X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=0e4312a65654d8b3da25235002743ee329c0ae1b;hb=9807ea8cc4e867378c52d51b832168d4bc611d29;hp=8e8b066e40c201afb9228d7c64ff7846f0872b66;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 8e8b066..0e4312a 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -24,7 +24,6 @@ import jalview.schemes.*;
 
 import java.awt.*;
 
-
 /**
  * DOCUMENT ME!
  *
@@ -40,6 +39,8 @@ public class SequenceRenderer
     SequenceGroup[] allGroups = null;
     Color resBoxColour;
     Graphics graphics;
+    boolean monospacedFont;
+    boolean forOverview = false;
 
     /**
      * Creates a new SequenceRenderer object.
@@ -61,22 +62,27 @@ public class SequenceRenderer
         renderGaps = b;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param cs DOCUMENT ME!
-     * @param seq DOCUMENT ME!
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+
+    public Color getResidueBoxColour(SequenceI seq, int i)
     {
-        getBoxColour(cs, seq, i);
+      allGroups = av.alignment.findAllGroups(seq);
 
-        return resBoxColour;
+      if (inCurrentSequenceGroup(i))
+      {
+        if (currentSequenceGroup.getDisplayBoxes())
+        {
+          getBoxColour(currentSequenceGroup.cs, seq, i);
+        }
+      }
+      else if (av.getShowBoxes())
+      {
+          getBoxColour(av.globalColourScheme, seq, i);
+      }
+
+      return resBoxColour;
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -90,9 +96,13 @@ 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;
+          resBoxColour = Color.white;
         }
     }
 
@@ -110,16 +120,19 @@ public class SequenceRenderer
      * @param height DOCUMENT ME!
      */
     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);
+        drawBoxes(seq, start, end, y1);
 
         fm = g.getFontMetrics();
-        drawText(seq, start, end, x1, y1, (int) width, height);
+
+        monospacedFont = fm.getStringBounds("M",g).getWidth()==fm.getStringBounds("|",g).getWidth();
+
+        drawText(seq, start, end, y1);
     }
 
     /**
@@ -133,61 +146,61 @@ public class SequenceRenderer
      * @param width DOCUMENT ME!
      * @param height DOCUMENT ME!
      */
-    public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
-        int width, int height)
+    public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)
     {
-        int i = start;
-        int length = seq.getLength();
+      int i = start;
+      int length = seq.getLength();
 
-        int curStart = -1;
-        int curWidth = width;
+      int curStart = -1;
+      int curWidth = av.charWidth;
 
-        Color tempColour = null;
+      Color tempColour = null;
 
-        while (i <= end)
-        {
-          resBoxColour = Color.white;
+      while (i <= end)
+      {
+        resBoxColour = Color.white;
 
-          if (i < length)
+        if (i < length)
+        {
+          if (inCurrentSequenceGroup(i))
           {
-            if (inCurrentSequenceGroup(i))
+            if (currentSequenceGroup.getDisplayBoxes())
             {
-              if (currentSequenceGroup.getDisplayBoxes())
-              {
-                getBoxColour(currentSequenceGroup.cs, seq, i);
-              }
+              getBoxColour(currentSequenceGroup.cs, seq, i);
             }
-            else if (av.getShowBoxes())
-            {
-              getBoxColour(av.getGlobalColourScheme(), seq, i);
-            }
-
+          }
+          else if (av.getShowBoxes())
+          {
+            getBoxColour(av.globalColourScheme, seq, i);
           }
 
-            if (resBoxColour != tempColour)
-            {
-                if (tempColour != null)
-                {
-                    graphics.fillRect(x1 + (width * (curStart - start)), y1,
-                        curWidth, height);
-                }
+        }
 
-                graphics.setColor(resBoxColour);
+          if (resBoxColour != tempColour)
+          {
+              if (tempColour != null)
+              {
+                  graphics.fillRect( av.charWidth * (curStart - start), y1,
+                      curWidth, av.charHeight);
+              }
 
-                curStart = i;
-                curWidth = width;
-                tempColour = resBoxColour;
-            }
-            else
-            {
-                curWidth += width;
-            }
+              graphics.setColor(resBoxColour);
 
-            i++;
-        }
+              curStart = i;
+              curWidth = av.charWidth;
+              tempColour = resBoxColour;
+          }
+          else
+          {
+              curWidth += av.charWidth;
+          }
+
+          i++;
+      }
+
+      graphics.fillRect( av.charWidth * (curStart - start), y1, curWidth,
+          av.charHeight);
 
-        graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,
-            height);
     }
 
     /**
@@ -201,76 +214,76 @@ public class SequenceRenderer
      * @param width DOCUMENT ME!
      * @param height DOCUMENT ME!
      */
-    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;
+      y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+      int charOffset = 0;
+      char s;
 
-        float fwidth = width + ((float)av.charWidth/(float)width)/width;
+        if(end+1>=seq.getLength())
+          end = seq.getLength()-1;
+        graphics.setColor(Color.black);
 
 
-        if(av.charWidth != (av.charWidth/width)*width)
+        if(monospacedFont && av.showText && allGroups.length==0 && !av.getColourText())
         {
-
+          graphics.drawString(seq.getSequence(start, end + 1), 0, y1);
         }
-
-        // Need to find the sequence position here.
-        String sequence = seq.getSequence();
-
-        if(end+1>=seq.getLength())
-          end = seq.getLength()-1;
-
-        for (int i = start; i <= end; i++)
+        else
         {
+          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;
+              continue;
             }
 
             if (inCurrentSequenceGroup(i))
             {
-                if (!currentSequenceGroup.getDisplayText())
-                {
-                    continue;
-                }
+              if (!currentSequenceGroup.getDisplayText())
+              {
+                continue;
+              }
 
-                if (currentSequenceGroup.getColourText())
-                {
-                    getBoxColour(currentSequenceGroup.cs, seq, i);
-                    graphics.setColor(resBoxColour.darker());
-                }
+              if (currentSequenceGroup.getColourText())
+              {
+                getBoxColour(currentSequenceGroup.cs, seq, i);
+                graphics.setColor(resBoxColour.darker());
+              }
             }
             else
             {
-                if (!av.getShowText())
+              if (!av.getShowText())
+              {
+                continue;
+              }
+
+              if (av.getColourText())
+              {
+                getBoxColour(av.globalColourScheme, seq, i);
+
+                if (av.getShowBoxes())
                 {
-                    continue;
+                  graphics.setColor(resBoxColour.darker());
                 }
-
-                if (av.getColourText())
+                else
                 {
-                    getBoxColour(av.getGlobalColourScheme(), seq, i);
-
-                    if (av.getShowBoxes())
-                    {
-                        graphics.setColor(resBoxColour.darker());
-                    }
-                    else
-                    {
-                        graphics.setColor(resBoxColour);
-                    }
+                  graphics.setColor(resBoxColour);
                 }
+              }
             }
 
-            charOffset = (width - fm.charWidth(s)) / 2;
+            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+
+          //  System.out.print(s);
             graphics.drawString(String.valueOf(s),
-                charOffset + x1 + (int)(fwidth * (i - start)), (y1 + height) - pady);
+                                charOffset + av.charWidth * (i - start),
+                                y1);
+
+          }
+        //  System.out.println("\n");
         }
     }