConsSymbols(cprof.getState());
+ aaa.groupRef.setshowSequenceLogo(cprofl.getState());
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
- pop.add(cprof);
- } else {
+ pop.add(cprofl);
+ }
+ else
+ {
final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
"Show Histogram", av.isShowConsensusHistogram());
chist.addActionListener(new ActionListener()
});
pop.add(chist);
final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
- "Show Logo", av.isShowConsensusProfile());
+ "Show Logo", av.isShowSequenceLogo());
cprof.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
// view
// can be
// updated.
- av.setShowConsensusProfile(cprof.getState());
+ av.setShowSequenceLogo(cprof.getState());
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
- pop.add(cprof);
+ pop.add(cprof);
}
final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
consclipbrd.addActionListener(this);
* do a single sequence copy to jalview and the system clipboard
*
* @param sq
- * sequence to be copied to clipboard
+ * sequence to be copied to clipboard
*/
protected void copy_annotseqtoclipboard(SequenceI sq)
{
Desktop.jalviewClipboard = new Object[]
{ seqs, ds, // what is the dataset of a consensus sequence ? need to flag
- // sequence as special.
+ // sequence as special.
hiddenColumns };
}
* DOCUMENT ME!
*
* @param g1
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void paintComponent(Graphics g)
{
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void drawComponent(Graphics g, int width)
{
if (aa != null)
{
+ hasHiddenRows = false;
for (int i = 0; i < aa.length; i++)
{
g.setColor(Color.black);
if (!aa[i].visible)
{
+ hasHiddenRows = true;
continue;
}
git://source.jalview.org / jalview.git / blobdiff