/*
- * 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 2.7)
+ * Copyright (C) 2011 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;
import java.util.*;
+import java.util.regex.Pattern;
import java.awt.*;
import java.awt.datatransfer.*;
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)
{
{
}
- 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);
* 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(HIDE))
{
aa[selectedRow].visible = false;
-
- if (aa[selectedRow].label.equals("Quality"))
- {
- ap.av.quality = null;
- }
}
else if (evt.getActionCommand().equals(DELETE))
{
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();
- ap.annotationScroller.validate();
- ap.paintAlignment(true);
+ ap.validateAnnotationDimensions(false);
+ ap.addNotify();
+ ap.repaint();
+ //validate();
+ //ap.paintAlignment(true);
}
/**
* 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)
{
&& ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
{
AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow];
-
- StringBuffer desc = new StringBuffer("<html>");
-
+
+ StringBuffer desc = new StringBuffer();
if (aa.description != null
&& !aa.description.equals("New description"))
{
- desc.append(aa.getDescription(true));
- if (aa.hasScore)
- desc.append("<br>");
+ // 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(Pattern.compile("<").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/>");
+ }
+
+
+ } else {
+ // begin the tooltip's html fragment
+ desc.append("<html>");
}
if (aa.hasScore())
{
- desc.append("Score: " + aa.score);
+ // 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("</html>");
this.setToolTipText(desc.toString());
* 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)
{
- ap.seqPanel.ap.idPanel.highlightSearchResults(aa[selectedRow].groupRef.getSequences(null));
- if (evt.getClickCount()>=2)
+ if (evt.getClickCount() >= 2)
{
- // todo: make the ap scroll to the selection
- ap.av.setSelectionGroup(new SequenceGroup(aa[selectedRow].groupRef));
+ // 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){
+ }
+ 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)
{
- // display 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);
+ 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 (aa[selectedRow].label.indexOf("Consensus") > -1)
{
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
"Ignore Gaps In Consensus",
(aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
- .getIgnoreGapsConsensus()
- : ap.av.getIgnoreGapsConsensus());
+ .getIgnoreGapsConsensus() : ap.av
+ .getIgnoreGapsConsensus());
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addActionListener(new ActionListener()
{
{
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
// av and sequencegroup need to implement same interface for
if (aaa.groupRef != null)
{
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ "Show Group Histogram",
+ aa[selectedRow].groupRef.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ "Show Group Logo",
+ aa[selectedRow].groupRef.isShowSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setshowSequenceLogo(cprofl.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprofl);
+ }
+ else
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ "Show Histogram", av.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(chist);
final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
- "Show Full Profile", aa[selectedRow].groupRef
- .isIncludeAllConsSymbols());
+ "Show Logo", av.isShowSequenceLogo());
cprof.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
// view
// can be
// updated.
- aaa.groupRef.setIncludeAllConsSymbols(cprof.getState());
- ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ av.setShowSequenceLogo(cprof.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
});
pop.add(cprof);
* 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)
{
String output = new FormatAdapter().formatSequences("Fasta", seqs,
omitHidden);
- Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
- new StringSelection(output), Desktop.instance);
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(output), Desktop.instance);
Vector hiddenColumns = null;
if (av.hasHiddenColumns)
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;
}
g.setColor(aa[gg].annotations[0].colour);
}
- g.drawLine(x, y - graphExtras - 3, x
- + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
+ g.drawLine(x, y - graphExtras - 3,
+ x + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
g.setColor(Color.black);
graphExtras += fontHeight + 8;
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() - scrollOffset);
}
if ((aa == null) || (aa.length < 1))
git://source.jalview.org / jalview.git / blobdiff