From a11e13d8fffacf8115a4d83e4254bf94a87d6600 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 3 Dec 2004 16:32:23 +0000
Subject: [PATCH] Preparing for groupselect mode

---
 src/jalview/gui/SeqCanvas.java        |  170 ++++++++++++++++++++++-----------
 src/jalview/gui/SeqPanel.java         |  105 +++++++++++++++++---
 src/jalview/gui/SequenceRenderer.java |   75 ++++++++++-----
 3 files changed, 259 insertions(+), 91 deletions(-)

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 3850244..00b4e95 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -2,7 +2,7 @@ package jalview.gui;
 
 import java.awt.*;
 import javax.swing.*;
-import java.util.*;
+import java.awt.event.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 import jalview.analysis.*;
@@ -10,6 +10,7 @@ import jalview.analysis.*;
 
 public class SeqCanvas extends JPanel
 {
+    ColourSchemeI globalColorScheme = null;
     Image             img;
     Graphics          gg;
     int               imgWidth;
@@ -30,15 +31,15 @@ public class SeqCanvas extends JPanel
     int chunkHeight;
     int chunkWidth;
 
-    ColourSchemeI   cs = new ZappoColourScheme();
 
     public SeqCanvas(AlignViewport av)
     {
 	this.av         = av;
        setLayout(new BorderLayout());
+
     }
 
-  public void drawScale(int startx, int endx,double charWidth, int charHeight,int ypos) {
+  public void drawScale(int startx, int endx,int charWidth, int charHeight,int ypos) {
       int scalestartx = startx - startx%10 + 10;
 
       gg.setColor(Color.black);
@@ -92,10 +93,10 @@ public class SeqCanvas extends JPanel
     int endx   = av.getEndRes();
     int endy   = av.getEndSeq();
 
-    double charWidth  = av.getCharWidth();
-    int charHeight    = av.getCharHeight();
+    int charWidth  = av.getCharWidth();
+    int charHeight = av.getCharHeight();
 
-    chunkWidth = (int)(getWidth()/charWidth);
+    chunkWidth  =   getWidth()/charWidth;
     chunkHeight =  (da.getHeight() + 2)*charHeight;
 
     av.setChunkHeight(chunkHeight);
@@ -187,8 +188,8 @@ public class SeqCanvas extends JPanel
     {
       // This is dragging horizontal scrollbar to the right
 
-      int delx  = (int)((startx - oldstartx) * charWidth);
-      int delx2 = (int)((oldendx - startx + 1)   * charWidth);
+      int delx  = (startx - oldstartx)   * charWidth;
+      int delx2 = (oldendx - startx + 1) * charWidth;
 
       gg.copyArea(delx,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),-delx,0);
 
@@ -205,8 +206,8 @@ public class SeqCanvas extends JPanel
     {
      // Horizontal scrollbar pulled to the left
 
-      int delx  = (int)((oldstartx - startx) * charWidth);
-      int delx2 = (int)((endx - oldstartx +1)   * charWidth);
+      int delx  = (oldstartx - startx)    * charWidth;
+      int delx2 = (endx - oldstartx +1)   * charWidth;
 
       gg.copyArea(0,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),delx,0);
 
@@ -224,7 +225,7 @@ public class SeqCanvas extends JPanel
       int dely  = AlignmentUtil.getPixelHeight(oldstarty,starty,charHeight);
       int dely2 = AlignmentUtil.getPixelHeight(starty,oldendy,charHeight);
 
-      gg.copyArea(0,dely,(int)((endx-startx+1)*charWidth),dely2,0,-dely);
+      gg.copyArea(0,dely,(endx-startx+1)*charWidth,dely2,0,-dely);
 
       if (starty > oldendy) {
 	drawPanel(gg,startx,endx,starty,endy,startx,starty,0);
@@ -241,7 +242,7 @@ public class SeqCanvas extends JPanel
       int dely  = AlignmentUtil.getPixelHeight(endy,oldendy,charHeight);
       int dely2 = AlignmentUtil.getPixelHeight(oldstarty,endy,charHeight);
 
