X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=70f67d7656f7aea0b03cb0dadd28142ca51f18ef;hb=e9217775986fbca85770d7fe5b3763b6920b0c3f;hp=82124cef35ffe78efb91fecb77dccfd79d04094d;hpb=c9f0ef34e578218c8ffabaac9c405fd86d1196e2;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 82124ce..70f67d7 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,162 +1,434 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * 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 java.awt.*;
+
 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;
-  Color color;
-
+  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)
   {
-   Color c = Color.white;
-try{
-     if (cs != null)
-       c = cs.findColour(seq.getSequence(i, i + 1), i, av.getConsensus(false));
-   }catch(Exception ex){}
+    allGroups = av.alignment.findAllGroups(seq);
 
-    return c;
+    if (inCurrentSequenceGroup(i))
+    {
+      if (currentSequenceGroup.getDisplayBoxes())
+      {
+        getBoxColour(currentSequenceGroup.cs, seq, i);
+      }
+    }
+    else if (av.getShowBoxes())
+    {
+      getBoxColour(av.globalColourScheme, seq, i);
+    }
+
+    return resBoxColour;
   }
 
-  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)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param cs DOCUMENT ME!
+   * @param seq DOCUMENT ME!
+   * @param i DOCUMENT ME!
+   */
+  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
-    currentSequenceGroup = sg;
+    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;
+    }
+  }
 
-    drawBoxes(g, seq, start, end, x1, y1, (int) width, height, pid);
+  /**
+   * 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;
 
-    fm = g.getFontMetrics();
-    drawText(g,seq,start,end,x1,y1,(int)width,height);
+    drawBoxes(seq, start, end, y1);
 
+    if (av.validCharWidth)
+    {
+      drawText(seq, start, end, y1);
+    }
   }
 
-  public void drawBoxes(Graphics g, SequenceI seq,int start, int end, int x1, int y1, int width, int height,Vector freq) {
-    int i      = start;
+  /**
+   * 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();
 
-    Color currentColor = Color.WHITE;
+    int curStart = -1;
+    int curWidth = av.charWidth;
 
-    int curStart = x1;
-    int curWidth = width;
+    Color tempColour = null;
 
-    while (i <= end && i < length)
+    while (i <= end)
     {
-      color = color.white;
+      resBoxColour = Color.white;
 
-      if(inCurrentSequenceGroup(i))
+      if (i < length)
       {
-        if( currentSequenceGroup.getDisplayBoxes())
-             color = getResidueBoxColour(currentSequenceGroup.cs, seq, i);
-      }
-      else if(av.getShowBoxes())
-           color = getResidueBoxColour(av.getGlobalColourScheme(), seq, i);
+        if (inCurrentSequenceGroup(i))
+        {
+          if (currentSequenceGroup.getDisplayBoxes())
+          {
+            getBoxColour(currentSequenceGroup.cs, seq, i);
+          }
+        }
+        else if (av.getShowBoxes())
+        {
+          getBoxColour(av.globalColourScheme, seq, i);
+        }
 
+      }
 
-      if (color != currentColor || color != null)
+      if (resBoxColour != tempColour)
       {
-        g.fillRect(x1+width*(curStart-start),y1,curWidth,height);
+        if (tempColour != null)
+        {
+          graphics.fillRect(av.charWidth * (curStart - start), y1,
+                            curWidth, av.charHeight);
+        }
 
-        currentColor = color;
-        g.setColor(color);
+        graphics.setColor(resBoxColour);
 
         curStart = i;
-        curWidth = width;
+        curWidth = av.charWidth;
+        tempColour = resBoxColour;
       }
       else
-        curWidth += width;
+      {
+        curWidth += av.charWidth;
+      }
 
       i++;
     }
-    g.fillRect(x1+width*(curStart-start),y1,curWidth,height);
+
+    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
+                      av.charHeight);
+
   }
 
-  public void drawText(Graphics g, 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;
-    int charOffset=0;
-    g.setColor(Color.black);
-
+    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+    int charOffset = 0;
     char s;
-    // Need to find the sequence position here.
-    for (int i = start; i <= end; i++)
+
+    if (end + 1 >= seq.getLength())
     {
-        if(i<seq.getLength())
-          s = seq.getSequence().charAt(i);
-        else
-          s = ' ';
+      end = seq.getLength() - 1;
+    }
+    graphics.setColor(av.textColour);
 
-        if(!renderGaps && (s=='-' || s=='.' || s==' '))
+    if (monospacedFont
+        && av.showText
+        && allGroups.length == 0
+        && !av.getColourText()
+        && av.thresholdTextColour == 0)
+    {
+      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);
+      }
+    }
+    else
+    {
+      boolean getboxColour = false;
+      for (int i = start; i <= end; i++)
+      {
+        graphics.setColor(av.textColour);
+        getboxColour = false;
+        s = seq.getCharAt(i);
+        if (!renderGaps && jalview.util.Comparison.isGap(s))
+        {
           continue;
-
-        g.setColor(Color.black);
+        }
 
         if (inCurrentSequenceGroup(i))
         {
-          if(!currentSequenceGroup.getDisplayText())
+          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(currentSequenceGroup.getColourText())
-            g.setColor(getResidueBoxColour(currentSequenceGroup.cs, seq, i).darker());
         }
         else
         {
-          if(!av.getShowText())
+          if (!av.getShowText())
+          {
             continue;
+          }
+
+          if (av.getColourText())
+          {
+            getboxColour = true;
+            getBoxColour(av.globalColourScheme, seq, i);
+
+            if (av.getShowBoxes())
+            {
+              graphics.setColor(resBoxColour.darker());
+            }
+            else
+            {
+              graphics.setColor(resBoxColour);
+            }
+          }
+
+          if (av.thresholdTextColour > 0)
+          {
+            if (!getboxColour)
+            {
+              getBoxColour(av.globalColourScheme, seq, i);
+            }
+
+            if (resBoxColour.getRed() +
+                resBoxColour.getBlue() +
+                resBoxColour.getGreen() < av.thresholdTextColour)
+            {
+              graphics.setColor(av.textColour2);
+            }
+          }
 
-          if(av.getColourText())
-            g.setColor(getResidueBoxColour(av.getGlobalColourScheme(), seq, i).darker());
         }
 
-      charOffset =  (width - fm.charWidth(s))/2;
-      g.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(currentSequenceGroup==null)
+    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 (currentSequenceGroup.getStartRes()<=res && currentSequenceGroup.getEndRes()>=res)?true:false;
+        return true;
+      }
+    }
+
+    return false;
   }
 
-  public void drawHighlightedText(Graphics g, 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 drawHighlightedText(SequenceI seq, int start, int end, int x1,
+                                  int y1)
   {
-    int pady = height/5;
-    int charOffset=0;
-    g.setColor(Color.BLACK);
-    g.fillRect(x1,y1,width*(end-start+1),height);
-    g.setColor(Color.white);
+    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 = '~';
 
-    char s='~';
     // Need to find the sequence position here.
-    for (int i = start; i <= end; i++)
+    if (av.validCharWidth)
     {
-       if(i<seq.getLength())
-          s = seq.getSequence().charAt(i);
+      for (int i = start; i <= end; i++)
+      {
+        if (i < seq.getLength())
+        {
+          s = seq.getCharAt(i);
+        }
 
-      charOffset =  (width - fm.charWidth(s))/2;
-      g.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 + 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);
+
+      char s = seq.getCharAt(res);
 
+      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+      graphics.drawString(String.valueOf(s),
+                          charOffset + x1,
+                          (y1 + av.charHeight) - pady);
+    }
+
+  }
 }