/*
- * 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 (Version 2.5)
+ * 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;
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, SelectionListener
+ 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)
{
* 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)
{
if (av.followHighlight)
{
ap.scrollToPosition(results, false);
+ seqCanvas.revalidate();
}
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)
+ tooltipText2.append(features[i].getType() + " ");
+ if (rpos != 0)
{
- tmpString = tmpString.substring(startTag + 6);
+ // we are marking a positional feature
+ tooltipText2.append(features[i].begin);
}
- int endTag = tmpString.toUpperCase().indexOf("</BODY>");
- if (endTag > -1)
+ if (features[i].begin != features[i].end)
{
- tmpString = tmpString.substring(0, endTag);
- }
- endTag = tmpString.toUpperCase().indexOf("</HTML>");
- if (endTag > -1)
- {
- 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].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)
+ // check score should be shown
+ if (features[i].getScore() != Float.NaN)
{
- tooltipText2.append("; (" + features[i].getValue("status")
- + ")");
+ 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)
+ {
+ 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)
{
public void mouseClicked(MouseEvent evt)
{
+ SequenceGroup sg = null;
SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
if (evt.getClickCount() > 1)
{
- if (av.getSelectionGroup().getSize() == 1
- && av.getSelectionGroup().getEndRes()
- - av.getSelectionGroup().getStartRes() < 2)
+ sg = av.getSelectionGroup();
+ if (sg != null && sg.getSize() == 1
+ && sg.getEndRes() - sg.getStartRes() < 2)
{
av.setSelectionGroup(null);
}
{
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;
* 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)
+ // TODO: fix this hack - source of messages is align viewport, but SeqPanel
+ // handles selection messages...
+ // TODO: extend config options to allow user to control if selections may be
+ // shared between viewports.
+ if (av == source
+ || !av.followSelection
+ || (source instanceof AlignViewport && ((AlignViewport) source)
+ .getSequenceSetId().equals(av.getSequenceSetId())))
{
return;
}
- // do we want to thread this ? (contention with seqsel and colsel locks, I suspect)
- boolean repaint=false;
- if (av.followSelection)
+ // do we want to thread this ? (contention with seqsel and colsel locks, I
+ // suspect)
+ // rules are: colsel is copied if there is a real intersection between sequence selection
+ boolean repaint = false,copycolsel=true;
+ if (av.selectionGroup == null || !av.isSelectionGroupChanged())
{
- if (av.selectionGroup==null || !av.isSelectionGroupChanged())
+ SequenceGroup sgroup = null;
+ if (seqsel != null)
{
- SequenceGroup sgroup = (seqsel!=null) ? seqsel.intersect(av.alignment, (av.hasHiddenRows) ? av.hiddenRepSequences : null)
- : null;
- if (sgroup!=null && sgroup.getSize()>0)
+ if (av.alignment == null)
{
- av.setSelectionGroup(sgroup);
- } else {
- av.setSelectionGroup(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) && (colsel==null || colsel.size()==0))
+ {
+ // don't copy columns if the region didn't intersect.
+ copycolsel=false;
}
- repaint = av.isSelectionGroupChanged();
}
- if (av.colSel==null || !av.isColSelChanged())
+ if (sgroup != null && sgroup.getSize() > 0)
+ {
+ av.setSelectionGroup(sgroup);
+ }
+ else
{
- // Check to see if the current selection is from a previous message
- if (colsel==null || colsel.size()==0)
+ av.setSelectionGroup(null);
+ }
+ repaint = av.isSelectionGroupChanged();
+ }
+ if (copycolsel && (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 {
+ }
+ }
+ else
+ {
+ // TODO: shift colSel according to the intersecting sequences
+ if (av.colSel == null)
+ {
av.colSel = new ColumnSelection(colsel);
- }
- repaint |= av.isColSelChanged();
+ }
+ else
+ {
+ av.colSel.setElementsFrom(colsel);
+ }
}
+ repaint |= av.isColSelChanged();
+ }
+ if (copycolsel && av.hasHiddenColumns
+ && (av.colSel == null || av.colSel.getHiddenColumns() == null))
+ {
+ System.err.println("Bad things");
}
if (repaint)
{