-      gg.copyArea(0,0,(int)((endx-startx+1)*charWidth),dely2,0,dely);
+      gg.copyArea(0,0,(endx-startx+1)*charWidth,dely2,0,dely);
 
       if (oldstarty > endy) {
 	drawPanel(gg,startx,endx,starty,endy,startx,starty,0);
@@ -253,9 +254,9 @@ public class SeqCanvas extends JPanel
       oldendy   = endy;
     }
 
-    if ((oldendy -oldstarty) > (int)((getWidth() / av.getCharWidth()))) {
+    if ((oldendy -oldstarty) > (getWidth() / av.getCharWidth())) {
       System.out.println("LIMITS ERROR LIMITS ERROR");
-      System.out.println("Corrds " + (oldendy-oldstarty) + " " + (int)(getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth());
+      System.out.println("Corrds " + (oldendy-oldstarty) + " " + (getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth());
     }
 
 
@@ -274,6 +275,16 @@ public class SeqCanvas extends JPanel
   public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
 
 /*
+    Startx and starty appear to be the same as x1, y1, unless you find different
+      x1                                               x2
+    y1**************************************************
+      *                                                *
+      *                                                *
+      *                                                *
+      *                                                *
+      **************************************************y2
+
+/*
     System.out.println("drawPanel called with g      = " + g);
     System.out.println("                      x1     = " + x1);
     System.out.println("                      x2     = " + x2);
@@ -284,8 +295,8 @@ public class SeqCanvas extends JPanel
 */
 
     g.setFont(av.getFont());
-    double            charWidth  = av.getCharWidth();
-    int               charHeight = av.getCharHeight();
+    int            charWidth  = av.getCharWidth();
+    int            charHeight = av.getCharHeight();
     RendererI sr = av.getRenderer();
 
 
@@ -309,56 +320,64 @@ public class SeqCanvas extends JPanel
     {
        fillBackground(g,
                    Color.WHITE,
-                   (int)((x1-startx)*charWidth),
+                   (x1-startx)*charWidth,
                    offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()),
-                   (int)((x2-x1+1)*charWidth),
+                   (x2-x1+1)*charWidth,
                    offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight()));
     }
 
     SequenceI nextSeq;
-    SequenceGroup group;
+    SequenceGroup group=null;
+    boolean newGroup=false;
+    int sx, sy, ex, ey;
+    int oldStartX=0,oldEndX=0,oldY=0;
     for (int i = y1 ; i < y2 ;i++)
     {
-    /*  if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {
-          r = fr;
-          System.out.println("use feature renderer");
-      } else if ( i == 0) {
-        //  r = br;
-      } else if (av.getAlignment().getSequenceAt(i).getName().equals("CpG")) {
-          r = cgr;
-          System.out.println("cg renderer");
-      }
-*/
      nextSeq = av.getAlignment().getSequenceAt(i);
-     group = av.alignment.findGroup( nextSeq );
-     if( group!=null )
-     {
-       sr.drawSequence(g, group.cs, nextSeq,
-                      x1,
-                      x2,
-                      (int) ( (x1 - startx) * charWidth),
-                      offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),
-                      charWidth, charHeight,
-                      false, group.getDisplayBoxes(), group.getDisplayText(), group.getColourText(),
-                      null, i);
-     }
+     if(group==null || group!=av.alignment.findGroup( nextSeq ))
+        newGroup = true;
      else
+        newGroup = false;
+
+    group = av.alignment.findGroup( nextSeq );
+
+    sr.drawSequence(g, nextSeq, group,x1,x2,
+                 (x1 - startx) * charWidth,
+                 offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),
+                 charWidth,charHeight,null, i);
+
+
+     if( group!=null )
      {
-       sr.drawSequence(g, cs, nextSeq,
-                      x1,
-                      x2,
-                      (int) ( (x1 - startx) * charWidth),
-                      offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),
-                      charWidth,charHeight,
-                      showScores, av.getShowBoxes(),  av.getShowText(), av.getColourText(),
-                      null, i);
 
