/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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;
}
}
+ {
+ // 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");
+ if (srsPos > -1)
+ {
+ links.setElementAt(
+ "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
+ srsPos);
+ }
+ }
if (links.size() < 1)
{
links = new java.util.Vector();
- links.addElement("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+ links.addElement("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
}
}
// DEFAULT LINK IS FIRST IN THE LINK LIST
int seq = alignPanel.seqPanel.findSeq(e);
SequenceI sq = av.getAlignment().getSequenceAt(seq);
- if (sq==null)
+ if (sq == null)
{
return;
}
if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
-
+
// build a new links menu based on the current links + any non-positional
// features
Vector nlinks = new Vector();
{
nlinks.addElement(links.elementAt(l));
}
- SequenceFeature sf[] = sq==null ? null:sq.getSequenceFeatures();
+ SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
for (int sl = 0; sf != null && sl < sf.length; sl++)
{
if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
{
lastid = seq;
SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
- av.getSelectionGroup().addOrRemove(pickedSeq, false);
+ av.getSelectionGroup().addOrRemove(pickedSeq, true);
}
void selectSeqs(int start, int end)
for (int i = start; i <= end; i++)
{
av.getSelectionGroup().addSequence(
- av.getAlignment().getSequenceAt(i), i==end);
+ av.getAlignment().getSequenceAt(i), i == end);
}
}