X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=ec93abf246f244f59897e1ba794ce5c91b17450e;hb=e02486484d33e20dedb020a34f31f6024d5720a2;hp=896fda5a7c916879d9775e8f65371050c0e3c672;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 896fda5..ec93abf 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -18,237 +18,359 @@
  */
 package jalview.gui;
 
-import java.awt.*;
-
 import jalview.datamodel.*;
+
 import jalview.schemes.*;
 
+import java.awt.*;
+
+/**
+ * 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;
-
-  public SequenceRenderer(AlignViewport av)
-  {
-    this.av = av;
-  }
-
-  public void renderGaps(boolean b)
-  {
-    renderGaps = b;
-  }
-
-  public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
-  {
-    getBoxColour(cs, seq, i);
-
-    return resBoxColour;
-  }
-
-  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
-  {
-    if (cs != null)
+    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)
     {
-      resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
+        this.av = av;
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void prepare(Graphics g, boolean renderGaps)
     {
-      resBoxColour = Color.white;
+        graphics = g;
+        fm = g.getFontMetrics();
+        monospacedFont = fm.getStringBounds("M",g).getWidth()==fm.getStringBounds("|",g).getWidth();
+        this.renderGaps = renderGaps;
     }
-  }
-
-  public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
-                           int start, int end, int x1, int y1, int width,
-                           int height)
-  {
-    allGroups = sg;
-
-    graphics = g;
-
-    drawBoxes(seq, start, end, x1, y1, (int) width, height);
-
-    fm = g.getFontMetrics();
-    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;
-    int length = seq.getLength();
 
-    int curStart = -1;
-    int curWidth = width;
 
-    Color tempColour = null;
-
-    while ( (i <= end) && (i < length))
+    public Color getResidueBoxColour(SequenceI seq, int i)
     {
+      allGroups = av.alignment.findAllGroups(seq);
+
       if (inCurrentSequenceGroup(i))
       {
         if (currentSequenceGroup.getDisplayBoxes())
         {
           getBoxColour(currentSequenceGroup.cs, seq, i);
         }
-        else
-        {
-          resBoxColour = Color.white;
-        }
       }
       else if (av.getShowBoxes())
       {
-        getBoxColour(av.getGlobalColourScheme(), seq, i);
+          getBoxColour(av.globalColourScheme, seq, i);
       }
-      else
-      {
-        resBoxColour = Color.white;
-      }
-
-      if (resBoxColour != tempColour)
-      {
-        if (tempColour != null)
-        {
-          graphics.fillRect(x1 + (width * (curStart - start)), y1,
-                            curWidth, height);
-        }
 
-        graphics.setColor(resBoxColour);
+      return resBoxColour;
+    }
 
-        curStart = i;
-        curWidth = width;
-        tempColour = resBoxColour;
-      }
-      else
-      {
-        curWidth += width;
-      }
 
-      i++;
+    /**
+     * 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 if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+        {
+            resBoxColour = Color.lightGray;
+        }
+        else
+        {
+          resBoxColour = Color.white;
+        }
     }
 
-    graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,
-                      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;
 
-  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;
+        drawBoxes(seq, start, end, y1);
 
-    // Need to find the sequence position here.
-    String sequence = seq.getSequence();
+        drawText(seq, start, end, y1);
+    }
 
-    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 synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)
     {
-      graphics.setColor(Color.black);
+      int i = start;
+      int length = seq.getLength();
 
-      if (i < sequence.length())
-      {
-        s = sequence.charAt(i);
-      }
-      else
-      {
-        s = ' ';
-      }
+      int curStart = -1;
+      int curWidth = av.charWidth;
 
-      if (!renderGaps && jalview.util.Comparison.isGap(s))
-      {
-        continue;
-      }
+      Color tempColour = null;
 
-      if (inCurrentSequenceGroup(i))
+      while (i <= end)
       {
-        if (!currentSequenceGroup.getDisplayText())
-        {
-          continue;
-        }
+        resBoxColour = Color.white;
 