-     }
+        g.setColor(Color.GREEN);
 
+        sx = (group.getStartRes()-startx)*charWidth;
+        sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight());
+        ex = (group.getEndRes()+1-startx)*charWidth;
+        ey = offset + AlignmentUtil.getPixelHeight(starty, i+1, av.getCharHeight());
 
-    }
 
+        if (newGroup)
+        {
+          g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box
+          g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box
+        }
+
+        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;
+
+     }
+
+    }
 
+    /// Highlight search Results once all sequences have been drawn
     if(displaySearch)
     {
       for(int r=0; r<searchResults.length; r+=3)
@@ -373,18 +392,61 @@ public class SeqCanvas extends JPanel
           ssr.drawHighlightedText(g, av.getAlignment().getSequenceAt(searchSeq),
                                   searchStart,
                                   searchEnd,
-                                  (int) ( (searchStart - startx) * charWidth),
+                                  (searchStart - startx) * charWidth,
                                   offset +
                                   AlignmentUtil.getPixelHeight(starty, searchSeq,
               charHeight),
-                                  (int) charWidth,
+                                  charWidth,
                                   charHeight);
-
         }
       }
     }
 
 
+
+
+    /*bg.drawImage(image,0,0,null);
+  int size=width*height;
+  int pixel, b, x,y;
+  if(value!=0 )
+  {
+    if(painted!=null)
+    {
+     for(int i=0; i<size; i++)
+     {
+      if(painted[i] == value)
+      {
+         x = (i%width);
+         y = (i-x)/width;
+         pixel = buf.getRGB(x,y);
+         b = pixel & 0x000000ff;
+         pixel = (105<<24) | (0<<16)+32 | (0<<8)+32 | b;
+         buf.setRGB(x,y,pixel);
+     }
+     }
+
+    }
+    else
+    {
+     for(int i=0; i<size; i++)
+     {
+      if(paintedShort[i] == value)
+      {
+       x = (i%width);
+       y = (i-x)/width;
+       pixel = buf.getRGB(x,y);
+       b = pixel & 0x000000ff;
+       pixel = (105<<24) | (0<<16) | (0<<8) | b;
+       buf.setRGB(x,y,pixel);
+     }
+     }
+    }
+
+   }
+   oldvalue = value;
+   return (Image)buf;
+*/
+
   }
 
  // public int groupX, groupY, groupendX, groupendY;
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 1714a31..ebcbc76 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -27,10 +27,10 @@ public class SeqPanel extends JPanel
   // if character is inserted or deleted, we will need to recalculate the conservation
   int seqEditOccurred = -1;
 
-  public SeqPanel(AlignViewport av, AlignmentPanel p) {
-    this.av         = av;
+  public SeqPanel(AlignViewport avp, AlignmentPanel p) {
+    this.av         = avp;
 
-    seqCanvas  = new SeqCanvas(av);
+    seqCanvas  = new SeqCanvas(avp);
     setLayout(new BorderLayout());
     add(seqCanvas, BorderLayout.CENTER);
 
@@ -41,15 +41,30 @@ public class SeqPanel extends JPanel
       public void mouseMoved(MouseEvent evt)
       {  doMouseMoved(evt);   }
       public void mouseDragged(MouseEvent evt)
-      {      doMouseDragged(evt);  }
+      {
+        if(av.groupDefiningMode)
+          doMouseDraggedDefineMode(evt);
+        else
+          doMouseDragged(evt);
+      }
     });
 
     addMouseListener( new MouseAdapter()
     {
       public void mouseReleased(MouseEvent evt)
-      {  doMouseReleased(evt);  }
+      {
+        if(av.groupDefiningMode)
+          doMouseReleasedDefineMode(evt);
+        else
+          doMouseReleased(evt);
+      }
       public void mousePressed(MouseEvent evt)
-      {  doMousePressed(evt);   }
+      {
+        if(av.groupDefiningMode)
+          doMousePressedDefineMode(evt);
+        else
+          doMousePressed(evt);
+      }
 
