/*
- * 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
* Creates a new SeqPanel object.
*
* @param avp
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param p
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public SeqPanel(AlignViewport av, AlignmentPanel ap)
{
* 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)
{
* 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(tooltipText.toString());
lastTooltip = tooltipText.toString();
}
-
+
}
-
- }
- /* (non-Javadoc)
+ }
+ 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 = (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 p;
+ 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;
}
/**
* @param linkImageURL
* @param rpos
* @param features
- * TODO refactor to Jalview 'utilities' somehow.
+ * TODO refactor to Jalview 'utilities' somehow.
*/
- public static void appendFeatures(StringBuffer tooltipText2,
+ 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)
{
}
}
}
- // TODO: check min/max range for this feature type to decide if
- // score should be shown
- if (features[i].getScore() != Float.NaN)
- {
- tooltipText2.append(" Score=" + features[i].getScore());
+ // 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)
{
* 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)
{
* 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;
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void doMouseDraggedDefineMode(MouseEvent evt)
{
{
if (av.selectionGroup == null || !av.isSelectionGroupChanged())
{
- SequenceGroup sgroup = (seqsel != null) ? seqsel.intersect(
- av.alignment, (av.hasHiddenRows) ? av.hiddenRepSequences
- : null) : null;
+ 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);
}
if (av.colSel == null || !av.isColSelChanged())
{
- // Check to see if the current selection is from a previous message
+ // the current selection is unset or from a previous message
+ // so import the new colsel.
if (colsel == null || colsel.size() == 0)
{
- av.colSel.clear();
+ if (av.colSel!=null)
+ {
+ av.colSel.clear();
+ }
}
else
{
- av.colSel = new ColumnSelection(colsel);
+ 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
git://source.jalview.org / jalview.git / blobdiff