X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=6c7fb37cd615f5a85e52eab5f2be52076f20c43d;hb=cca1d315fd19ddcc7c67a5aba91dafa98be097cf;hp=192e252cbf0b522c1a6e3ee554ee78ee651e8649;hpb=b0e7370d001804e563320570d2a11453954c393e;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 192e252..6c7fb37 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,155 +1,421 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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
 {
-  FontMetrics fm;
-  boolean renderGaps = true;
+    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();
 
-  public void renderGaps(boolean b)
-  {
-    renderGaps = b;
-  }
+        monospacedFont =
+               (dwidth == fm.getStringBounds("|",g).getWidth()
+               && (float)av.charWidth == dwidth);
 
-  public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
-  {
-   Color c = Color.white;
-    try{
-       c = cs.findColour(seq, seq.getSequence(i, i + 1), i, null);
-    }catch(Exception ex){}
+        this.renderGaps = renderGaps;
+    }
 
-    return c;
-  }
 
+    public Color getResidueBoxColour(SequenceI seq, int i)
+    {
+      allGroups = av.alignment.findAllGroups(seq);
 
-  public void drawSequence(Graphics g,ColourSchemeI cs,SequenceI seq,int start, int end, int x1, int y1, double width, int height,boolean showScores, boolean displayBoxes, boolean displayText, boolean colourText,Vector freq, int seqnum) {
+      if (inCurrentSequenceGroup(i))
+      {
+        if (currentSequenceGroup.getDisplayBoxes())
+        {
+          getBoxColour(currentSequenceGroup.cs, seq, i);
+        }
+      }
+      else if (av.getShowBoxes())
+      {
+          getBoxColour(av.globalColourScheme, seq, i);
+      }
 
+      return resBoxColour;
+    }
 
-    if (displayBoxes)
-        drawBoxes(g,cs,seq,start,end,x1,y1,(int)width, height,freq);
 
-    if (displayText)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cs DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     * @param i DOCUMENT ME!
+     */
+    void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
     {
-        fm = g.getFontMetrics();
-        drawText(g,cs,colourText,seq,start,end,x1,y1,(int)width,height);
+        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;
+        }
     }
-  }
 
-  public void drawBoxes(Graphics g,ColourSchemeI cs, SequenceI seq,int start, int end, int x1, int y1, int width, int height,Vector freq) {
-    int i      = start;
-    int length = seq.getLength();
+    /**
+     * 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;
 
-    Color currentColor = Color.WHITE;
+        drawBoxes(seq, start, end, y1);
 
-    int curStart = x1;
-    int curWidth = width;
+        if (av.validCharWidth)
+          drawText(seq, start, end, y1);
+    }
 
-  //  int threshold = 80;
+    /**
+     * 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();
 
-    while (i <= end && i < length) {
-      Color c = getResidueBoxColour(cs,seq,i);
+      int curStart = -1;
+      int curWidth = av.charWidth;
 
-    //  Hashtable hash  = (Hashtable)freq.elementAt(i-start);
-    //  String    s     = (String)hash.get("maxResidue");
-    //  int       count = ((Integer)hash.get("maxCount")).intValue();
-  //    int       max   = ((Integer)hash.get("size")).intValue();
-   //   int       nongap = ((Integer)hash.get("nongap")).intValue();
-   //   float     frac  = (float)(count*1.0/(1.0*nongap));
+      Color tempColour = null;
 
-      //System.out.println("Frac/count/nongap " + frac + " " + count + " " + nongap);
-    /*  if (!seq.getSequence().substring(i,i+1).equals(s) ||
-	  s.equals("-") ||
-	  s.equals(".") ||
-	  s.equals(" "))
-      {
-	c = Color.white;
-      } else {
-	if (frac > 0.9) {
-	  c = Color.red;
-	} else if (frac > 0.8) {
-	  c = Color.orange;
-	} else if (frac > 0.7) {
-	  c = Color.pink;
-	} else if (frac > 0.5) {
-	  c = Color.yellow;
-	} else if (frac> 0.3) {
-	    c = Color.lightGray;
-	}
-      }*/
-
-      if (c != currentColor || c != null)
+      while (i <= end)
       {
-        g.fillRect(x1+width*(curStart-start),y1,curWidth,height);
+        resBoxColour = Color.white;
 