     });
     repaint();
@@ -59,7 +74,7 @@ public class SeqPanel extends JPanel
   public void doMouseReleased(MouseEvent evt) {
 
     int x = evt.getX();
-    int res = (int)(x/av.getCharWidth()) + av.getStartRes();
+    int res = x/av.getCharWidth() + av.getStartRes();
 
     endres = res;
 
@@ -79,15 +94,15 @@ public class SeqPanel extends JPanel
   }
 
   public void doMousePressed(MouseEvent evt) {
-  parent.alignFrame.addHistoryItem("sequence edit");
+    parent.alignFrame.addHistoryItem("sequence edit");
     int seq;
     int res;
 
     int x = evt.getX();
     int y = evt.getY();
 
-    res = (int)(x/av.getCharWidth()) + av.getStartRes();
-    seq = (y)/av.getCharHeight() + av.getStartSeq();
+    res = x/av.getCharWidth() + av.getStartRes();
+    seq = y/av.getCharHeight() + av.getStartSeq();
 
     if (seq < av.getAlignment().getHeight() && res < av.getAlignment().getSequenceAt(seq).getLength())
     {
@@ -126,7 +141,7 @@ public class SeqPanel extends JPanel
       int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
 
 
-      res =   (int)((y/chunkHeight)*(getWidth()/av.charWidth)) +  (int)(x/av.getCharWidth()) + av.getStartRes();
+      res =   (int)((y/chunkHeight)*(getWidth()/av.charWidth)) +  x/av.getCharWidth() + av.getStartRes();
 
       System.out.println( ((y/chunkHeight)*(getWidth()/av.charWidth)) +" "+((x / av.getCharWidth()) + av.getStartRes()) );
       y %= chunkHeight;
@@ -137,7 +152,7 @@ public class SeqPanel extends JPanel
     }
     else
     {
-      res = (int) (x / av.getCharWidth()) + av.getStartRes();
+      res = x / av.getCharWidth()  + av.getStartRes();
       seq = y / av.getCharHeight() + av.getStartSeq();
     }
 
@@ -163,7 +178,7 @@ public class SeqPanel extends JPanel
     editFlag = true;
     int x = evt.getX();
 
-    int res = (int)(x/av.getCharWidth()) + av.getStartRes();
+    int res = x/av.getCharWidth() + av.getStartRes();
     if (res < 0) {res = 0;}
 
     if (res  != lastres) {
@@ -318,7 +333,7 @@ public class SeqPanel extends JPanel
     seqCanvas.paintFlag = true;
     if (av.getSelection().size() == 0)
     {
-      seqCanvas.cs = cs;
+      seqCanvas.globalColorScheme = cs;
       for (int i = 0; i < av.alignment.getGroups().size();i++)
       {
         SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);
@@ -392,6 +407,9 @@ public class SeqPanel extends JPanel
 
   boolean isNewSelection(SequenceGroup sg)
   {
+    if(sg==null)
+      return true;
+
     if(sg.getSize()!=av.getSelection().size())
       return true;
 
