X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=70f67d7656f7aea0b03cb0dadd28142ca51f18ef;hb=890bd0eac47a4b0f55bd062a359c16a43c3780a0;hp=896fda5a7c916879d9775e8f65371050c0e3c672;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 896fda5..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
@@ -23,6 +23,12 @@ import java.awt.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class SequenceRenderer
 {
   AlignViewport av;
@@ -32,29 +38,74 @@ public class SequenceRenderer
   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;
   }
 
-  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();
+
+    // 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(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;
   }
 
+  /**
+   * 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);
+      resBoxColour = cs.findColour(seq.getCharAt(i), i);
+    }
+    else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+    {
+      resBoxColour = Color.lightGray;
     }
     else
     {
@@ -62,149 +113,243 @@ public class SequenceRenderer
     }
   }
 
-  public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
-                           int start, int end, int x1, int y1, int width,
-                           int height)
+  /**
+   * 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;
 
-    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);
+    }
   }
 
-  public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
-                        int width, int height)
+  /**
+   * 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 = width;
+    int curWidth = av.charWidth;
 
     Color tempColour = null;
 
-    while ( (i <= end) && (i < length))
+    while (i <= end)
     {
-      if (inCurrentSequenceGroup(i))
+      resBoxColour = Color.white;
+
+      if (i < length)
       {
-        if (currentSequenceGroup.getDisplayBoxes())
+        if (inCurrentSequenceGroup(i))
         {
-          getBoxColour(currentSequenceGroup.cs, seq, i);
+          if (currentSequenceGroup.getDisplayBoxes())
+          {
+            getBoxColour(currentSequenceGroup.cs, seq, i);
+          }
         }
-        else
+        else if (av.getShowBoxes())
         {
-          resBoxColour = Color.white;
+          getBoxColour(av.globalColourScheme, 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.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)
+  /**
+   * 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)
   {
-    int pady = height / 5;
+    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
     int charOffset = 0;
     char s;
 
-    // Need to find the sequence position here.
-    String sequence = seq.getSequence();
-
-    for (int i = start; i <= end; i++)
+    if (end + 1 >= seq.getLength())
     {
-      graphics.setColor(Color.black);
+      end = seq.getLength() - 1;
+    }
+    graphics.setColor(av.textColour);
 
-      if (i < sequence.length())
+    if (monospacedFont
+        && av.showText
+        && allGroups.length == 0
+        && !av.getColourText()
+        && av.thresholdTextColour == 0)
+    {
+      if (av.renderGaps)
       {
-        s = sequence.charAt(i);
+        graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
       }
       else
       {
-        s = ' ';
+        char gap = av.getGapCharacter();
+        graphics.drawString(seq.getSequenceAsString(start, end + 1).replace(gap,
+            ' '), 0, y1);
       }
-
-      if (!renderGaps && jalview.util.Comparison.isGap(s))
-      {
-        continue;
-      }
-
-      if (inCurrentSequenceGroup(i))
+    }
+    else
+    {
+      boolean getboxColour = false;
+      for (int i = start; i <= end; i++)
       {
-        if (!currentSequenceGroup.getDisplayText())
+        graphics.setColor(av.textColour);
+        getboxColour = false;
+        s = seq.getCharAt(i);
+        if (!renderGaps && jalview.util.Comparison.isGap(s))
         {
           continue;
         }
 
-        if (currentSequenceGroup.getColourText())
+        if (inCurrentSequenceGroup(i))
         {
-          getBoxColour(currentSequenceGroup.cs, seq, i);
-          graphics.setColor(resBoxColour.darker());
-        }
-      }
-      else
-      {
-        if (!av.getShowText())
-        {
-          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)
+            {
+              if (resBoxColour.getRed() +
+                  resBoxColour.getBlue() +
+                  resBoxColour.getGreen() <
+                  currentSequenceGroup.thresholdTextColour)
+              {
+                graphics.setColor(currentSequenceGroup.textColour2);
+              }
+            }
+          }
+          else
+          {
+            graphics.setColor(currentSequenceGroup.textColour);
+          }
 
-        if (av.getColourText())
+        }
+        else
         {
-          getBoxColour(av.getGlobalColourScheme(), seq, i);
+          if (!av.getShowText())
+          {
+            continue;
+          }
 
-          if (av.getShowBoxes())
+          if (av.getColourText())
           {
-            graphics.setColor(resBoxColour.darker());
+            getboxColour = true;
+            getBoxColour(av.globalColourScheme, seq, i);
+
+            if (av.getShowBoxes())
+            {
+              graphics.setColor(resBoxColour.darker());
+            }
+            else
+            {
+              graphics.setColor(resBoxColour);
+            }
           }
-          else
+
+          if (av.thresholdTextColour > 0)
           {
-            graphics.setColor(resBoxColour);
+            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 + (width * (i - start)),
-                          (y1 + height) - pady);
+        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)
@@ -226,29 +371,64 @@ public class SequenceRenderer
     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 width, int height)
+                                  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.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.black);
+    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+
+    if (av.validCharWidth)
+    {
+      graphics.setColor(Color.white);
 
-      charOffset = (width - fm.charWidth(s)) / 2;
+      char s = seq.getCharAt(res);
+
+      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);
     }
+
   }
 }