-        if (currentSequenceGroup.getColourText())
-        {
-          getBoxColour(currentSequenceGroup.cs, seq, i);
-          graphics.setColor(resBoxColour.darker());
-        }
-      }
-      else
-      {
-        if (!av.getShowText())
+        if (i < length)
         {
-          continue;
-        }
+          if (inCurrentSequenceGroup(i))
+          {
+            if (currentSequenceGroup.getDisplayBoxes())
+            {
+              getBoxColour(currentSequenceGroup.cs, seq, i);
+            }
+          }
+          else if (av.getShowBoxes())
+          {
+            getBoxColour(av.globalColourScheme, seq, i);
+          }
 
-        if (av.getColourText())
-        {
-          getBoxColour(av.getGlobalColourScheme(), seq, i);
+        }
 
-          if (av.getShowBoxes())
+          if (resBoxColour != tempColour)
           {
-            graphics.setColor(resBoxColour.darker());
+              if (tempColour != null)
+              {
+                  graphics.fillRect( av.charWidth * (curStart - start), y1,
+                      curWidth, av.charHeight);
+              }
+
+              graphics.setColor(resBoxColour);
+
+              curStart = i;
+              curWidth = av.charWidth;
+              tempColour = resBoxColour;
           }
           else
           {
-            graphics.setColor(resBoxColour);
+              curWidth += av.charWidth;
           }
-        }
+
+          i++;
       }
 
-      charOffset = (width - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s),
-                          charOffset + x1 + (width * (i - start)),
-                          (y1 + height) - pady);
+      graphics.fillRect( av.charWidth * (curStart - start), y1, curWidth,
+          av.charHeight);
+
     }
-  }
 
-  boolean inCurrentSequenceGroup(int res)
-  {
-    if (allGroups == null)
+    /**
+     * 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)
     {
-      return false;
+      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())
+        {
+          if(av.renderGaps)
+          graphics.drawString(seq.getSequence(start, end + 1), 0, y1);
+         else
+         {
+           char gap = av.getGapCharacter();
+           graphics.drawString( seq.getSequence(start, end+1).replace(gap, ' '), 0, y1);
+         }
+        }
+        else
+        {
+          for (int i = start; i <= end; i++)
+          {
+            graphics.setColor(Color.black);
+            s = seq.getCharAt(i);
+            if (!renderGaps && jalview.util.Comparison.isGap(s))
+            {
+              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.globalColourScheme, seq, i);
+
+                if (av.getShowBoxes())
+                {
+                  graphics.setColor(resBoxColour.darker());
+                }
+                else
+                {
+                  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");
+        }
     }
 
-    for (int i = 0; i < allGroups.length; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param res DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    boolean inCurrentSequenceGroup(int res)
     {
-      if ( (allGroups[i].getStartRes() <= res) &&
-          (allGroups[i].getEndRes() >= res))
-      {
-        currentSequenceGroup = allGroups[i];
+        if (allGroups == null)
+        {
+            return false;
+        }
 
-        return true;
-      }
+        for (int i = 0; i < allGroups.length; i++)
+        {
+            if ((allGroups[i].getStartRes() <= res) &&
+                    (allGroups[i].getEndRes() >= res))
+            {
+                currentSequenceGroup = allGroups[i];
+
+                return true;
+            }
+        }
+
+        return false;
     }
 
-    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);
 
-  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);
+        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);
+            }
+
+            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+            graphics.drawString(String.valueOf(s),
+                charOffset + x1 + (av.charWidth * (i - start)),
+                (y1 + av.charHeight) - pady);
+        }
+    }
 
-    // Need to find the sequence position here.
-    for (int i = start; i <= end; i++)
+    public void drawCursor(SequenceI seq, int res, int x1, int y1)
     {
-      if (i < seq.getLength())
-      {
-        s = seq.getSequence().charAt(i);
-      }
+      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);
+
+      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);
+
+
     }
-  }
 }