X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=d3b56bea723690c97915ba89278711467ed02302;hb=4059c82f431d3f98931b290d9a72da2a54a0fc95;hp=a05c6c0120e280c5862c95c106781f7ec3f95323;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index a05c6c0..d3b56be 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
@@ -53,7 +53,7 @@ public class IdCanvas extends JPanel
     {
         setLayout(new BorderLayout());
         this.av = av;
-        PaintRefresher.Register(this, av.alignment);
+        PaintRefresher.Register(this, av.getSequenceSetId());
     }
 
     /**
@@ -65,8 +65,7 @@ public class IdCanvas extends JPanel
      * @param starty DOCUMENT ME!
      * @param ypos DOCUMENT ME!
      */
-    public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
-        int ypos)
+    public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty, int ypos)
     {
         int charHeight = av.charHeight;
 
@@ -96,6 +95,11 @@ public class IdCanvas extends JPanel
 
         gg.drawString( s.getDisplayId(av.getShowJVSuffix()),
                       0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
+
+        if (av.hasHiddenRows && av.showHiddenMarkers)
+          drawMarker(i, starty, ypos);
+
+
     }
 
     /**
@@ -169,6 +173,8 @@ public class IdCanvas extends JPanel
             return;
         }
 
+        int oldHeight = imgHeight;
+
         imgHeight = getHeight();
         imgHeight -= (imgHeight % av.charHeight);
 
@@ -177,15 +183,17 @@ public class IdCanvas extends JPanel
             return;
         }
 
-        image = new BufferedImage(getWidth(), imgHeight,
-                BufferedImage.TYPE_INT_RGB);
-        gg = (Graphics2D) image.getGraphics();
+        if(oldHeight!=imgHeight || image.getWidth(this)!=getWidth())
+        {
+          image = new BufferedImage(getWidth(), imgHeight,
+                                    BufferedImage.TYPE_INT_RGB);
+        }
 
+        gg = (Graphics2D) image.getGraphics();
         //Fill in the background
         gg.setColor(Color.white);
         gg.fillRect(0, 0, getWidth(), imgHeight);
 
-
         drawIds(av.getStartSeq(), av.endSeq);
 
         g.drawImage(image, 0, 0, this);
@@ -249,7 +257,7 @@ public class IdCanvas extends JPanel
               {
                 if (av.hasHiddenRows)
                 {
-                  setHiddenFont(i, starty);
+                  setHiddenFont(i);
                 }
                 else
                   gg.setFont(italic);
@@ -264,16 +272,20 @@ public class IdCanvas extends JPanel
                   labels.drawComponent(gg, getWidth());
                   gg.translate(0, -ypos-(alheight * av.charHeight));
                 }
+
+
             }
         }
         else
         {
+          //Now draw the id strings
+
             //Now draw the id strings
             for (int i = starty; i < endy; i++)
             {
               if (av.hasHiddenRows)
               {
-                setHiddenFont(i, starty);
+                setHiddenFont(i);
               }
 
                 // Selected sequence colours
@@ -308,34 +320,84 @@ public class IdCanvas extends JPanel
                 gg.drawString(string, 0,
                     (((i - starty) * av.charHeight) + av.charHeight) -
                     (av.charHeight / 5));
+
+               if(av.hasHiddenRows && av.showHiddenMarkers)
+                 drawMarker(i, starty, 0);
+
             }
 
         }
     }
 
-    void setHiddenFont(int i, int starty)
+    void drawMarker(int i, int starty, int yoffset)
     {
-      Font italic = new Font(av.getFont().getName(), Font.ITALIC,
-                             av.getFont().getSize());
-      Font bold = new Font(av.getFont().getName(), Font.BOLD,
-                           av.getFont().getSize());
 
-      int tmp, hiddenIndex = starty;
-      tmp = av.adjustForHiddenSeqs(i);
+      SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+      //Use this method here instead of calling hiddenSeq adjust
+      //3 times.
+      int hSize = hseqs.length;
 
-      if (av.adjustForHiddenSeqs(i - 1) == tmp - 1)
-      {
-        hiddenIndex = tmp;
-      }
+      int hiddenIndex = i;
+      int lastIndex = i - 1;
+      int nextIndex = i + 1;
 
-      if (hiddenIndex != tmp)
+      for(int j=0; j<hSize; j++)
       {
-        hiddenIndex = tmp;
+        if (hseqs[j] != null)
+        {
+          if(j-1<hiddenIndex)
+            hiddenIndex++;
+          if(j-1<lastIndex)
+            lastIndex++;
+          if(j-1<nextIndex)
+            nextIndex++;
+        }
       }
 
-      hiddenIndex++;
+      boolean below = (hiddenIndex > lastIndex + 1);
+      boolean above = (nextIndex > hiddenIndex+1);
+
+
+        gg.setColor(Color.blue);
+        if(below)
+        {
+          gg.fillPolygon(new int[]
+                         {getWidth()- av.charHeight,
+                         getWidth()- av.charHeight,
+                         getWidth()},
+                         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[]
+                        {getWidth()- av.charHeight,
+                        getWidth()- av.charHeight,
+                        getWidth() },
+                        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)
+    {
+      Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+                             av.getFont().getSize());
+      Font bold = new Font(av.getFont().getName(), Font.BOLD,
+                           av.getFont().getSize());
+
 
-      if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)
+      if (av.alignment.getSequenceAt(i)!=null
+          && av.alignment.getSequenceAt(i).getHiddenSequences() != null)
         gg.setFont(bold);
       else
         gg.setFont(italic);