/*
- * 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 2.7)
+ * 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;
* DOCUMENT ME!
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.130 $
*/
public class SeqPanel extends JPanel implements MouseListener,
MouseMotionListener, MouseWheelListener, SequenceListener,
* Creates a new SeqPanel object.
*
* @param avp
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param p
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public SeqPanel(AlignViewport av, AlignmentPanel ap)
{
addMouseMotionListener(this);
addMouseListener(this);
addMouseWheelListener(this);
- ssm = StructureSelectionManager.getStructureSelectionManager();
+ ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
}
else
{
+ if (x>seqCanvas.getWidth()+seqCanvas.getWidth())
+ {
+ // make sure we calculate relative to visible alignment, rather than right-hand gutter
+ x = seqCanvas.getX()+seqCanvas.getWidth();
+ }
res = (x / av.getCharWidth()) + av.getStartRes();
}
y -= hgap;
- seq = Math.min((y % cHeight) / av.getCharHeight(), av.alignment
- .getHeight() - 1);
+ seq = Math.min((y % cHeight) / av.getCharHeight(),
+ av.alignment.getHeight() - 1);
}
else
{
* 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 (lastMessage == null || !lastMessage.equals(tmp))
{
// System.err.println("mouseOver Sequence: "+tmp);
- ssm.mouseOverSequence(sequence, index, pos);
+ ssm.mouseOverSequence(sequence, index, pos, av);
}
lastMessage = tmp;
}
{
if (av.followHighlight)
{
- ap.scrollToPosition(results, false);
+ if (ap.scrollToPosition(results, false))
+ {
+ seqCanvas.revalidate();
+ }
}
seqCanvas.highlightSearchResults(results);
}
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void mouseMoved(MouseEvent evt)
{
if (av.showSequenceFeatures)
{
int rpos;
- SequenceFeature[] features = findFeaturesAtRes(sequence
- .getDatasetSequence(), rpos = sequence.findPosition(res));
- appendFeatures(tooltipText, linkImageURL.toString(), rpos, features);
+ SequenceFeature[] features = findFeaturesAtRes(
+ sequence.getDatasetSequence(),
+ rpos = sequence.findPosition(res));
+ 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)
{
.getType()))
{
tmpString = features[i].getDescription();
- int startTag = tmpString.toUpperCase().indexOf("<HTML>");
+ String tmp2up=tmpString.toUpperCase();
+ int startTag = tmp2up.indexOf("<HTML>");
if (startTag > -1)
{
tmpString = tmpString.substring(startTag + 6);
+ tmp2up = tmp2up.substring(startTag+6);
}
- int endTag = tmpString.toUpperCase().indexOf("</BODY>");
+ int endTag = tmp2up.indexOf("</BODY>");
if (endTag > -1)
{
tmpString = tmpString.substring(0, endTag);
+ tmp2up = tmp2up.substring(0, endTag);
}
- endTag = tmpString.toUpperCase().indexOf("</HTML>");
+ endTag = tmp2up.indexOf("</HTML>");
if (endTag > -1)
{
tmpString = tmpString.substring(0, endTag);
}
}
}
- // TODO: check min/max range for this feature type to decide if
- // score should be shown
+ // check score should be shown
if (features[i].getScore() != Float.NaN)
{
- tooltipText2.append(" Score=" + features[i].getScore());
+ 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)
{
// Which is bigger, left-right or up-down?
