X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=c68e85c9636221067ffd39bba43cda20a809991e;hb=f6235770cfcf11c4970e9dbe96ca293966611f24;hp=ea857cbcda7c7b6bb4662218ca5ab5ae09836804;hpb=6d6d6bc08bca95676a8175c634c03c163fb88684;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index ea857cb..c68e85c 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,8 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+
 package jalview.appletgui;
 
+import java.awt.*;
+
 import jalview.datamodel.*;
 import jalview.schemes.*;
-import java.awt.*;
 
 public class SequenceRenderer
 {
@@ -10,7 +30,7 @@ public class SequenceRenderer
   FontMetrics fm;
   boolean renderGaps = true;
   SequenceGroup currentSequenceGroup = null;
-  SequenceGroup [] allGroups = null;
+  SequenceGroup[] allGroups = null;
   Color resBoxColour;
   Graphics graphics;
 
@@ -19,27 +39,53 @@ public class SequenceRenderer
     this.av = av;
   }
 
-
   public void renderGaps(boolean b)
   {
     renderGaps = b;
   }
 
-  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)
   {
-   if (cs != null)
-       resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
-   else
-       resBoxColour = Color.white;
+    if (cs != null)
+    {
+      resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
+    }
+    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);
+    return resBoxColour;
   }
 
-  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)
+  public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
+                           int start, int end, int x1, int y1, int width,
+                           int height)
   {
     allGroups = sg;
 
@@ -48,37 +94,46 @@ public class SequenceRenderer
     drawBoxes(seq, start, end, x1, y1, (int) width, height);
 
     fm = g.getFontMetrics();
-    drawText(seq,start,end,x1,y1,(int)width,height);
+    drawText(seq, start, end, x1, y1, (int) width, height);
 
   }
 
-  public void drawBoxes(SequenceI seq,int start, int end, int x1, int y1, int width, int height) {
-    int i      = start;
+  public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
+                        int width, int height)
+  {
+    int i = start;
     int length = seq.getLength();
 
     int curStart = -1;
     int curWidth = width;
 
     Color tempColour = null;
-    while (i <= end && i < length)
+    while (i <= end)
     {
-      if(inCurrentSequenceGroup(i))
+      resBoxColour = Color.white;
+      if(i < length)
       {
-        if( currentSequenceGroup.getDisplayBoxes())
-             getBoxColour(currentSequenceGroup.cs, seq, i);
-        else
-             resBoxColour = Color.white;
+        if (inCurrentSequenceGroup(i))
+        {
+          if (currentSequenceGroup.getDisplayBoxes())
+          {
+            getBoxColour(currentSequenceGroup.cs, seq, i);
+          }
+        }
+        else if (av.getShowBoxes())
+        {
+          getBoxColour(av.getGlobalColourScheme(), seq, i);
+        }
       }
-      else if(av.getShowBoxes())
-            getBoxColour(av.getGlobalColourScheme(), seq, i);
-      else
-        resBoxColour = Color.white;
 
 
       if (resBoxColour != tempColour)
       {
-        if(tempColour!=null)
-          graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
+        if (tempColour != null)
+        {
+          graphics.fillRect(x1 + width * (curStart - start), y1, curWidth,
+                            height);
+        }
         graphics.setColor(resBoxColour);
 
         curStart = i;
@@ -87,105 +142,124 @@ public class SequenceRenderer
 
       }
       else
+      {
         curWidth += width;
+      }
 
       i++;
     }
 
-
-     graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
+    graphics.fillRect(x1 + width * (curStart - start), y1, curWidth, height);
   }
 
-  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 x1, int y1,
+                       int width, int height)
   {
-    int pady = height/5;
-    int charOffset=0;
-    char s;
+    int pady = height / 5;
+    int charOffset = 0;
+    char s=' ';
     // Need to find the sequence position here.
 
-    String sequence  = seq.getSequence();
+    String sequence = seq.getSequence();
+
+    if(end+1>=seq.getLength())
+          end = seq.getLength()-1;
+
     for (int i = start; i <= end; i++)
     {
-        if(i<sequence.length())
-          s = sequence.charAt(i);
-        else
-          s = ' ';
+      graphics.setColor(Color.black);
 
-        if(!renderGaps && jalview.util.Comparison.isGap(s))
-          continue;
+      s = sequence.charAt(i);
 
+      if (!renderGaps && jalview.util.Comparison.isGap(s))
+      {
+        continue;
+      }
 
-        if (inCurrentSequenceGroup(i))
+      if (inCurrentSequenceGroup(i))
+      {
+        if (!currentSequenceGroup.getDisplayText())
+        {
+          continue;
+        }
+
+        if (currentSequenceGroup.getColourText())
         {
-          if(!currentSequenceGroup.getDisplayText())
-            continue;
-
-            if (currentSequenceGroup.getColourText())
-            {
-              getBoxColour(currentSequenceGroup.cs, seq, i);
-              graphics.setColor(resBoxColour.darker());
-            }
+          getBoxColour(currentSequenceGroup.cs, seq, i);
+          graphics.setColor(resBoxColour.darker());
         }
-        else
+      }
+      else
+      {
+        if (!av.getShowText())
         {
-          if(!av.getShowText())
-            continue;
-
-          if(av.getColourText())
-           {
-             getBoxColour(av.getGlobalColourScheme(), seq, i);
-             if(av.getShowBoxes())
-              graphics.setColor(resBoxColour.darker());
-            else
-              graphics.setColor(resBoxColour);
-           }
-           else
-             graphics.setColor(Color.black);
+          continue;
         }
 
-          charOffset =  (width - fm.charWidth(s))/2;
-          graphics.drawString(String.valueOf(s),
-                              charOffset + x1 + width * (i - start),
-                              y1 + height - pady);
+        if (av.getColourText())
+        {
+          getBoxColour(av.getGlobalColourScheme(), seq, i);
+          if (av.getShowBoxes())
+          {
+            graphics.setColor(resBoxColour.darker());
+          }
+          else
+          {
+            graphics.setColor(resBoxColour);
+          }
         }
+      }
 
+      charOffset = (width - fm.charWidth(s)) / 2;
+      graphics.drawString(String.valueOf(s),
+                          charOffset + x1 + width * (i - start),
+                          y1 + height - pady);
+    }
 
   }
 
   boolean inCurrentSequenceGroup(int res)
   {
-    if(allGroups ==null)
+    if (allGroups == null)
+    {
       return false;
+    }
 
-    for(int i=0; i<allGroups.length; i++)
-      if(allGroups[i].getStartRes()<=res && allGroups[i].getEndRes()>=res)
+    for (int i = 0; i < allGroups.length; i++)
+    {
+      if (allGroups[i].getStartRes() <= res && allGroups[i].getEndRes() >= res)
       {
-         currentSequenceGroup = allGroups[i];
-         return true;
+        currentSequenceGroup = allGroups[i];
+        return true;
       }
+    }
 
     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 width, int height)
   {
-    int pady = height/5;
-    int charOffset=0;
+    int pady = height / 5;
+    int charOffset = 0;
     graphics.setColor(Color.black);
-    graphics.fillRect(x1,y1,width*(end-start+1),height);
+    graphics.fillRect(x1, y1, width * (end - start + 1), height);
     graphics.setColor(Color.white);
 
-    char s='~';
+    char s = '~';
     // Need to find the sequence position here.
     for (int i = start; i <= end; i++)
     {
-       if(i<seq.getLength())
-          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;
+      graphics.drawString(String.valueOf(s),
+                          charOffset + x1 + width * (i - start),
+                          y1 + height - pady);
     }
   }
 
-
 }