/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
import java.awt.*;
import java.awt.event.*;
+
import javax.swing.*;
import jalview.commands.*;
* @version $Revision$
*/
public class SeqPanel extends JPanel implements MouseListener,
- MouseMotionListener, MouseWheelListener, SequenceListener
+ MouseMotionListener, MouseWheelListener, SequenceListener,
+ SelectionListener
{
/** DOCUMENT ME!! */
* Creates a new SeqPanel object.
*
* @param avp
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param p
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public SeqPanel(AlignViewport av, AlignmentPanel ap)
{
addMouseWheelListener(this);
ssm = StructureSelectionManager.getStructureSelectionManager();
ssm.addStructureViewerListener(this);
+ ssm.addSelectionListener(this);
}
}
}
ap.paintAlignment(false);
+ av.sendSelection();
}
void insertGapAtCursor(boolean group)
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseReleased(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mousePressed(MouseEvent evt)
{
public void highlightSequence(SearchResults results)
{
+ if (av.followHighlight)
+ {
+ ap.scrollToPosition(results, false);
+ }
seqCanvas.highlightSearchResults(results);
}
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseMoved(MouseEvent evt)
{
int rpos;
SequenceFeature[] features = findFeaturesAtRes(sequence
.getDatasetSequence(), rpos = sequence.findPosition(res));
- appendFeatures(tooltipText, linkImageURL.toString(), rpos, features);
+ appendFeatures(tooltipText, linkImageURL.toString(), rpos, features,this.ap.seqPanel.seqCanvas.fr.minmax);
}
if (tooltipText.length() == 6) // <html></html>
{
setToolTipText(null);
+ lastTooltip = null;
}
else
{
tooltipText.append("</html>");
if (lastTooltip == null
|| !lastTooltip.equals(tooltipText.toString()))
+ {
setToolTipText(tooltipText.toString());
+ lastTooltip = tooltipText.toString();
+ }
- lastTooltip = tooltipText.toString();
}
}
+ private Point lastp=null;
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
+ */
+ public Point getToolTipLocation(MouseEvent event)
+ {
+ int x = event.getX(), w = getWidth();
+ int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
+ // close to edge
+ Point p = lastp;
+ if (!event.isShiftDown() || p==null) {
+ p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
+ event.getX() + wdth, event.getY() - 20)
+ : null;
+ }
+ /*
+ * TODO: try to modify position region is not obcured by tooltip
+ */
+ return lastp=p;
+ }
+
/**
- * appends the features at rpos to the given stringbuffer ready for display in a tooltip
+ * appends the features at rpos to the given stringbuffer ready for display in
+ * a tooltip
+ *
* @param tooltipText2
* @param linkImageURL
* @param rpos
* @param features
- * TODO refactor to Jalview 'utilities' somehow.
+ * TODO refactor to Jalview 'utilities' somehow.
*/
- public static void appendFeatures(StringBuffer tooltipText2, String linkImageURL,
- int rpos, SequenceFeature[] features)
+ public void appendFeatures(StringBuffer tooltipText2,
+ String linkImageURL, int rpos, SequenceFeature[] features)
+ {
+ appendFeatures(tooltipText2,linkImageURL,rpos,features,null);
+ }
+ public void appendFeatures(StringBuffer tooltipText2, String string,
+ int rpos, SequenceFeature[] features, Hashtable minmax)
{
String tmpString;
if (features != null)
{
tooltipText2.append("<br>");
}
-
- tooltipText2.append(features[i].getType() + " ");
- if (rpos!=0)
- {
- // we are marking a positional feature
- tooltipText2.append(features[i].begin);
- }
- if (features[i].begin != features[i].end)
+ // TODO: remove this hack to display link only features
+ boolean linkOnly = features[i].getValue("linkonly") != null;
+ if (!linkOnly)
{
- tooltipText2.append(" " + features[i].end);
- }
-
- if (features[i].getDescription() != null
- && !features[i].description.equals(features[i]
- .getType()))
- {
- tmpString = features[i].getDescription();
- int startTag = tmpString.toUpperCase().indexOf("<HTML>");
- if (startTag > -1)
- {
- tmpString = tmpString.substring(startTag + 6);
- }
- int endTag = tmpString.toUpperCase().indexOf("</BODY>");
- if (endTag > -1)
+ tooltipText2.append(features[i].getType() + " ");
+ if (rpos != 0)
{
- tmpString = tmpString.substring(0, endTag);
+ // we are marking a positional feature
+ tooltipText2.append(features[i].begin);
}
- endTag = tmpString.toUpperCase().indexOf("</HTML>");
- if (endTag > -1)
+ if (features[i].begin != features[i].end)
{
- tmpString = tmpString.substring(0, endTag);
+ tooltipText2.append(" " + features[i].end);
}
- if (startTag > -1)
+ if (features[i].getDescription() != null
+ && !features[i].description.equals(features[i]
+ .getType()))
{
- tooltipText2.append("; " + tmpString);
- }
- else
- {
- if (tmpString.indexOf("<") > -1
- || tmpString.indexOf(">") > -1)
+ tmpString = features[i].getDescription();
+ int startTag = tmpString.toUpperCase().indexOf("<HTML>");
+ if (startTag > -1)
{
- // The description does not specify html is to
- // be used, so we must remove < > symbols
- tmpString = tmpString.replaceAll("<", "<");
- tmpString = tmpString.replaceAll(">", ">");
-
- tooltipText2.append("; ");
- tooltipText2.append(tmpString);
+ tmpString = tmpString.substring(startTag + 6);
+ }
+ int endTag = tmpString.toUpperCase().indexOf("</BODY>");
+ if (endTag > -1)
