X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=ac82e12a36e8925fd8478c825e4e2bfc3c05cf6d;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=dd057a347e4a3839445d9742282026c87d63874e;hpb=da144cfa9b7997a6e8dd04ef10d55bcea3b02c71;p=jalview.git

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index dd057a3..ac82e12 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, 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
@@ -43,7 +43,7 @@ public class IdCanvas
   {
     setLayout(null);
     this.av = av;
-    PaintRefresher.Register(this, av.alignment);
+    PaintRefresher.Register(this, av.getSequenceSetId());
   }
 
   public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
@@ -54,33 +54,34 @@ public class IdCanvas
     if (searchResults != null && searchResults.contains(s))
     {
       gg.setColor(Color.black);
-      gg.fillRect(0, ((i - starty) * charHeight) + ypos,
+      gg.fillRect(0, ( (i - starty) * charHeight) + ypos,
                   getSize().width, charHeight);
       gg.setColor(Color.white);
     }
     else if (av.getSelectionGroup() != null &&
-             av.getSelectionGroup().getSequences(false).contains(s))
+             av.getSelectionGroup().getSequences(null).contains(s))
     {
       gg.setColor(Color.lightGray);
-      gg.fillRect(0, ((i - starty) * charHeight) + ypos,
+      gg.fillRect(0, ( (i - starty) * charHeight) + ypos,
                   getSize().width, charHeight);
       gg.setColor(Color.white);
     }
     else
     {
-      gg.setColor(s.getColor());
-      gg.fillRect(0, ((i - starty) * charHeight) + ypos,
+      gg.setColor(av.getSequenceColour(s));
+      gg.fillRect(0, ( (i - starty) * charHeight) + ypos,
                   getSize().width, charHeight);
       gg.setColor(Color.black);
     }
 
-
-    gg.drawString( s.getDisplayId(av.getShowJVSuffix()), 0,
-                  ((i - starty) * charHeight) + ypos +
+    gg.drawString(s.getDisplayId(av.getShowJVSuffix()), 0,
+                  ( (i - starty) * charHeight) + ypos +
                   charHeight - (charHeight / 5));
 
     if (av.hasHiddenRows && av.showHiddenMarkers)
-          drawMarker(i, starty, ypos);
+    {
+      drawMarker(i, starty, ypos);
+    }
 
   }
 
@@ -186,7 +187,9 @@ public class IdCanvas
       int alheight = av.alignment.getHeight();
 
       if (av.hasHiddenColumns)
+      {
         maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      }
 
       int annotationHeight = 0;
       AnnotationLabels labels = null;
@@ -200,7 +203,9 @@ public class IdCanvas
 
       int hgap = av.charHeight;
       if (av.scaleAboveWrapped)
+      {
         hgap += av.charHeight;
+      }
 
       int cHeight = alheight * av.charHeight
           + hgap
@@ -220,7 +225,9 @@ public class IdCanvas
             setHiddenFont(i);
           }
           else
+          {
             gg.setFont(italic);
+          }
 
           SequenceI s = av.alignment.getSequenceAt(i);
           drawIdString(gg, s, i, 0, ypos);
@@ -240,6 +247,7 @@ public class IdCanvas
       //Now draw the id strings
 
       //Now draw the id strings
+      SequenceI seq;
       for (int i = starty; i < endy; i++)
       {
         if (av.hasHiddenRows)
@@ -247,23 +255,28 @@ public class IdCanvas
           setHiddenFont(i);
         }
 
+        seq = av.alignment.getSequenceAt(i);
+        if (seq == null)
+        {
+          continue;
+        }
+
         // Selected sequence colours
         if ( (searchResults != null) &&
-            searchResults.contains(av.alignment.getSequenceAt(i)))
+            searchResults.contains(seq))
         {
           currentColor = Color.black;
           currentTextColor = Color.white;
         }
         else if ( (av.getSelectionGroup() != null) &&
-                 av.getSelectionGroup().getSequences(false).contains(
-                     av.alignment.getSequenceAt(i)))
+                 av.getSelectionGroup().getSequences(null).contains(seq))
         {
           currentColor = Color.lightGray;
           currentTextColor = Color.black;
         }
         else
         {
-          currentColor = av.alignment.getSequenceAt(i).getColor();
+          currentColor = av.getSequenceColour(seq);
           currentTextColor = Color.black;
         }
 
@@ -274,15 +287,15 @@ public class IdCanvas
 
         gg.setColor(currentTextColor);
 
-        String string = av.alignment.getSequenceAt(i).getDisplayId(av.
-            getShowJVSuffix());
-
-        gg.drawString(string, 0,
+        gg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
+                      0,
                       ( ( (i - starty) * av.charHeight) + av.charHeight) -
                       (av.charHeight / 5));
 
         if (av.hasHiddenRows && av.showHiddenMarkers)
+        {
           drawMarker(i, starty, 0);
+        }
       }
     }
   }
@@ -295,7 +308,7 @@ public class IdCanvas
 
   void drawMarker(int i, int starty, int yoffset)
   {
-    SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+    SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
     //Use this method here instead of calling hiddenSeq adjust
     //3 times.
     int hSize = hseqs.length;
@@ -307,59 +320,64 @@ public class IdCanvas
     boolean below = (hiddenIndex > lastIndex + 1);
     boolean above = (nextIndex > hiddenIndex + 1);
 
-
-
-    for(int j=0; j<hSize; j++)
+    for (int j = 0; j < hSize; j++)
     {
       if (hseqs[j] != null)
       {
-        if(j-1<hiddenIndex)
+        if (j - 1 < hiddenIndex)
+        {
           hiddenIndex++;
-        if(j-1<lastIndex)
+        }
+        if (j - 1 < lastIndex)
+        {
           lastIndex++;
-        if(j-1<nextIndex)
+        }
+        if (j - 1 < nextIndex)
+        {
           nextIndex++;
+        }
       }
-      }
+    }
 
-      gg.setColor(Color.blue);
-      if(below)
-      {
-        gg.fillPolygon(new int[]
-                       {getSize().width- av.charHeight,
-                       getSize().width- av.charHeight,
-                       getSize().width},
-                       new int[]
-                       {
-                       (i - starty) * av.charHeight +yoffset,
-                       (i - starty) * av.charHeight +yoffset+ av.charHeight / 4,
-                       (i - starty) * av.charHeight+yoffset
-        }, 3);
-      }
-      if(above)
-      {
-        gg.fillPolygon(new int[]
-                      {getSize().width- av.charHeight,
-                      getSize().width - av.charHeight,
-                      getSize().width },
-                      new int[]
-                      {
-                      (i - starty+1) * av.charHeight +yoffset,
-                      (i - starty+1) * av.charHeight +yoffset- av.charHeight / 4,
-                      (i - starty+1) * av.charHeight +yoffset
-       }, 3);
+    gg.setColor(Color.blue);
+    if (below)
+    {
+      gg.fillPolygon(new int[]
+                     {getSize().width - av.charHeight,
+                     getSize().width - av.charHeight,
+                     getSize().width},
+                     new int[]
+                     {
+                     (i - starty) * av.charHeight + yoffset,
+                     (i - starty) * av.charHeight + yoffset + av.charHeight / 4,
+                     (i - starty) * av.charHeight + yoffset
+      }, 3);
+    }
+    if (above)
+    {
+      gg.fillPolygon(new int[]
+                     {getSize().width - av.charHeight,
+                     getSize().width - av.charHeight,
+                     getSize().width},
+                     new int[]
+                     {
+                     (i - starty + 1) * av.charHeight + yoffset,
+                     (i - starty + 1) * av.charHeight + yoffset -
+                     av.charHeight / 4,
+                     (i - starty + 1) * av.charHeight + yoffset
+      }, 3);
 
-      }
+    }
   }
 
   void setHiddenFont(int i)
   {
-  /*  System.out.println(i+" "+av.alignment.getHeight());
-    if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)
-      gg.setFont(new Font(av.getFont().getName(), Font.BOLD,
-                          av.getFont().getSize()));
-    else
-      gg.setFont(new Font(av.getFont().getName(), Font.ITALIC,
-                          av.getFont().getSize()));*/
+    /*  System.out.println(i+" "+av.alignment.getHeight());
+      if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)
+        gg.setFont(new Font(av.getFont().getName(), Font.BOLD,
+                            av.getFont().getSize()));
+      else
+        gg.setFont(new Font(av.getFont().getName(), Font.ITALIC,
+                            av.getFont().getSize()));*/
   }
 }