if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
- .getX()
- - lastMousePress.getX()))
+ .getX() - lastMousePress.getX()))
{
int fontSize = av.font.getSize();
fontSize = 1;
}
- av
- .setFont(new Font(av.font.getName(), av.font.getStyle(),
- fontSize));
+ av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
av.charWidth = oldWidth;
ap.fontChanged();
}
* 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);
}
- SequenceFeature[] features = findFeaturesAtRes(sequence
- .getDatasetSequence(), sequence.findPosition(findRes(evt)));
+ SequenceFeature[] features = findFeaturesAtRes(
+ sequence.getDatasetSequence(),
+ sequence.findPosition(findRes(evt)));
if (features != null && features.length > 0)
{
SearchResults highlight = new SearchResults();
- highlight.addResult(sequence, features[0].getBegin(), features[0]
- .getEnd());
+ highlight.addResult(sequence, features[0].getBegin(),
+ features[0].getEnd());
seqCanvas.highlightSearchResults(highlight);
}
if (features != null && features.length > 0)
{
ap.scrollUp(true);
}
+ // TODO Update tooltip for new position.
}
/**
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void doMousePressedDefineMode(MouseEvent evt)
{
if (javax.swing.SwingUtilities.isRightMouseButton(evt))
{
- SequenceFeature[] allFeatures = findFeaturesAtRes(sequence
- .getDatasetSequence(), sequence.findPosition(res));
+ SequenceFeature[] allFeatures = findFeaturesAtRes(
+ sequence.getDatasetSequence(), sequence.findPosition(res));
Vector links = new Vector();
for (int i = 0; i < allFeatures.length; i++)
{
* 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)
{
- ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup
- .getSequences(av.hiddenRepSequences), stretchGroup
- .getWidth());
- }
-
- if (stretchGroup.cs instanceof Blosum62ColourScheme
- || stretchGroup.cs instanceof PIDColourScheme
- || stretchGroup.cs.conservationApplied()
- || stretchGroup.cs.getThreshold() > 0)
- {
- stretchGroup.recalcConservation();
+ ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
+ stretchGroup.getSequences(av.hiddenRepSequences),
+ stretchGroup.getWidth());
}
if (stretchGroup.cs.conservationApplied())
{
- SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup
- .getName());
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+ stretchGroup.getName());
}
else
{
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup
- .getName());
+ 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)
{
{
// TODO: fix this hack - source of messages is align viewport, but SeqPanel
// handles selection messages...
- if (av == source)
+ // TODO: extend config options to allow user to control if selections may be
+ // shared between viewports.
+ if (av == source
+ || !av.followSelection
+ || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
+ || (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)
+ // rules are: colsel is copied if there is a real intersection between
+ // sequence selection
+ boolean repaint = false, copycolsel = true;
+ // if (!av.isSelectionGroupChanged(false))
{
- if (av.selectionGroup == null || !av.isSelectionGroupChanged())
+ SequenceGroup sgroup = null;
+ if (seqsel != null && seqsel.getSize()>0)
{
- 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);
+ jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
+ + av.getSequenceSetId() + " ViewId=" + av.getViewId()
+ + " 's alignment is NULL! returning immediatly.");
+ return;
}
- else
+ sgroup = seqsel.intersect(av.alignment,
+ (av.hasHiddenRows) ? av.hiddenRepSequences : null);
+ if ((sgroup == null || sgroup.getSize() == 0)
+ || (colsel == null || colsel.size() == 0))
{
- av.setSelectionGroup(null);
+ // 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
+ {
+ av.setSelectionGroup(null);
+ }
+ av.isSelectionGroupChanged(true);
+ repaint = true;
+ }
+ if (copycolsel)
+ {
+ // the current selection is unset or from a previous message
+ // so import the new colsel.
+ if (colsel == null || colsel.size() == 0)
{
- // Check to see if the current selection is from a previous message
- if (colsel == null || colsel.size() == 0)
+ if (av.colSel != null)
{
av.colSel.clear();
+ repaint=true;
}
- 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);
+ }
}
+ av.isColSelChanged(true);
+ repaint = true;
+ }
+ if (copycolsel && av.hasHiddenColumns
+ && (av.colSel == null || av.colSel.getHiddenColumns() == null))
+ {
+ System.err.println("Bad things");
}
if (repaint)
{
git://source.jalview.org / jalview.git / blobdiff