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JAL-2282 Renamed internal use of sequence id / db accession for
[jalview.git]
/
src
/
jalview
/
appletgui
/
IdPanel.java
diff --git
a/src/jalview/appletgui/IdPanel.java
b/src/jalview/appletgui/IdPanel.java
index
eba52d5
..
182f20e
100755
(executable)
--- a/
src/jalview/appletgui/IdPanel.java
+++ b/
src/jalview/appletgui/IdPanel.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 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.
*
*
* This file is part of Jalview.
*
@@
-20,6
+20,9
@@
*/
package jalview.appletgui;
*/
package jalview.appletgui;
+import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.SRS_STRING;
+
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
@@
-82,24
+85,22
@@
public class IdPanel extends Panel implements MouseListener,
}
{
// upgrade old SRS link
}
{
// 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)
{
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();
}
}
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;
}
}
Tooltip tooltip;
+ @Override
public void mouseMoved(MouseEvent e)
{
int seq = alignPanel.seqPanel.findSeq(e);
public void mouseMoved(MouseEvent e)
{
int seq = alignPanel.seqPanel.findSeq(e);
@@
-188,6
+189,7
@@
public class IdPanel extends Panel implements MouseListener,
tooltiptext = null;
}
tooltiptext = null;
}
+ @Override
public void mouseDragged(MouseEvent e)
{
mouseDragging = true;
public void mouseDragged(MouseEvent e)
{
mouseDragging = true;
@@
-207,6
+209,7
@@
public class IdPanel extends Panel implements MouseListener,
alignPanel.paintAlignment(false);
}
alignPanel.paintAlignment(false);
}
+ @Override
public void mouseClicked(MouseEvent e)
{
if (e.getClickCount() < 2)
public void mouseClicked(MouseEvent e)
{
if (e.getClickCount() < 2)
@@
-243,7
+246,14
@@
public class IdPanel extends Panel implements MouseListener,
url = null;
continue;
}
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());
if (!urlLink.isValid())
{
System.err.println(urlLink.getInvalidMessage());
@@
-270,6
+280,7
@@
public class IdPanel extends Panel implements MouseListener,
}
}
}
}
+ @Override
public void mouseEntered(MouseEvent e)
{
if (scrollThread != null)
public void mouseEntered(MouseEvent e)
{
if (scrollThread != null)
@@
-278,6
+289,7
@@
public class IdPanel extends Panel implements MouseListener,
}
}
}
}
+ @Override
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
@@
-297,6
+309,7
@@
public class IdPanel extends Panel implements MouseListener,
}
}
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
if (e.getClickCount() > 1)
public void mousePressed(MouseEvent e)
{
if (e.getClickCount() > 1)
@@
-345,8
+358,8
@@
public class IdPanel extends Panel implements MouseListener,
}
if ((av.getSelectionGroup() == null)
}
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);
{
av.setSelectionGroup(new SequenceGroup());
av.getSelectionGroup().setStartRes(0);
@@
-401,6
+414,7
@@
public class IdPanel extends Panel implements MouseListener,
}
}
+ @Override
public void mouseReleased(MouseEvent e)
{
if (scrollThread != null)
public void mouseReleased(MouseEvent e)
{
if (scrollThread != null)
@@
-455,6
+469,7
@@
public class IdPanel extends Panel implements MouseListener,
running = false;
}
running = false;
}
+ @Override
public void run()
{
running = true;
public void run()
{
running = true;