X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=81daef79b7122b9b1a00e0f8b9b1bb830cff41fd;hb=4377073e4bb83612169bf0565e1561b872b069e6;hp=54785ef0e4bbc42237350d9ef5367ecbe4e1147b;hpb=4932359fd4e14cbe82294b76d66f693cc8d3ffa8;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 54785ef..81daef7 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,189 +1,332 @@
+/*
+ * 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.gui;
 
 import jalview.datamodel.*;
+
 import jalview.schemes.*;
+
 import java.awt.*;
-import java.util.*;
 
-public class SequenceRenderer implements RendererI
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceRenderer
 {
-  AlignViewport av;
-  FontMetrics fm;
-  boolean renderGaps = true;
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup [] allGroups = null;
-  Color resBoxColour;
-  Graphics graphics;
+    AlignViewport av;
+    FontMetrics fm;
+    boolean renderGaps = true;
+    SequenceGroup currentSequenceGroup = null;
+    SequenceGroup[] allGroups = null;
+    Color resBoxColour;
+    Graphics graphics;
+
+    /**
+     * Creates a new SequenceRenderer object.
+     *
+     * @param av DOCUMENT ME!
+     */
+    public SequenceRenderer(AlignViewport av)
+    {
+        this.av = av;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void renderGaps(boolean b)
+    {
+        renderGaps = b;
+    }
 
-  public SequenceRenderer(AlignViewport av)
-  {
-    this.av = av;
-  }
+    /**
+     * 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)
+    {
+        getBoxColour(cs, seq, i);
+
+        return resBoxColour;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cs DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     * @param i DOCUMENT ME!
+     */
+    void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+    {
+        if (cs != null)
+        {
+            resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
+        }
+        else
+        {
+            resBoxColour = Color.white;
+        }
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     * @param sg DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     * @param x1 DOCUMENT ME!
+     * @param y1 DOCUMENT ME!
+     * @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)
+    {
+        allGroups = sg;
 
-  public void renderGaps(boolean b)
-  {
-    renderGaps = b;
-  }
+        graphics = g;
 
-  public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
-  {
-    getBoxColour(cs, seq, i);
-    return resBoxColour;
-  }
+        drawBoxes(seq, start, end, x1, y1, (int) width, height);
 
-  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
-  {
-   if (cs != null)
-       resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
-   else
-       resBoxColour = Color.white;
-  }
+        fm = g.getFontMetrics();
+        drawText(seq, start, end, x1, y1, (int) width, height);
+    }
 
-  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)
-  {
-    allGroups = sg;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     * @param x1 DOCUMENT ME!
+     * @param y1 DOCUMENT ME!
+     * @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)
+    {
+        int i = start;
+        int length = seq.getLength();
 
-    graphics = g;
+        int curStart = -1;
+        int curWidth = width;
 
-    drawBoxes(seq, start, end, x1, y1, (int) width, height);
+        Color tempColour = null;
 
-    fm = g.getFontMetrics();
-    drawText(seq,start,end,x1,y1,(int)width,height);
+        while (i <= end)
+        {
+          resBoxColour = Color.white;
 
-  }
+          if (i < length)
+          {
+            if (inCurrentSequenceGroup(i))
+            {
+              if (currentSequenceGroup.getDisplayBoxes())
+              {
+                getBoxColour(currentSequenceGroup.cs, seq, i);
+              }
+            }
+            else if (av.getShowBoxes())
+            {
+              getBoxColour(av.getGlobalColourScheme(), seq, i);
+            }
 
-  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;
+            if (resBoxColour != tempColour)
+            {
+                if (tempColour != null)
+                {
+                    graphics.fillRect(x1 + (width * (curStart - start)), y1,
+                        curWidth, height);
+                }
 
-    Color tempColour = null;
-    while (i <= end && i < length)
-    {
-      if(inCurrentSequenceGroup(i))
-      {
-        if( currentSequenceGroup.getDisplayBoxes())
-             getBoxColour(currentSequenceGroup.cs, 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);
-        graphics.setColor(resBoxColour);
-
-        curStart = i;
-        curWidth = width;
-        tempColour = resBoxColour;
-
-      }
-      else
-        curWidth += width;
-
-      i++;
-    }
+                graphics.setColor(resBoxColour);
 
+                curStart = i;
+                curWidth = width;
+                tempColour = resBoxColour;
+            }
+            else
+            {
+                curWidth += width;
+            }
 