-        currentColor = c;
-        g.setColor(c);
+        if (i < length)
+        {
+          if (inCurrentSequenceGroup(i))
+          {
+            if (currentSequenceGroup.getDisplayBoxes())
+            {
+              getBoxColour(currentSequenceGroup.cs, seq, i);
+            }
+          }
+          else if (av.getShowBoxes())
+          {
+            getBoxColour(av.globalColourScheme, seq, i);
+          }
+
+        }
 
-        curStart = i;
-        curWidth = width;
+          if (resBoxColour != tempColour)
+          {
+              if (tempColour != null)
+              {
+                  graphics.fillRect( av.charWidth * (curStart - start), y1,
+                      curWidth, av.charHeight);
+              }
+
+              graphics.setColor(resBoxColour);
+
+              curStart = i;
+              curWidth = av.charWidth;
+              tempColour = resBoxColour;
+          }
+          else
+          {
+              curWidth += av.charWidth;
+          }
+
+          i++;
       }
-      else
-        curWidth += width;
 
-      i++;
+      graphics.fillRect( av.charWidth * (curStart - start), y1, curWidth,
+          av.charHeight);
+
     }
-    g.fillRect(x1+width*(curStart-start),y1,curWidth,height);
-  }
-
-  public void drawText(Graphics g, ColourSchemeI cs, boolean colText, SequenceI seq,int start, int end, int x1, int y1, int width, int height)
-  {
-    int pady = height/5;
-    int charOffset=0;
-    g.setColor(Color.black);
-
-    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 drawText(SequenceI seq, int start, int end, int y1)
     {
-        if(i<seq.getLength())
-          s = seq.getSequence().charAt(i);
-        else
-          s = ' ';
+      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(av.textColour);
 
-        if(!renderGaps && (s=='-' || s=='.' || s==' '))
-          continue;
 
-        if (colText)
+        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;
+            }
+
+            if (inCurrentSequenceGroup(i))
+            {
+              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);
+
+            }
+            else
+            {
+              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);
+              }
+
+            }
+
+
+
+          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)
         {
-            Color c = getResidueBoxColour(cs, seq, i);
-            g.setColor(c.darker());
+            return false;
         }
 
-      charOffset =  (width - fm.charWidth(s))/2;
+        for (int i = 0; i < allGroups.length; i++)
+        {
+            if ((allGroups[i].getStartRes() <= res) &&
+                    (allGroups[i].getEndRes() >= res))
+            {
+                currentSequenceGroup = allGroups[i];
 
+                return true;
+            }
+        }
 
-      g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);
+        return false;
     }
-  }
-
-  public void drawHighlightedText(Graphics g, SequenceI seq,int start, int end, int x1, int y1, int width, int height)
-  {
-    int pady = height/5;
-    int charOffset=0;
-    g.setColor(Color.BLACK);
-    g.fillRect(x1,y1,width*(end-start+1),height);
-    g.setColor(Color.white);
-
-    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)
     {
-       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 * (end - start + 1), av.charHeight);
+        graphics.setColor(Color.white);
 
-      charOffset =  (width - fm.charWidth(s))/2;
-      g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);
+        char s = '~';
+
+        // Need to find the sequence position here.
+        if(av.validCharWidth)
+        {
+          for (int i = start; i <= end; 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);
+
+        char s = seq.getCharAt(res);
 
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s),
+                            charOffset + x1,
+                            (y1 + av.charHeight) - pady);
+      }
+
+    }
 }