javatidy

[jalview.git] / src / jalview / appletgui / IdPanel.java

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 43da907..0042856 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,6 +1,6 @@
 /*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -19,6 +19,7 @@ package jalview.appletgui;
 
 import java.awt.*;
 import java.awt.event.*;
+import java.util.List;
 import java.util.Vector;
 
 import jalview.datamodel.*;
@@ -89,61 +90,62 @@ 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
@@ -196,7 +198,12 @@ 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;
@@ -266,7 +273,7 @@ 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);
     }
@@ -290,6 +297,7 @@ 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();
@@ -297,7 +305,7 @@ 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)
@@ -324,7 +332,7 @@ 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)
@@ -363,7 +371,10 @@ 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(
@@ -390,16 +401,16 @@ public class IdPanel extends Panel implements MouseListener,
     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)
@@ -444,7 +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);
           }