X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=9bf0128d3ce10a55a5e6055da45b7287e5581bba;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=b1a9a36bf45cf0278ec3ea24dd150c9e81d1776b;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index b1a9a36..9bf0128 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,24 +1,26 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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.
- *
+ *
* 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 .
+ * 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 jalview.datamodel.*;
@@ -72,11 +74,21 @@ public class IdPanel extends Panel implements MouseListener,
}
}
+ {
+ // 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=$SEQUENCE_ID$");
}
}
@@ -90,61 +102,62 @@ public class IdPanel extends Panel implements MouseListener,
// look for non-pos features
StringBuffer tooltiptext = new StringBuffer();
-
- if (sequence.getDescription() != null)
+ if (sequence != null)
{
- tooltiptext.append(sequence.getDescription());
- tooltiptext.append("\n");
- }
+ if (sequence.getDescription() != null)
+ {
+ tooltiptext.append(sequence.getDescription());
+ tooltiptext.append("\n");
+ }
- SequenceFeature sf[] = sequence.getSequenceFeatures();
- for (int sl = 0; sf != null && sl < sf.length; sl++)
- {
- if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+ SequenceFeature sf[] = sequence.getSequenceFeatures();
+ for (int sl = 0; sf != null && sl < sf.length; sl++)
{
- boolean nl = false;
- if (sf[sl].getFeatureGroup() != null)
- {
- tooltiptext.append(sf[sl].getFeatureGroup());
- nl = true;
- }
- ;
- if (sf[sl].getType() != null)
- {
- tooltiptext.append(" ");
- tooltiptext.append(sf[sl].getType());
- nl = true;
- }
- ;
- if (sf[sl].getDescription() != null)
- {
- tooltiptext.append(" ");
- tooltiptext.append(sf[sl].getDescription());
- nl = true;
- }
- ;
- if (sf[sl].getScore() != Float.NaN && sf[sl].getScore() != 0f)
- {
- tooltiptext.append(" Score = ");
- tooltiptext.append(sf[sl].getScore());
- nl = true;
- }
- ;
- if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
- {
- tooltiptext.append(" (");
- tooltiptext.append(sf[sl].getStatus());
- tooltiptext.append(")");
- nl = true;
- }
- ;
- if (nl)
+ if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
{
- tooltiptext.append("\n");
+ boolean nl = false;
+ if (sf[sl].getFeatureGroup() != null)
+ {
+ tooltiptext.append(sf[sl].getFeatureGroup());
+ nl = true;
+ }
+ ;
+ if (sf[sl].getType() != null)
+ {
+ tooltiptext.append(" ");
+ tooltiptext.append(sf[sl].getType());
+ nl = true;
+ }
+ ;
+ if (sf[sl].getDescription() != null)
+ {
+ tooltiptext.append(" ");
+ tooltiptext.append(sf[sl].getDescription());
+ nl = true;
+ }
+ ;
+ if (sf[sl].getScore() != Float.NaN && sf[sl].getScore() != 0f)
+ {
+ tooltiptext.append(" Score = ");
+ tooltiptext.append(sf[sl].getScore());
+ nl = true;
+ }
+ ;
+ if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
+ {
+ tooltiptext.append(" (");
+ tooltiptext.append(sf[sl].getStatus());
+ tooltiptext.append(")");
+ nl = true;
+ }
+ ;
+ if (nl)
+ {
+ tooltiptext.append("\n");
+ }
}
}
}
-
if (tooltiptext.length() == 0)
{
// nothing to display - so clear tooltip if one is visible
@@ -197,7 +210,12 @@ public class IdPanel extends Panel implements MouseListener,
// DEFAULT LINK IS FIRST IN THE LINK LIST
int seq = alignPanel.seqPanel.findSeq(e);
- String id = av.getAlignment().getSequenceAt(seq).getName();
+ SequenceI sq = av.getAlignment().getSequenceAt(seq);
+ if (sq == null)
+ {
+ return;
+ }
+ String id = sq.getName();
String target = null;
String url = null;
@@ -267,7 +285,7 @@ public class IdPanel extends Panel implements MouseListener,
}
if (mouseDragging && e.getY() >= getSize().height
- && av.alignment.getHeight() > av.getEndSeq())
+ && av.getAlignment().getHeight() > av.getEndSeq())
{
scrollThread = new ScrollThread(false);
}
@@ -291,6 +309,7 @@ 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
Vector nlinks = new Vector();
@@ -298,7 +317,7 @@ public class IdPanel extends Panel implements MouseListener,
{
nlinks.addElement(links.elementAt(l));
}
- SequenceFeature sf[] = 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)
@@ -325,7 +344,7 @@ public class IdPanel extends Panel implements MouseListener,
{
av.setSelectionGroup(new SequenceGroup());
av.getSelectionGroup().setStartRes(0);
- av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+ av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
}
if (e.isShiftDown() && lastid != -1)
@@ -344,7 +363,7 @@ public class IdPanel extends Panel implements MouseListener,
{
lastid = seq;
SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
- av.getSelectionGroup().addOrRemove(pickedSeq, false);
+ av.getSelectionGroup().addOrRemove(pickedSeq, true);
}
void selectSeqs(int start, int end)
@@ -364,11 +383,14 @@ public class IdPanel extends Panel implements MouseListener,
end = tmp;
lastid = end;
}
-
+ if (av.getSelectionGroup() == null)
+ {
+ av.setSelectionGroup(new SequenceGroup());
+ }
for (int i = start; i <= end; i++)
{
av.getSelectionGroup().addSequence(
- av.getAlignment().getSequenceAt(i), false);
+ av.getAlignment().getSequenceAt(i), i == end);
}
}
@@ -387,18 +409,20 @@ public class IdPanel extends Panel implements MouseListener,
mouseDragging = false;
PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // always send selection message when mouse is released
+ av.sendSelection();
}
- public void highlightSearchResults(java.util.Vector found)
+ public void highlightSearchResults(List 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)
@@ -443,7 +467,7 @@ 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);
}