X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=480a50600f573a5e338c1a34a734e11ba5bc50a2;hb=6d50f49d0e32b01c57733c4b6e5ece33aa9664af;hp=c413588cbcfffec4b73667815d73c228183fe3b7;hpb=4377073e4bb83612169bf0565e1561b872b069e6;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index c413588..480a506 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/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
@@ -33,22 +33,44 @@ public class SequenceRenderer
   SequenceGroup[] allGroups = null;
   Color resBoxColour;
   Graphics graphics;
+  boolean forOverview = false;
 
   public SequenceRenderer(AlignViewport av)
   {
     this.av = av;
   }
 
-  public void renderGaps(boolean b)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void prepare(Graphics g, boolean renderGaps)
   {
-    renderGaps = b;
-  }
+      graphics = g;
+      fm = g.getFontMetrics();
+
+      this.renderGaps = renderGaps;
+    }
 
-  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);
+
+    if (inCurrentSequenceGroup(i))
+    {
+      if (currentSequenceGroup.getDisplayBoxes())
+      {
+        getBoxColour(currentSequenceGroup.cs, seq, i);
+      }
+    }
+    else if (av.getShowBoxes())
+    {
+        getBoxColour(av.globalColourScheme, seq, i);
+    }
+
     return resBoxColour;
-  }
+    }
 
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
@@ -56,35 +78,47 @@ 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;
     }
+
   }
 
-  public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
-                           int start, int end, int x1, int y1, int width,
-                           int height)
+  public Color findSequenceColour(SequenceI seq, int i)
   {
-    allGroups = sg;
+    allGroups = av.alignment.findAllGroups(seq);
+    drawBoxes(seq, i,i, 0);
+    return resBoxColour;
+  }
 
-    graphics = g;
+  public void drawSequence(SequenceI seq, SequenceGroup[] sg,
+                           int start, int end,  int y1)
+  {
+    if(seq==null)
+      return;
 
-    drawBoxes(seq, start, end, x1, y1, (int) width, height);
+    allGroups = sg;
 
-    fm = g.getFontMetrics();
-    drawText(seq, start, end, x1, y1, (int) width, height);
+    drawBoxes(seq, start, end,  y1);
 
+    if(av.validCharWidth)
+    {
+      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)
@@ -110,46 +144,53 @@ 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.
+   Font boldFont = null;
+   boolean bold = false;
+   if(av.upperCasebold)
+   {
+     boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
 
-    String sequence = seq.getSequence();
+     graphics.setFont(av.getFont());
+   }
 
+    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;
@@ -189,10 +230,30 @@ public class SequenceRenderer
         }
       }
 
-      charOffset = (width - fm.charWidth(s)) / 2;
+      if (av.upperCasebold)
+      {
+        fm = graphics.getFontMetrics();
+        if ('A' <= s && s <= 'Z')
+        {
+          if(!bold)
+          {
+
+            graphics.setFont(boldFont);
+          }
+          bold = true;
+        }
+        else if(bold)
+        {
+          graphics.setFont(av.font);
+          bold = false;
+        }
+
+      }
+
+      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 );
     }
 
   }
@@ -216,29 +277,52 @@ public class SequenceRenderer
     return false;
   }
 
-  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)
     {
-      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 = (av.charWidth - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s),
+                            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);
+    graphics.setColor(Color.white);
+
+    graphics.setColor(Color.white);
 
-      charOffset = (width - fm.charWidth(s)) / 2;
+    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);
+    }
     }
-  }
 
 }