X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=7981634355f84715fae6cd55cf38188c3ffb3108;hb=70c81d16f9b2bbcfcfb1479954c1caebff8e08cc;hp=3153301f52fef85bff43842f7b26535eb6cd2a77;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 3153301..7981634 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,25 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * 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.*;
@@ -58,6 +61,7 @@ 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++)
@@ -72,11 +76,21 @@ 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=$SEQUENCE_ID$");
     }
   }
 
@@ -87,33 +101,66 @@ 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<sf.length;sl++)
+    if (sequence != null)
     {
-      if (sf[sl].begin==sf[sl].end && sf[sl].begin==0)
+      if (sequence.getDescription() != null)
       {
-        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"); }
+        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)
+        {
+          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)
+    if (tooltiptext.length() == 0)
     {
       // nothing to display - so clear tooltip if one is visible
       if (tooltip != null)
@@ -134,7 +181,7 @@ public class IdPanel extends Panel implements MouseListener,
       tooltip.setTip(sequence.getDisplayId(true) + "\n"
               + tooltiptext.toString());
     }
-    tooltiptext=null;
+    tooltiptext = null;
   }
 
   public void mouseDragged(MouseEvent e)
@@ -165,7 +212,12 @@ 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;
@@ -235,7 +287,7 @@ 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);
     }
@@ -258,29 +310,30 @@ 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();l<lSize; l++)
+      for (int l = 0, lSize = links.size(); l < lSize; l++)
       {
         nlinks.addElement(links.elementAt(l));
       }
-      SequenceFeature sf[] = sq.getSequenceFeatures();
-      for (int sl=0;sf!=null && sl<sf.length;sl++)
+      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)
+        if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
         {
-          if (sf[sl].links!=null && sf[sl].links.size()>0)
+          if (sf[sl].links != null && sf[sl].links.size() > 0)
           {
-            for (int l=0, lSize=sf[sl].links.size(); l<lSize; l++)
-            { 
+            for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
+            {
               nlinks.addElement(sf[sl].links.elementAt(l));
             }
           }
         }
       }
-      
+
       APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
       this.add(popup);
       popup.show(this, e.getX(), e.getY());
@@ -293,7 +346,7 @@ 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)
@@ -312,7 +365,7 @@ 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)
@@ -332,11 +385,14 @@ 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);
     }
 
   }
@@ -355,18 +411,20 @@ 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<SequenceI> 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 +469,7 @@ 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);
           }