X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=3adaa14af2a3813d0985392832ba8b12fe4f550e;hb=46d6d8de867a35ce4082c3be437e5f5cdc31ba34;hp=b973913802ed7d06bd0c9190d708155de885c4a6;hpb=7d4f1d8e997964bef5c351d04fbdafe4401cf5d7;p=jalview.git
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index b973913..3adaa14 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,25 +1,25 @@
/*
- * 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 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.appletgui;
import java.awt.*;
import java.awt.event.*;
+import java.util.List;
import java.util.Vector;
import jalview.datamodel.*;
@@ -58,6 +58,7 @@ public class IdPanel extends Panel implements MouseListener,
idCanvas.addMouseMotionListener(this);
String label, url;
+ // TODO: add in group link parameter
if (av.applet != null)
{
for (int i = 1; i < 10; i++)
@@ -75,8 +76,7 @@ public class IdPanel extends Panel implements MouseListener,
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("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
}
}
@@ -87,33 +87,66 @@ public class IdPanel extends Panel implements MouseListener,
int seq = alignPanel.seqPanel.findSeq(e);
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-
+
// look for non-pos features
StringBuffer tooltiptext = new StringBuffer();
-
-
- if (sequence.getDescription() != null)
- {
- tooltiptext.append(sequence.getDescription());
- tooltiptext.append("\n");
- }
-
- SequenceFeature sf[] = sequence.getSequenceFeatures();
- for (int sl=0;sf!=null && sl= getSize().height
- && av.alignment.getHeight() > av.getEndSeq())
+ && av.getAlignment().getHeight() > av.getEndSeq())
{
scrollThread = new ScrollThread(false);
}
@@ -258,29 +296,30 @@ public class IdPanel extends Panel implements MouseListener,
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
+ 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();
- for (int l=0,lSize=links.size();l0)
+ if (sf[sl].links != null && sf[sl].links.size() > 0)
{
- for (int l=0, lSize=sf[sl].links.size(); l list)
{
- idCanvas.setHighlighted(found);
+ idCanvas.setHighlighted(list);
- if (found == null)
+ if (list == null)
{
return;
}
- int index = av.alignment.findIndex((SequenceI) found.elementAt(0));
+ int index = av.getAlignment().findIndex(list.get(0));
// do we need to scroll the panel?
if (av.getStartSeq() > index || av.getEndSeq() < index)
@@ -411,7 +455,7 @@ public class IdPanel extends Panel implements MouseListener,
{
selectSeqs(lastid - 1, seq);
}
- else if (seq > lastid && seq < av.alignment.getHeight())
+ else if (seq > lastid && seq < av.getAlignment().getHeight())
{
selectSeqs(lastid + 1, seq);
}