+ {
+ tmpString = tmpString.substring(0, endTag);
+ }
+ endTag = tmpString.toUpperCase().indexOf("</HTML>");
+ if (endTag > -1)
+ {
+ tmpString = tmpString.substring(0, endTag);
+ }
+ if (startTag > -1)
+ {
+ tooltipText2.append("; " + tmpString);
}
else
{
- tooltipText2.append("; " + tmpString);
+ if (tmpString.indexOf("<") > -1
+ || tmpString.indexOf(">") > -1)
+ {
+ // The description does not specify html is to
+ // be used, so we must remove < > symbols
+ tmpString = tmpString.replaceAll("<", "<");
+ tmpString = tmpString.replaceAll(">", ">");
+
+ tooltipText2.append("; ");
+ tooltipText2.append(tmpString);
+
+ }
+ else
+ {
+ tooltipText2.append("; " + tmpString);
+ }
}
}
- }
- if (features[i].getValue("status") != null)
- {
- String status = features[i].getValue("status").toString();
- if (status.length() > 0)
+ // check score should be shown
+ if (features[i].getScore() != Float.NaN) {
+ float[][] rng=(minmax==null) ? null : ((float[][])minmax.get(features[i].getType()));
+ if (rng!=null && rng[0]!=null && rng[0][0]!=rng[0][1]) {
+ tooltipText2.append(" Score=" + features[i].getScore());
+ }
+ }
+ if (features[i].getValue("status") != null)
{
- tooltipText2.append("; (" + features[i].getValue("status")
- + ")");
+ String status = features[i].getValue("status").toString();
+ if (status.length() > 0)
+ {
+ tooltipText2.append("; (" + features[i].getValue("status")
+ + ")");
+ }
}
}
-
if (features[i].links != null)
{
tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
* Set status message in alignment panel
*
* @param sequence
- * aligned sequence object
+ * aligned sequence object
* @param res
- * alignment column
+ * alignment column
* @param seq
- * index of sequence in alignment
+ * index of sequence in alignment
* @return position of res in sequence
*/
int setStatusMessage(SequenceI sequence, int res, int seq)
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseDragged(MouseEvent evt)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseEntered(MouseEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseExited(MouseEvent e)
{
{
ap.scrollUp(true);
}
+ // TODO Update tooltip for new position.
}
/**
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void doMousePressedDefineMode(MouseEvent evt)
{
sg.setEndRes(res);
sg.addSequence(sequence, false);
av.setSelectionGroup(sg);
+
stretchGroup = sg;
if (av.getConservationSelected())
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void doMouseReleasedDefineMode(MouseEvent evt)
{
return;
}
+ stretchGroup.recalcConservation(); // always do this - annotation has own state
if (stretchGroup.cs != null)
{
if (stretchGroup.cs instanceof ClustalxColourScheme)
.getWidth());
}
- if (stretchGroup.cs instanceof Blosum62ColourScheme
- || stretchGroup.cs instanceof PIDColourScheme
- || stretchGroup.cs.conservationApplied()
- || stretchGroup.cs.getThreshold() > 0)
- {
- stretchGroup.recalcConservation();
- }
-
if (stretchGroup.cs.conservationApplied())
{
SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup
SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup
.getName());
}
- PaintRefresher.Refresh(this, av.getSequenceSetId());
- ap.paintAlignment(true);
}
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ ap.paintAlignment(true);
changeEndRes = false;
changeStartRes = false;
stretchGroup = null;
-
+ av.sendSelection();
}
/**
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void doMouseDraggedDefineMode(MouseEvent evt)
{
}
}
}
+
+ /**
+ * modify current selection according to a received message.
+ */
+ public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+ SelectionSource source)
+ {
+ // TODO: fix this hack - source of messages is align viewport, but SeqPanel
+ // handles selection messages...
+ if (av == source)
+ {
+ return;
+ }
+ // do we want to thread this ? (contention with seqsel and colsel locks, I
+ // suspect)
+ boolean repaint = false;
+ if (av.followSelection)
+ {
+ if (av.selectionGroup == null || !av.isSelectionGroupChanged())
+ {
+ SequenceGroup sgroup = null;
+ if (seqsel != null)
+ {
+ if (av.alignment==null)
+ {
+ jalview.bin.Cache.log.warn("alignviewport av SeqSetId="+av.getSequenceSetId()+" ViewId="+av.getViewId()+" 's alignment is NULL! returning immediatly.");
+ return;
+ }
+ sgroup = seqsel.intersect(av.alignment,
+ (av.hasHiddenRows) ? av.hiddenRepSequences : null);
+ }
+ if (sgroup != null && sgroup.getSize() > 0)
+ {
+ av.setSelectionGroup(sgroup);
+ }
+ else
+ {
+ av.setSelectionGroup(null);
+ }
+ repaint = av.isSelectionGroupChanged();
+ }
+ if (av.colSel == null || !av.isColSelChanged())
+ {
+ // the current selection is unset or from a previous message
+ // so import the new colsel.
+ if (colsel == null || colsel.size() == 0)
+ {
+ if (av.colSel!=null)
+ {
+ av.colSel.clear();
+ }
+ }
+ else
+ {
+ if (av.colSel == null)
+ {
+ av.colSel = new ColumnSelection(colsel);
+ } else {
+ av.colSel.setElementsFrom(colsel);
+ }
+ }
+ repaint |= av.isColSelChanged();
+ }
+ }
+ if (av.hasHiddenColumns && (av.colSel==null || av.colSel.getHiddenColumns()==null))
+ {
+ System.err.println("Bad things");
+ }
+ if (repaint)
+ {
+ // probably finessing with multiple redraws here
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // ap.paintAlignment(false);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff