X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=70f67d7656f7aea0b03cb0dadd28142ca51f18ef;hb=d704670a936df11fbaf75abbb6d07493d70993a9;hp=ab6c1aba4ff84585b3dad6aa52c59953edfd57b4;hpb=c77ccc33971183dba9cb66b40886a6b61fe8eaa0;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index ab6c1ab..70f67d7 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) 2007 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
@@ -18,12 +18,11 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
+import java.awt.*;
 
+import jalview.datamodel.*;
 import jalview.schemes.*;
 
-import java.awt.*;
-
 /**
  * DOCUMENT ME!
  *
@@ -32,339 +31,404 @@ import java.awt.*;
  */
 public class SequenceRenderer
 {
-    AlignViewport av;
-    FontMetrics fm;
-    boolean renderGaps = true;
-    SequenceGroup currentSequenceGroup = null;
-    SequenceGroup[] allGroups = null;
-    Color resBoxColour;
-    Graphics graphics;
-    boolean monospacedFont;
-    boolean forOverview = false;
-
-    /**
-     * Creates a new SequenceRenderer object.
-     *
-     * @param av DOCUMENT ME!
-     */
-    public SequenceRenderer(AlignViewport av)
+  AlignViewport av;
+  FontMetrics fm;
+  boolean renderGaps = true;
+  SequenceGroup currentSequenceGroup = null;
+  SequenceGroup[] allGroups = null;
+  Color resBoxColour;
+  Graphics graphics;
+  boolean monospacedFont;
+  boolean forOverview = false;
+
+  /**
+   * Creates a new SequenceRenderer object.
+   *
+   * @param av DOCUMENT ME!
+   */
+  public SequenceRenderer(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void prepare(Graphics g, boolean renderGaps)
+  {
+    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;
+  }
+
+  public Color getResidueBoxColour(SequenceI seq, int i)
+  {
+    allGroups = av.alignment.findAllGroups(seq);
+
+    if (inCurrentSequenceGroup(i))
+    {
+      if (currentSequenceGroup.getDisplayBoxes())
+      {
+        getBoxColour(currentSequenceGroup.cs, seq, i);
+      }
+    }
+    else if (av.getShowBoxes())
     {
-        this.av = av;
+      getBoxColour(av.globalColourScheme, seq, i);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void prepare(Graphics g, boolean renderGaps)
+    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.getCharAt(i), i);
+    }
+    else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+    {
+      resBoxColour = Color.lightGray;
+    }
+    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(SequenceI seq, SequenceGroup[] sg,
+                           int start, int end, int y1)
+  {
+    allGroups = sg;
+
+    drawBoxes(seq, start, end, y1);
+
+    if (av.validCharWidth)
     {
-        graphics = g;
-        fm = g.getFontMetrics();
-        monospacedFont = fm.getStringBounds("M",g).getWidth()==fm.getStringBounds("|",g).getWidth();
-        this.renderGaps = renderGaps;
+      drawText(seq, start, end, y1);
     }
+  }
+
+  /**
+   * 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 synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)
+  {
+    int i = start;
+    int length = seq.getLength();
+
+    int curStart = -1;
+    int curWidth = av.charWidth;
+
+    Color tempColour = null;
+
+    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.globalColourScheme, seq, i);
+        }
 
-    public Color getResidueBoxColour(SequenceI seq, int i)
-    {
-      allGroups = av.alignment.findAllGroups(seq);
+      }
 
-      if (inCurrentSequenceGroup(i))
+      if (resBoxColour != tempColour)
       {
-        if (currentSequenceGroup.getDisplayBoxes())
+        if (tempColour != null)
         {
-          getBoxColour(currentSequenceGroup.cs, seq, i);
+          graphics.fillRect(av.charWidth * (curStart - start), y1,
+                            curWidth, av.charHeight);
         }
+
+        graphics.setColor(resBoxColour);
+
+        curStart = i;
+        curWidth = av.charWidth;
+        tempColour = resBoxColour;
       }
-      else if (av.getShowBoxes())
+      else
       {
-          getBoxColour(av.globalColourScheme, seq, i);
+        curWidth += av.charWidth;
       }
 
-      return resBoxColour;
+      i++;
     }
 
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param cs DOCUMENT ME!
-     * @param seq DOCUMENT ME!
-     * @param i DOCUMENT ME!
-     */
-    void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
+                      av.charHeight);
+
+  }
+
+  /**
+   * 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 y1)
+  {
+    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+    int charOffset = 0;
+    char s;
+
+    if (end + 1 >= seq.getLength())
     {
-        if (cs != null)
-        {
-            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;
-        }
+      end = seq.getLength() - 1;
     }
+    graphics.setColor(av.textColour);
 
-    /**
-     * 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(SequenceI seq, SequenceGroup[] sg,
-        int start, int end, int y1)
+    if (monospacedFont
+        && av.showText
+        && allGroups.length == 0
+        && !av.getColourText()
+        && av.thresholdTextColour == 0)
     {
-        allGroups = sg;
-
-        drawBoxes(seq, start, end, y1);
-
-        drawText(seq, start, end, y1);
+      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);
+      }
     }
-
-    /**
-     * 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 synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)
+    else
     {
-      int i = start;
-      int length = seq.getLength();
-
-      int curStart = -1;
-      int curWidth = av.charWidth;
-
-      Color tempColour = null;
-
-      while (i <= end)
+      boolean getboxColour = false;
+      for (int i = start; i <= end; i++)
       {
-        resBoxColour = Color.white;
+        graphics.setColor(av.textColour);
+        getboxColour = false;
+        s = seq.getCharAt(i);
+        if (!renderGaps && jalview.util.Comparison.isGap(s))
+        {
+          continue;
+        }
 
