From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 21 Mar 2005 18:47:17 +0000 (+0000)
Subject: new method for outlining groups
X-Git-Tag: Release_2_0~534
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=09b64bea954c283bde1d21c0a230f51f1ae89373;p=jalview.git

new method for outlining groups
---

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 96dea90..f9ab015 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -2,9 +2,7 @@ package jalview.gui;
 
 import java.awt.*;
 import javax.swing.*;
-import java.awt.event.*;
 import jalview.datamodel.*;
-import jalview.schemes.*;
 import jalview.analysis.*;
 
 
@@ -157,111 +155,97 @@ public class SeqCanvas extends JPanel
     }*/
 
     SequenceI nextSeq;
-    SequenceGroup group=null;
-    SequenceGroup [] groups=null;
-    boolean inGroup=false; // are we in a defined group?
-    boolean inRB=false; //Are we in a rubberband group?
-    int sx=-1, sy=-1, ex=-1, ey=-1;
-    int oldStartX=0,oldEndX=0,oldY=0;
-    int oldRStartX=0,oldREndX=0,oldRY=0;
+
+    /// First draw the sequences
+    /////////////////////////////
     for (int i = y1 ; i < y2 ;i++)
     {
      nextSeq = av.getAlignment().getSequenceAt(i);
 
-     group = av.alignment.findGroup( nextSeq );
-     groups = av.alignment.findAllGroups( nextSeq );
-
-     sr.drawSequence(g, nextSeq, groups,x1,x2,
+     sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2,
                  (x1 - startx) * av.charWidth,
                  offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
                  av.charWidth,av.charHeight,null, i);
 
      if(av.showSequenceFeatures)
      {
-       fr.drawSequence(g, nextSeq, groups, x1, x2,
+       fr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ), x1, x2,
                        (x1 - startx) * av.charWidth,
                        offset +
                        AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
                        av.charWidth, av.charHeight, null, i);
      }
+    }
+    //
+    /////////////////////////////////////
 
+    // Now outline any areas if necessary
+    /////////////////////////////////////
+    SequenceGroup group = av.getSelectionGroup();
+    java.util.Vector groups = av.alignment.getGroups();
 
+    int sx = -1, sy = -1, ex = -1;
+    int groupIndex = -1;
+    if (group == null && groups.size() > 0)
+    {
+      group = (SequenceGroup) groups.elementAt(0);
+      groupIndex = 0;
+    }
 
-
-     if( group!=null )
-     {
-
-        g.setColor(Color.lightGray);
-
-        sx = (group.getStartRes()-startx)*av.charWidth;
-        sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
-        ex = (group.getEndRes()+1-startx)*av.charWidth;
-        ey = offset + AlignmentUtil.getPixelHeight(starty, i+1, av.charHeight);
-
-
-        if (!inGroup)
+    if (group != null)
+      do
+      {
+        int oldY = -1;
+        int i = 0;
+        boolean inGroup = false;
+        for (i = y1; i < y2; i++)
         {
-          g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box
-          inGroup=true;
+          sx = (group.getStartRes() - startx) * av.charWidth;
+          sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
+          ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth;
+
+          if (group.sequences.contains(av.alignment.getSequenceAt(i))
+              && sx < getWidth()
+              && ex > 0)
+          {
+            if (!inGroup)
+            {
+              oldY = sy;
+              inGroup = true;
+              if (group == av.getSelectionGroup())
+                g.setColor(Color.RED.brighter());
+              else
+                g.setColor(group.getOutlineColour());
+            }
+          }
+          else
+          {
+            if (inGroup)
+            {
+              g.drawRect(sx, oldY, ex, (sy - oldY));
+              inGroup = false;
+            }
+          }
+        }
+        if (inGroup)
+        {
+          sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
+          g.drawRect(sx, oldY, ex, (sy - oldY));
+          inGroup = false;
         }
 
-        g.drawLine(sx, sy, sx, ey ); // vertical line, left hand side
-        g.drawLine( ex,sy,ex,ey);    // vertical line, right hand side
-        if (i == y2 - 1)// last line of alignment, seal the box
-          g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box
-
-        oldStartX = sx;
-        oldEndX = ex;
-        oldY = ey;
+        groupIndex++;
+        if (groupIndex >= groups.size())
+          break;
 
-     }
-     else if(inGroup)
-     {
-       g.setColor(Color.lightGray);
-       g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box
-     }
-     else
-       inGroup = false;
+        group = (SequenceGroup) groups.elementAt(groupIndex);
 
-     group = av.getSelectionGroup();
-     if( group != null && group.sequences.contains(nextSeq) )
-     {
-         g.setColor(Color.RED.brighter());
-         sx = (group.getStartRes() - startx) * av.charWidth;
-         sy = offset +
-             AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
-         ex = (group.getEndRes() + 1 - startx) * av.charWidth;
-         ey = offset +
-             AlignmentUtil.getPixelHeight(starty, i + 1, av.charHeight);
-
-         if (!inRB)
-         {
-
-           g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box
-           inRB = true;
-         }
-
-         g.drawLine(sx, sy, sx, ey); // vertical line, left hand side
-         g.drawLine(ex, sy, ex, ey); // vertical line, right hand side
-         if (i == y2 - 1) // last line of alignment, seal the box
-           g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box
-
-          oldRStartX = sx;
-          oldREndX = ex;
-          oldRY = ey;
-     }
-     else if(inRB)
-     {
-       g.setColor(Color.RED.brighter());
-       g.drawLine(oldRStartX, oldRY, oldREndX, oldRY); // Horizontal, bottom of old box
-       inRB = false;
-     }
-     else
-       inRB = false;
+      }
+      while (groupIndex < groups.size());
 
-    }
 
     /// Highlight search Results once all sequences have been drawn
+    //////////////////////////////////////////////////////////
     if(displaySearch)
     {
       for(int r=0; r<searchResults.length; r+=3)