@@ -408,8 +426,65 @@ public class SeqPanel extends JPanel
     if(av.getSelection().size()>0)
        return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;
     else
-      return seqCanvas.cs;
+      return seqCanvas.globalColorScheme;
+  }
+
+  public void doMousePressedDefineMode(MouseEvent evt)
+  {
+    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
+    int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
+
+    stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq));
+
+    if(stretchGroup!=null  && stretchGroup.getEndRes()==res)
+    {
+      // Edit end res position of selected group
+      changeEndRes = true;
+    }
+    else if(stretchGroup!=null  && stretchGroup.getStartRes()==res)
+    {
+      // Edit end res position of selected group
+      changeStartRes = true;
+    }
+
+
+  }
+
+  boolean changeEndRes = false;
+  boolean changeStartRes = false;
+  SequenceGroup stretchGroup = null;
+
+  public void doMouseReleasedDefineMode(MouseEvent evt)
+  {
+    changeEndRes = false;
+    changeStartRes = false;
+  }
+
+  public void doMouseDraggedDefineMode(MouseEvent evt)
+  {
+    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
+    int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
+
+    if(res<av.getStartRes())
+      res = av.getStartRes();
+    else if(res>av.getEndRes())
+      res = av.getEndRes();
+
+    if(changeEndRes)
+    {
+      if(res>stretchGroup.getStartRes()-1)
+        stretchGroup.setEndRes( res );
+    }
+    else if(changeStartRes)
+    {
+      if(res<stretchGroup.getEndRes()+1)
+        stretchGroup.setStartRes( res );
+    }
+    seqCanvas.paintFlag = true;
+    repaint();
+
   }
+
 }
 
 
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 192e252..4264c64 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -2,14 +2,22 @@ package jalview.gui;
 
 import jalview.datamodel.*;
 import jalview.schemes.*;
-
 import java.awt.*;
 import java.util.*;
 
 public class SequenceRenderer implements RendererI
 {
+  AlignViewport av;
   FontMetrics fm;
   boolean renderGaps = true;
+  SequenceGroup currentSequenceGroup = null;
+  Color color;
+
+  public SequenceRenderer(AlignViewport av)
+  {
+    this.av = av;
+  }
+
 
   public void renderGaps(boolean b)
   {
@@ -26,21 +34,18 @@ public class SequenceRenderer implements RendererI
     return c;
   }
 
+  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;
 
-  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) {
-
+    drawBoxes(g, seq, start, end, x1, y1, (int) width, height, pid);
 
-    if (displayBoxes)
-        drawBoxes(g,cs,seq,start,end,x1,y1,(int)width, height,freq);
+    fm = g.getFontMetrics();
+    drawText(g,seq,start,end,x1,y1,(int)width,height);
 
-    if (displayText)
-    {
-        fm = g.getFontMetrics();
-        drawText(g,cs,colourText,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();
 
@@ -49,10 +54,22 @@ public class SequenceRenderer implements RendererI
     int curStart = x1;
     int curWidth = width;
 
+    if(currentSequenceGroup!=null && currentSequenceGroup.getDisplayBoxes())
+    {
+      curStart = currentSequenceGroup.getStartRes();
+      curWidth = currentSequenceGroup.getEndRes();
+    }
+
   //  int threshold = 80;
 
-    while (i <= end && i < length) {
-      Color c = getResidueBoxColour(cs,seq,i);
+    while (i <= end && i < length)
+    {
+      if(inCurrentSequenceGroup(i))
+      {
+        color = getResidueBoxColour(currentSequenceGroup.cs, seq, i);
+      }
+      else
+        color = getResidueBoxColour(av.getGlobalColourScheme(), seq, i);
 
     //  Hashtable hash  = (Hashtable)freq.elementAt(i-start);
     //  String    s     = (String)hash.get("maxResidue");
@@ -82,12 +99,12 @@ public class SequenceRenderer implements RendererI
 	}
       }*/
 
-      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;
@@ -100,7 +117,7 @@ public class SequenceRenderer implements RendererI
     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)
+  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;
@@ -118,17 +135,31 @@ public class SequenceRenderer implements RendererI
         if(!renderGaps && (s=='-' || s=='.' || s==' '))
           continue;
 
-        if (colText)
+
+        if (inCurrentSequenceGroup(i))
         {
-            Color 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
+          g.setColor(Color.black);
 
       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)
-- 
1.7.10.2