X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=5022050ab72a3f83bb6dd98f439127ee63da9b3f;hb=8af8289df86798d5e283e1d0aa275b8f98e563dc;hp=7df91496894483b6ceec6c5f50602345162a6a45;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 7df9149..5022050 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -2,41 +2,51 @@ package jalview.gui;
 
 import jalview.datamodel.*;
 import jalview.schemes.*;
-
 import java.awt.*;
 import java.util.*;
 
 public class SequenceRenderer implements RendererI
 {
-  FontMetrics fm;
   AlignViewport av;
+  FontMetrics fm;
+  boolean renderGaps = true;
+  SequenceGroup currentSequenceGroup = null;
+  Color color;
+
+  public SequenceRenderer(AlignViewport av)
+  {
+    this.av = av;
+  }
+
 
-  public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {
-    Color c = Color.WHITE;
+  public void renderGaps(boolean b)
+  {
+    renderGaps = b;
+  }
 
-    try{
-      if (cs != null)
-        c = cs.findColour(seq, seq.getSequence(i, i + 1), i, null);
-    }catch(Exception ex)
-    {    }
+  public Color getResidueBoxColour(ColourSchemeI cs, 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){}
 
     return c;
   }
 
-  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,Vector freq, int seqnum,AlignViewport av) {
+  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)
+  {
+    currentSequenceGroup = sg;
+
+    drawBoxes(g, seq, start, end, x1, y1, (int) width, height, pid);
 
-    this.av = av;
+    fm = g.getFontMetrics();
+    drawText(g,seq,start,end,x1,y1,(int)width,height);
 
-    if (displayBoxes == true) {
-        drawBoxes(g,cs,seq,start,end,x1,y1,(int)width, height,freq);
-    }
-    if (displayText == true) {
-        fm = g.getFontMetrics();
-        drawText(g,cs,seq,start,end,x1,y1,(int)width,height);
-    }
   }
 
-  public void drawBoxes(Graphics g,ColourSchemeI cs, SequenceI seq,int start, int end, int x1, int y1, int width, int height,Vector freq) {
+  public void drawBoxes(Graphics g, SequenceI seq,int start, int end, int x1, int y1, int width, int height,Vector freq) {
     int i      = start;
     int length = seq.getLength();
 
@@ -45,45 +55,25 @@ public class SequenceRenderer implements RendererI
     int curStart = x1;
     int curWidth = width;
 
-  //  int threshold = 80;
+    while (i <= end && i < length)
+    {
+      color = color.white;
 
-    while (i <= end && i < length) {
-      Color c = getResidueBoxColour(cs,seq,i);
+      if(inCurrentSequenceGroup(i))
+      {
+        if( currentSequenceGroup.getDisplayBoxes())
+             color = getResidueBoxColour(currentSequenceGroup.cs, seq, i);
+      }
+      else if(av.getShowBoxes())
+           color = getResidueBoxColour(av.getGlobalColourScheme(), seq, i);
 
-    //  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));
 
-      //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)
+      if (color != currentColor || color != null)
       {
         g.fillRect(x1+width*(curStart-start),y1,curWidth,height);
 
-        currentColor = c;
-        g.setColor(c);
+        currentColor = color;
+        g.setColor(color);
 
         curStart = i;
         curWidth = width;
@@ -96,35 +86,77 @@ public class SequenceRenderer implements RendererI
     g.fillRect(x1+width*(curStart-start),y1,curWidth,height);
   }
 
-  public void drawText(Graphics g, ColourSchemeI cs, SequenceI seq,int start, int end, int x1, int y1, int width, int height)
+  public void drawText(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);
-    boolean colourText = av.getColourText();
-    Color c;
+
     char s;
     // Need to find the sequence position here.
     for (int i = start; i <= end; i++)
     {
-        if (i < end && i < seq.getLength())
-          s = seq.getSequence().charAt(i);
-        else if(i<seq.getLength())
+        if(i<seq.getLength())
           s = seq.getSequence().charAt(i);
         else
           s = ' ';
 
-        if (colourText)
+        if(!renderGaps && jalview.util.Comparison.isGap(s))
+          continue;
+
+        g.setColor(Color.black);
+
+        if (inCurrentSequenceGroup(i))
         {
-            c = getResidueBoxColour(cs, seq, i);
-            g.setColor(c.darker());
+          if(!currentSequenceGroup.getDisplayText())
+            continue;
+
+          if(currentSequenceGroup.getColourText())
+            g.setColor(getResidueBoxColour(currentSequenceGroup.cs, seq, i).darker());
+        }
+        else
+        {
+          if(!av.getShowText())
+            continue;
+
+          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);
+    }
+
+
+  }
+
+  boolean inCurrentSequenceGroup(int res)
+  {
+    if(currentSequenceGroup==null)
+      return false;
 
+    return (currentSequenceGroup.getStartRes()<=res && currentSequenceGroup.getEndRes()>=res)?true: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++)
+    {
+       if(i<seq.getLength())
+          s = seq.getSequence().charAt(i);
 
+      charOffset =  (width - fm.charWidth(s))/2;
       g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);
     }
   }
 
+
 }