-     graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
-  }
+            i++;
+        }
 
-  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;
-    // Need to find the sequence position here.
+        graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,
+            height);
+    }
 
-    graphics.setColor(Color.black);
-    String sequence  = seq.getSequence();
-    for (int i = start; i <= end; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     * @param x1 DOCUMENT ME!
+     * @param y1 DOCUMENT ME!
+     * @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)
     {
-        if(i<sequence.length())
-          s = sequence.charAt(i);
-        else
-          s = ' ';
+        int pady = height / 5;
+        int charOffset = 0;
+        char s;
 
-        if(!renderGaps && jalview.util.Comparison.isGap(s))
-          continue;
+        // Need to find the sequence position here.
+        String sequence = seq.getSequence();
 
+        if(end+1>=seq.getLength())
+          end = seq.getLength()-1;
 
-        if (inCurrentSequenceGroup(i))
+        for (int i = start; i <= end; i++)
         {
-          if(!currentSequenceGroup.getDisplayText())
-            continue;
+            graphics.setColor(Color.black);
+
+            s = sequence.charAt(i);
 
-            if (currentSequenceGroup.getColourText())
+            if (!renderGaps && jalview.util.Comparison.isGap(s))
             {
-              getBoxColour(currentSequenceGroup.cs, seq, i);
-              graphics.setColor(resBoxColour.darker());
+                continue;
+            }
+
+            if (inCurrentSequenceGroup(i))
+            {
+                if (!currentSequenceGroup.getDisplayText())
+                {
+                    continue;
+                }
+
+                if (currentSequenceGroup.getColourText())
+                {
+                    getBoxColour(currentSequenceGroup.cs, seq, i);
+                    graphics.setColor(resBoxColour.darker());
+                }
             }
-        }
-        else
-        {
-          if(!av.getShowText())
-            continue;
-
-          if(av.getColourText())
-           {
-             getBoxColour(av.getGlobalColourScheme(), seq, i);
-             if(av.getShowBoxes())
-              graphics.setColor(resBoxColour.darker());
             else
-              graphics.setColor(resBoxColour);
-           }
-        }
+            {
+                if (!av.getShowText())
+                {
+                    continue;
+                }
+
+                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);
+            charOffset = (width - fm.charWidth(s)) / 2;
+            graphics.drawString(String.valueOf(s),
+                charOffset + x1 + (width * (i - start)), (y1 + height) - pady);
         }
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param res DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    boolean inCurrentSequenceGroup(int res)
+    {
+        if (allGroups == null)
+        {
+            return false;
+        }
 
-  }
-
-  boolean inCurrentSequenceGroup(int res)
-  {
-    if(allGroups ==null)
-      return false;
-
-    for(int i=0; i<allGroups.length; i++)
-      if(allGroups[i].getStartRes()<=res && allGroups[i].getEndRes()>=res)
-      {
-         currentSequenceGroup = allGroups[i];
-         return true;
-      }
+        for (int i = 0; i < allGroups.length; i++)
+        {
+            if ((allGroups[i].getStartRes() <= res) &&
+                    (allGroups[i].getEndRes() >= res))
+            {
+                currentSequenceGroup = allGroups[i];
 
-    return false;
-  }
+                return true;
+            }
+        }
 
-  public void drawHighlightedText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)
-  {
-    int pady = height/5;
-    int charOffset=0;
-    graphics.setColor(Color.BLACK);
-    graphics.fillRect(x1,y1,width*(end-start+1),height);
-    graphics.setColor(Color.white);
+        return false;
+    }
 
-    char s='~';
-    // Need to find the sequence position here.
-    for (int i = start; i <= end; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     * @param x1 DOCUMENT ME!
+     * @param y1 DOCUMENT ME!
+     * @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)
     {
-       if(i<seq.getLength())
-          s = seq.getSequence().charAt(i);
+        int pady = height / 5;
+        int charOffset = 0;
+        graphics.setColor(Color.BLACK);
+        graphics.fillRect(x1, y1, width * (end - start + 1), height);
+        graphics.setColor(Color.white);
 
-     charOffset =  (width - fm.charWidth(s))/2;
-      graphics.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);
-    }
-  }
+        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);
+            }
 
+            charOffset = (width - fm.charWidth(s)) / 2;
+            graphics.drawString(String.valueOf(s),
+                charOffset + x1 + (width * (i - start)), (y1 + height) - pady);
+        }
+    }
 }