X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=6c7fb37cd615f5a85e52eab5f2be52076f20c43d;hb=77c35fa912621cbadcf5ec74da4c6d45de6322e1;hp=0e4312a65654d8b3da25235002743ee329c0ae1b;hpb=3d1120fca6dd9dc2865ee6cde98760f65c2701da;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 0e4312a..6c7fb37 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.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
@@ -57,9 +57,19 @@ public class SequenceRenderer
      *
      * @param b DOCUMENT ME!
      */
-    public void renderGaps(boolean b)
+    public void prepare(Graphics g, boolean renderGaps)
     {
-        renderGaps = b;
+        graphics = g;
+        fm = g.getFontMetrics();
+
+        // If EPS graphics, stringWidth will be a double, not an int
+        double dwidth = fm.getStringBounds("M", g).getWidth();
+
+        monospacedFont =
+               (dwidth == fm.getStringBounds("|",g).getWidth()
+               && (float)av.charWidth == dwidth);
+
+        this.renderGaps = renderGaps;
     }
 
 
@@ -94,7 +104,7 @@ public class SequenceRenderer
     {
         if (cs != null)
         {
-            resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
+            resBoxColour = cs.findColour(seq.getCharAt(i), i);
         }
         else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
         {
@@ -119,20 +129,15 @@ public class SequenceRenderer
      * @param width DOCUMENT ME!
      * @param height DOCUMENT ME!
      */
-    public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
+    public void drawSequence(SequenceI seq, SequenceGroup[] sg,
         int start, int end, int y1)
     {
         allGroups = sg;
 
-        graphics = g;
-
         drawBoxes(seq, start, end, y1);
 
-        fm = g.getFontMetrics();
-
-        monospacedFont = fm.getStringBounds("M",g).getWidth()==fm.getStringBounds("|",g).getWidth();
-
-        drawText(seq, start, end, y1);
+        if (av.validCharWidth)
+          drawText(seq, start, end, y1);
     }
 
     /**
@@ -222,18 +227,30 @@ public class SequenceRenderer
 
         if(end+1>=seq.getLength())
           end = seq.getLength()-1;
-        graphics.setColor(Color.black);
+        graphics.setColor(av.textColour);
 
 
-        if(monospacedFont && av.showText && allGroups.length==0 && !av.getColourText())
+        if(monospacedFont
+           && av.showText
+           && allGroups.length==0
+           && !av.getColourText()
+           && av.thresholdTextColour==0)
         {
-          graphics.drawString(seq.getSequence(start, end + 1), 0, y1);
+          if (av.renderGaps)
+            graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
+          else
+         {
+           char gap = av.getGapCharacter();
+           graphics.drawString( seq.getSequenceAsString(start, end+1).replace(gap, ' '), 0, y1);
+         }
         }
         else
         {
+          boolean getboxColour = false;
           for (int i = start; i <= end; i++)
           {
-            graphics.setColor(Color.black);
+            graphics.setColor(av.textColour);
+            getboxColour = false;
             s = seq.getCharAt(i);
             if (!renderGaps && jalview.util.Comparison.isGap(s))
             {
@@ -247,11 +264,26 @@ public class SequenceRenderer
                 continue;
               }
 
-              if (currentSequenceGroup.getColourText())
+              if (currentSequenceGroup.thresholdTextColour > 0
+                  || currentSequenceGroup.getColourText())
               {
+                getboxColour = true;
                 getBoxColour(currentSequenceGroup.cs, seq, i);
-                graphics.setColor(resBoxColour.darker());
+
+                if (currentSequenceGroup.getColourText())
+                  graphics.setColor(resBoxColour.darker());
+
+                if (currentSequenceGroup.thresholdTextColour > 0)
+                {
+                  if (resBoxColour.getRed() +
+                      resBoxColour.getBlue() +
+                      resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour)
+                    graphics.setColor(currentSequenceGroup.textColour2);
+                }
               }
+              else
+                  graphics.setColor(currentSequenceGroup.textColour);
+
             }
             else
             {
@@ -262,6 +294,7 @@ public class SequenceRenderer
 
               if (av.getColourText())
               {
+                getboxColour = true;
                 getBoxColour(av.globalColourScheme, seq, i);
 
                 if (av.getShowBoxes())
@@ -273,17 +306,28 @@ public class SequenceRenderer
                   graphics.setColor(resBoxColour);
                 }
               }
+
+              if (av.thresholdTextColour > 0)
+              {
+                if (!getboxColour)
+                  getBoxColour(av.globalColourScheme, seq, i);
+
+                if (resBoxColour.getRed() +
+                    resBoxColour.getBlue() +
+                    resBoxColour.getGreen() < av.thresholdTextColour)
+                  graphics.setColor(av.textColour2);
+              }
+
             }
 
-            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
 
-          //  System.out.print(s);
-            graphics.drawString(String.valueOf(s),
-                                charOffset + av.charWidth * (i - start),
-                                y1);
+
+          charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+          graphics.drawString(String.valueOf(s),
+                              charOffset + av.charWidth * (i - start),
+                              y1);
 
           }
-        //  System.out.println("\n");
         }
     }
 
@@ -326,28 +370,52 @@ public class SequenceRenderer
      * @param width DOCUMENT ME!
      * @param height DOCUMENT ME!
      */
-    public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
-        int y1, int width, int height)
+    public void drawHighlightedText(SequenceI seq, int start, int end, int x1, int y1)
     {
-        int pady = height / 5;
+        int pady = av.charHeight / 5;
         int charOffset = 0;
         graphics.setColor(Color.BLACK);
-        graphics.fillRect(x1, y1, width * (end - start + 1), height);
+        graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
         graphics.setColor(Color.white);
 
         char s = '~';
 
         // Need to find the sequence position here.
-        for (int i = start; i <= end; i++)
+        if(av.validCharWidth)
         {
+          for (int i = start; i <= end; i++)
+          {
             if (i < seq.getLength())
             {
-                s = seq.getSequence().charAt(i);
+              s = seq.getCharAt(i);
             }
 
-            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 + x1 + (av.charWidth * (i - start)),
+                                (y1 + av.charHeight) - pady);
+          }
         }
     }
+
+    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);
+
+      if(av.validCharWidth)
+      {
+        graphics.setColor(Color.white);
+
+        char s = seq.getCharAt(res);
+
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s),
+                            charOffset + x1,
+                            (y1 + av.charHeight) - pady);
+      }
+
+    }
 }