X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=6c7fb37cd615f5a85e52eab5f2be52076f20c43d;hb=454688abf087254742210ace4c82bedc918e7590;hp=57cd0fc93c2b0aaa5188066818cf668517c49d69;hpb=9c5d69ef1e102b1eac18ec13c362522f40c9000d;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 57cd0fc..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
@@ -39,6 +39,8 @@ public class SequenceRenderer
     SequenceGroup[] allGroups = null;
     Color resBoxColour;
     Graphics graphics;
+    boolean monospacedFont;
+    boolean forOverview = false;
 
     /**
      * Creates a new SequenceRenderer object.
@@ -55,9 +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;
     }
 
 
@@ -92,11 +104,15 @@ 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)))
+        {
+            resBoxColour = Color.lightGray;
         }
         else
         {
-            resBoxColour = Color.white;
+          resBoxColour = Color.white;
         }
     }
 
@@ -113,17 +129,15 @@ public class SequenceRenderer
      * @param width DOCUMENT ME!
      * @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)
+    public void drawSequence(SequenceI seq, SequenceGroup[] sg,
+        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);
+        if (av.validCharWidth)
+          drawText(seq, start, end, y1);
     }
 
     /**
@@ -137,14 +151,13 @@ public class SequenceRenderer
      * @param width DOCUMENT ME!
      * @param height DOCUMENT ME!
      */
-    public synchronized 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 curStart = -1;
-      int curWidth = width;
+      int curWidth = av.charWidth;
 
       Color tempColour = null;
 
@@ -172,26 +185,26 @@ 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);
 
     }
 
@@ -206,70 +219,115 @@ 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;
-
-
-        // Need to find the sequence position here.
-        String sequence = seq.getSequence();
+      y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+      int charOffset = 0;
+      char s;
 
         if(end+1>=seq.getLength())
           end = seq.getLength()-1;
+        graphics.setColor(av.textColour);
 
-        for (int i = start; i <= end; i++)
-        {
-            graphics.setColor(Color.black);
-
-            s = sequence.charAt(i);
 
+        if(monospacedFont
+           && av.showText
+           && allGroups.length==0
+           && !av.getColourText()
+           && av.thresholdTextColour==0)
+        {
+          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(av.textColour);
+            getboxColour = false;
+            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.thresholdTextColour > 0
+                  || currentSequenceGroup.getColourText())
+              {
+                getboxColour = true;
+                getBoxColour(currentSequenceGroup.cs, seq, i);
 
                 if (currentSequenceGroup.getColourText())
+                  graphics.setColor(resBoxColour.darker());
+
+                if (currentSequenceGroup.thresholdTextColour > 0)
                 {
-                    getBoxColour(currentSequenceGroup.cs, seq, i);
-                    graphics.setColor(resBoxColour.darker());
+                  if (resBoxColour.getRed() +
+                      resBoxColour.getBlue() +
+                      resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour)
+                    graphics.setColor(currentSequenceGroup.textColour2);
                 }
+              }
+              else
+                  graphics.setColor(currentSequenceGroup.textColour);
+
             }
             else
             {
-                if (!av.getShowText())
+              if (!av.getShowText())
+              {
+                continue;
+              }
+
+              if (av.getColourText())
+              {
+                getboxColour = true;
+                getBoxColour(av.globalColourScheme, seq, i);
+
+                if (av.getShowBoxes())
                 {
-                    continue;
+                  graphics.setColor(resBoxColour.darker());
                 }
-
-                if (av.getColourText())
+                else
                 {
-                    getBoxColour(av.globalColourScheme, seq, i);
-
-                    if (av.getShowBoxes())
-                    {
-                        graphics.setColor(resBoxColour.darker());
-                    }
-                    else
-                    {
-                        graphics.setColor(resBoxColour);
-                    }
+                  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 = (width - fm.charWidth(s)) / 2;
-            graphics.drawString(String.valueOf(s),
-                charOffset + x1 + (int)(width * (i - start)), (y1 + height) - pady);
 
+
+          charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+          graphics.drawString(String.valueOf(s),
+                              charOffset + av.charWidth * (i - start),
+                              y1);
+
+          }
         }
     }
 
@@ -312,28 +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);
+      }
+
+    }
 }