X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=dbf6f38ea818481d987c7e34ee705102180074bc;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=d3467d46f9d6fef9595fead3741858967f88e11d;hpb=e87d402f10e23691d312a4ed6302d44b3e870203;p=jalview.git
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index d3467d4..dbf6f38 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,46 +1,53 @@
/*
- * 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 2.9.0b2)
+ * Copyright (C) 2015 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 .
+ * 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 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;
-import jalview.datamodel.*;
-import jalview.util.UrlLink;
-
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;
@@ -73,10 +80,21 @@ 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=$SEQUENCE_ID$");
}
}
@@ -124,7 +142,7 @@ public class IdPanel extends Panel implements MouseListener,
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());
@@ -199,7 +217,7 @@ public class IdPanel extends Panel implements MouseListener,
// 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;
}
@@ -289,7 +307,7 @@ public class IdPanel extends Panel implements MouseListener,
int y = e.getY();
if (av.getWrapAlignment())
{
- y -= 2 * av.charHeight;
+ y -= 2 * av.getCharHeight();
}
int seq = alignPanel.seqPanel.findSeq(e);
@@ -297,7 +315,7 @@ 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();
@@ -305,7 +323,7 @@ public class IdPanel extends Panel implements MouseListener,
{
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)
@@ -378,7 +396,7 @@ public class IdPanel extends Panel implements MouseListener,
for (int i = start; i <= end; i++)
{
av.getSelectionGroup().addSequence(
- av.getAlignment().getSequenceAt(i), i==end);
+ av.getAlignment().getSequenceAt(i), i == end);
}
}
@@ -477,5 +495,4 @@ public class IdPanel extends Panel implements MouseListener,
}
}
}
-
}