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!! */
addMouseWheelListener(this);
ssm = StructureSelectionManager.getStructureSelectionManager();
ssm.addStructureViewerListener(this);
+ ssm.addSelectionListener(this);
}
}
}
ap.paintAlignment(false);
+ av.sendSelection();
}
void insertGapAtCursor(boolean group)
public void highlightSequence(SearchResults results)
{
+ if (av.followHighlight)
+ {
+ ap.scrollToPosition(results, false);
+ }
seqCanvas.highlightSearchResults(results);
}
// use aa to see if the mouse pointer is on a
if (av.showSequenceFeatures)
{
+ int rpos;
SequenceFeature[] features = findFeaturesAtRes(sequence
- .getDatasetSequence(), sequence.findPosition(res));
+ .getDatasetSequence(), rpos = sequence.findPosition(res));
+ appendFeatures(tooltipText, linkImageURL.toString(), rpos, features);
+ }
+ 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();
+ }
+
+ }
+
+ }
- if (features != 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;
+ }
+
+ /**
+ * 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.
+ */
+ public static void appendFeatures(StringBuffer tooltipText2,
+ String linkImageURL, int rpos, SequenceFeature[] features)
+ {
+ String tmpString;
+ if (features != null)
+ {
+ for (int i = 0; i < features.length; i++)
{
- for (int i = 0; i < features.length; i++)
+ if (features[i].getType().equals("disulfide bond"))
{
- if (features[i].getType().equals("disulfide bond"))
+ if (features[i].getBegin() == rpos
+ || features[i].getEnd() == rpos)
{
- if (features[i].getBegin() == sequence.findPosition(res)
- || features[i].getEnd() == sequence.findPosition(res))
+ if (tooltipText2.length() > 6)
{
- if (tooltipText.length() > 6)
- {
- tooltipText.append("<br>");
- }
- tooltipText.append("disulfide bond " + features[i].getBegin()
- + ":" + features[i].getEnd());
- if (features[i].links != null)
- {
- tooltipText.append(" <img src=\"" + linkImageURL + "\">");
- }
+ tooltipText2.append("<br>");
+ }
+ tooltipText2.append("disulfide bond " + features[i].getBegin()
+ + ":" + features[i].getEnd());
+ if (features[i].links != null)
+ {
+ tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
}
}
- else
+ }
+ else
+ {
+ if (tooltipText2.length() > 6)
+ {
+ tooltipText2.append("<br>");
+ }
+ // TODO: remove this hack to display link only features
+ boolean linkOnly = features[i].getValue("linkonly") != null;
+ if (!linkOnly)
{
- if (tooltipText.length() > 6)
+ tooltipText2.append(features[i].getType() + " ");
+ if (rpos != 0)
{
- tooltipText.append("<br>");
+ // we are marking a positional feature
+ tooltipText2.append(features[i].begin);
}
-
- tooltipText.append(features[i].getType() + " "
- + features[i].begin);
if (features[i].begin != features[i].end)
{
- tooltipText.append(" " + features[i].end);
+ tooltipText2.append(" " + features[i].end);
}
if (features[i].getDescription() != null
if (startTag > -1)
{
- tooltipText.append("; " + tmpString);
+ tooltipText2.append("; " + tmpString);
}
else
{
tmpString = tmpString.replaceAll("<", "<");
tmpString = tmpString.replaceAll(">", ">");
- tooltipText.append("; ");
- tooltipText.append(tmpString);
+ tooltipText2.append("; ");
+ tooltipText2.append(tmpString);
}
else
{
- tooltipText.append("; " + tmpString);
+ tooltipText2.append("; " + tmpString);
}
}
}
+ // 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());
+ }
if (features[i].getValue("status") != null)
{
String status = features[i].getValue("status").toString();
if (status.length() > 0)
{
- tooltipText.append("; (" + features[i].getValue("status")
+ tooltipText2.append("; (" + features[i].getValue("status")
+ ")");
}
}
-
- if (features[i].links != null)
- {
- tooltipText.append(" <img src=\"" + linkImageURL + "\">");
- }
-
}
+ if (features[i].links != null)
+ {
+ tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
+ }
+
}
}
}
-
- if (tooltipText.length() == 6) // <html></html>
- {
- setToolTipText(null);
- }
- else
- {
- tooltipText.append("</html>");
- if (lastTooltip == null
- || !lastTooltip.equals(tooltipText.toString()))
- setToolTipText(tooltipText.toString());
-
- lastTooltip = tooltipText.toString();
- }
-
}
String lastTooltip;
sg.setEndRes(res);
sg.addSequence(sequence, false);
av.setSelectionGroup(sg);
+
stretchGroup = sg;
if (av.getConservationSelected())
changeEndRes = false;
changeStartRes = false;
stretchGroup = null;
-
+ av.sendSelection();
}
/**
}
}
}
+
+ /**
+ * 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 = (seqsel != null) ? seqsel.intersect(
+ av.alignment, (av.hasHiddenRows) ? av.hiddenRepSequences
+ : null) : null;
+ if (sgroup != null && sgroup.getSize() > 0)
+ {
+ av.setSelectionGroup(sgroup);
+ }
+ else
+ {
+ av.setSelectionGroup(null);
+ }
+ repaint = av.isSelectionGroupChanged();
+ }
+ if (av.colSel == null || !av.isColSelChanged())
+ {
+ // Check to see if the current selection is from a previous message
+ if (colsel == null || colsel.size() == 0)
+ {
+ av.colSel.clear();
+ }
+ else
+ {
+ av.colSel = new ColumnSelection(colsel);
+ }
+ repaint |= av.isColSelChanged();
+ }
+ }
+ if (repaint)
+ {
+ // probably finessing with multiple redraws here
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // ap.paintAlignment(false);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff