/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* 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.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.awt.*;
-import java.awt.event.*;
-import java.util.List;
-import java.util.Vector;
+import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.SRS_STRING;
-import jalview.datamodel.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
import jalview.util.UrlLink;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.Panel;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.List;
+import java.util.Vector;
public class IdPanel extends Panel implements MouseListener,
MouseMotionListener
protected IdCanvas idCanvas;
- protected AlignViewport av;
+ protected AlignmentViewport av;
protected AlignmentPanel alignPanel;
ScrollThread scrollThread = null;
- int offy;
-
- int width;
-
int lastid = -1;
boolean mouseDragging = false;
}
{
// upgrade old SRS link
- int srsPos = links
- .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+ int srsPos = links.indexOf(SRS_STRING);
if (srsPos > -1)
{
- links.setElementAt(
- "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
- srsPos);
+ links.setElementAt(EMBLEBI_STRING, srsPos);
}
}
if (links.size() < 1)
{
links = new java.util.Vector();
- links.addElement("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
+ links.addElement(EMBLEBI_STRING);
}
}
Tooltip tooltip;
+ @Override
public void mouseMoved(MouseEvent e)
{
int seq = alignPanel.seqPanel.findSeq(e);
nl = true;
}
;
- if (sf[sl].getScore() != Float.NaN && sf[sl].getScore() != 0f)
+ if (!Float.isNaN(sf[sl].getScore()) && sf[sl].getScore() != 0f)
{
tooltiptext.append(" Score = ");
tooltiptext.append(sf[sl].getScore());
tooltiptext = null;
}
+ @Override
public void mouseDragged(MouseEvent e)
{
mouseDragging = true;
alignPanel.paintAlignment(false);
}
+ @Override
public void mouseClicked(MouseEvent e)
{
if (e.getClickCount() < 2)
url = null;
continue;
}
- ;
+
+ if (urlLink.usesDBAccession())
+ {
+ // this URL requires an accession id, not the name of a sequence
+ url = null;
+ continue;
+ }
+
if (!urlLink.isValid())
{
System.err.println(urlLink.getInvalidMessage());
}
}
+ @Override
public void mouseEntered(MouseEvent e)
{
if (scrollThread != null)
}
}
+ @Override
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
if (e.getClickCount() > 1)
int y = e.getY();
if (av.getWrapAlignment())
{
- y -= 2 * av.charHeight;
+ y -= 2 * av.getCharHeight();
}
int seq = alignPanel.seqPanel.findSeq(e);
}
if ((av.getSelectionGroup() == null)
- || ((!e.isControlDown() && !e.isShiftDown()) && av
- .getSelectionGroup() != null))
+ || ((!jalview.util.Platform.isControlDown(e) && !e
+ .isShiftDown()) && av.getSelectionGroup() != null))
{
av.setSelectionGroup(new SequenceGroup());
av.getSelectionGroup().setStartRes(0);
}
+ @Override
public void mouseReleased(MouseEvent e)
{
if (scrollThread != null)
running = false;
}
+ @Override
public void run()
{
running = true;
}
}
}
-
}