X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=9dbb05ccb75a749e2211e02bc39b8f848b3067ad;hb=cd71fb9ef1a21678ad648ba13564b658b53ab834;hp=c68e85c9636221067ffd39bba43cda20a809991e;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index c68e85c..9dbb05c 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -33,6 +33,7 @@ public class SequenceRenderer
   SequenceGroup[] allGroups = null;
   Color resBoxColour;
   Graphics graphics;
+  boolean forOverview = false;
 
   public SequenceRenderer(AlignViewport av)
   {
@@ -69,43 +70,47 @@ public class SequenceRenderer
     {
       resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
     }
+    else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+    {
+        resBoxColour = Color.lightGray;
+    }
     else
     {
       resBoxColour = Color.white;
     }
+
   }
 
-  Image offscreen;
   public Color findSequenceColour(SequenceI seq, int i)
   {
     allGroups = av.alignment.findAllGroups(seq);
-    drawBoxes(seq, i,i, 0, 0, 1,1);
+    drawBoxes(seq, i,i, 0);
     return resBoxColour;
   }
 
   public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
-                           int start, int end, int x1, int y1, int width,
-                           int height)
+                           int start, int end,  int y1)
   {
     allGroups = sg;
 
     graphics = g;
 
-    drawBoxes(seq, start, end, x1, y1, (int) width, height);
-
-    fm = g.getFontMetrics();
-    drawText(seq, start, end, x1, y1, (int) width, height);
+    drawBoxes(seq, start, end,  y1);
 
+    if(av.validCharWidth)
+    {
+      fm = g.getFontMetrics();
+      drawText(seq, start, end, y1);
+    }
   }
 
-  public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
-                        int width, int height)
+  public void drawBoxes(SequenceI seq, int start, int end,  int y1)
   {
     int i = start;
     int length = seq.getLength();
 
     int curStart = -1;
-    int curWidth = width;
+    int curWidth = av.charWidth;
 
     Color tempColour = null;
     while (i <= end)
@@ -131,46 +136,45 @@ public class SequenceRenderer
       {
         if (tempColour != null)
         {
-          graphics.fillRect(x1 + width * (curStart - start), y1, curWidth,
-                            height);
+          graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
+                            av.charHeight);
         }
         graphics.setColor(resBoxColour);
 
         curStart = i;
-        curWidth = width;
+        curWidth = av.charWidth;
         tempColour = resBoxColour;
 
       }
       else
       {
-        curWidth += width;
+        curWidth += av.charWidth;
       }
 
       i++;
     }
 
-    graphics.fillRect(x1 + width * (curStart - start), y1, curWidth, height);
+    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth, av.charHeight);
   }
 
-  public void drawText(SequenceI seq, int start, int end, int x1, int y1,
-                       int width, int height)
+  public void drawText(SequenceI seq, int start, int end, int y1)
   {
-    int pady = height / 5;
-    int charOffset = 0;
-    char s=' ';
-    // Need to find the sequence position here.
 
-    String sequence = seq.getSequence();
+    y1 += av.charHeight - av.charHeight / 5;  // height/5 replaces pady
+
+    int charOffset = 0;
 
+    // Need to find the sequence position here.
     if(end+1>=seq.getLength())
           end = seq.getLength()-1;
 
+    char s = ' ';
+
     for (int i = start; i <= end; i++)
     {
       graphics.setColor(Color.black);
 
-      s = sequence.charAt(i);
-
+      s = seq.getCharAt(i);
       if (!renderGaps && jalview.util.Comparison.isGap(s))
       {
         continue;
@@ -210,10 +214,10 @@ public class SequenceRenderer
         }
       }
 
-      charOffset = (width - fm.charWidth(s)) / 2;
+      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
       graphics.drawString(String.valueOf(s),
-                          charOffset + x1 + width * (i - start),
-                          y1 + height - pady);
+                         charOffset + av.charWidth * (i - start),
+                        y1 );
     }
 
   }
@@ -248,18 +252,42 @@ public class SequenceRenderer
 
     char s = '~';
     // Need to find the sequence position here.
-    for (int i = start; i <= end; i++)
+    if(av.validCharWidth)
     {
-      if (i < seq.getLength())
+      for (int i = start; i <= end; i++)
       {
-        s = seq.getSequence().charAt(i);
+        if (i < seq.getLength())
+        {
+          s = seq.getSequence().charAt(i);
+        }
+
+        charOffset = (width - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s),
+                            charOffset + x1 + width * (i - start),
+                            y1 + height - pady);
       }
+    }
+  }
 
-      charOffset = (width - fm.charWidth(s)) / 2;
+  public void drawCursor(SequenceI seq, int res, int x1, int y1)
+  {
+    int pady = av.charHeight / 5;
+    int charOffset = 0;
+    graphics.setColor(Color.black);
+    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+    graphics.setColor(Color.white);
+
+    graphics.setColor(Color.white);
+
+    char s = seq.getCharAt(res);
+    if (av.validCharWidth)
+    {
+
+      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
       graphics.drawString(String.valueOf(s),
-                          charOffset + x1 + width * (i - start),
-                          y1 + height - pady);
+                          charOffset + x1,
+                          (y1 + av.charHeight) - pady);
+    }
     }
-  }
 
 }