-        if (i < length)
+        if (inCurrentSequenceGroup(i))
         {
-          if (inCurrentSequenceGroup(i))
+          if (!currentSequenceGroup.getDisplayText())
           {
-            if (currentSequenceGroup.getDisplayBoxes())
-            {
-              getBoxColour(currentSequenceGroup.cs, seq, i);
-            }
+            continue;
           }
-          else if (av.getShowBoxes())
+
+          if (currentSequenceGroup.thresholdTextColour > 0
+              || currentSequenceGroup.getColourText())
           {
-            getBoxColour(av.globalColourScheme, seq, i);
-          }
+            getboxColour = true;
+            getBoxColour(currentSequenceGroup.cs, seq, i);
 
-        }
+            if (currentSequenceGroup.getColourText())
+            {
+              graphics.setColor(resBoxColour.darker());
+            }
 
-          if (resBoxColour != tempColour)
-          {
-              if (tempColour != null)
+            if (currentSequenceGroup.thresholdTextColour > 0)
+            {
+              if (resBoxColour.getRed() +
+                  resBoxColour.getBlue() +
+                  resBoxColour.getGreen() <
+                  currentSequenceGroup.thresholdTextColour)
               {
-                  graphics.fillRect( av.charWidth * (curStart - start), y1,
-                      curWidth, av.charHeight);
+                graphics.setColor(currentSequenceGroup.textColour2);
               }
-
-              graphics.setColor(resBoxColour);
-
-              curStart = i;
-              curWidth = av.charWidth;
-              tempColour = resBoxColour;
+            }
           }
           else
           {
-              curWidth += av.charWidth;
+            graphics.setColor(currentSequenceGroup.textColour);
           }
 
-          i++;
-      }
-
-      graphics.fillRect( av.charWidth * (curStart - start), y1, curWidth,
-          av.charHeight);
-
-    }
-
-    /**
-     * 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 y1)
-    {
-      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(Color.black);
-
-
-        if(monospacedFont && av.showText && allGroups.length==0 && !av.getColourText())
-        {
-          graphics.drawString(seq.getSequence(start, end + 1), 0, y1);
         }
         else
         {
-          for (int i = start; i <= end; i++)
+          if (!av.getShowText())
           {
-            graphics.setColor(Color.black);
-            s = seq.getCharAt(i);
-            if (!renderGaps && jalview.util.Comparison.isGap(s))
-            {
-              continue;
-            }
+            continue;
+          }
 
-            if (inCurrentSequenceGroup(i))
-            {
-              if (!currentSequenceGroup.getDisplayText())
-              {
-                continue;
-              }
+          if (av.getColourText())
+          {
+            getboxColour = true;
+            getBoxColour(av.globalColourScheme, seq, i);
 
-              if (currentSequenceGroup.getColourText())
-              {
-                getBoxColour(currentSequenceGroup.cs, seq, i);
-                graphics.setColor(resBoxColour.darker());
-              }
+            if (av.getShowBoxes())
+            {
+              graphics.setColor(resBoxColour.darker());
             }
             else
             {
-              if (!av.getShowText())
-              {
-                continue;
-              }
-
-              if (av.getColourText())
-              {
-                getBoxColour(av.globalColourScheme, seq, i);
-
-                if (av.getShowBoxes())
-                {
-                  graphics.setColor(resBoxColour.darker());
-                }
-                else
-                {
-                  graphics.setColor(resBoxColour);
-                }
-              }
+              graphics.setColor(resBoxColour);
             }
-
-            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-
-          //  System.out.print(s);
-            graphics.drawString(String.valueOf(s),
-                                charOffset + av.charWidth * (i - start),
-                                y1);
-
           }
-        //  System.out.println("\n");
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param res DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    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))
+          if (av.thresholdTextColour > 0)
+          {
+            if (!getboxColour)
             {
-                currentSequenceGroup = allGroups[i];
+              getBoxColour(av.globalColourScheme, seq, i);
+            }
 
-                return true;
+            if (resBoxColour.getRed() +
+                resBoxColour.getBlue() +
+                resBoxColour.getGreen() < av.thresholdTextColour)
+            {
+              graphics.setColor(av.textColour2);
             }
+          }
+
         }
 
-        return false;
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s),
+                            charOffset + av.charWidth * (i - start),
+                            y1);
+
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param res DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  boolean inCurrentSequenceGroup(int res)
+  {
+    if (allGroups == null)
+    {
+      return false;
     }
 
-    /**
-     * 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)
+    for (int i = 0; i < allGroups.length; i++)
     {
-        int pady = av.charHeight / 5;
-        int charOffset = 0;
-        graphics.setColor(Color.BLACK);
-        graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
-        graphics.setColor(Color.white);
+      if ( (allGroups[i].getStartRes() <= res) &&
+          (allGroups[i].getEndRes() >= res))
+      {
+        currentSequenceGroup = allGroups[i];
 
-        char s = '~';
+        return true;
+      }
+    }
 
-        // Need to find the sequence position here.
-        for (int i = start; i <= end; i++)
+    return false;
+  }
+
+  /**
+   * 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 pady = av.charHeight / 5;
+    int charOffset = 0;
+    graphics.setColor(Color.BLACK);
+    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
+    graphics.setColor(Color.white);
+
+    char s = '~';
+
+    // Need to find the sequence position here.
+    if (av.validCharWidth)
+    {
+      for (int i = start; i <= end; i++)
+      {
+        if (i < seq.getLength())
         {
-            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);
+          s = seq.getCharAt(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.lightGray);
-      graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
-      graphics.setColor(Color.white);
+  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);
-
-
+                          charOffset + x1,
+                          (y1 + av.charHeight) - pady);
     }
+
+  }
 }