X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=f9ab0156721ee9f892cb37be967ef5d761238b9b;hb=09b64bea954c283bde1d21c0a230f51f1ae89373;hp=00b4e954f52b9a614f6eec87a7ae011260ca57a3;hpb=a11e13d8fffacf8115a4d83e4254bf94a87d6600;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 00b4e95..f9ab015 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -2,26 +2,20 @@ package jalview.gui;
 
 import java.awt.*;
 import javax.swing.*;
-import java.awt.event.*;
 import jalview.datamodel.*;
-import jalview.schemes.*;
 import jalview.analysis.*;
 
 
 public class SeqCanvas extends JPanel
 {
-    ColourSchemeI globalColorScheme = null;
+     FeatureRenderer fr;
     Image             img;
     Graphics          gg;
     int               imgWidth;
     int               imgHeight;
 
     AlignViewport     av;
-    int pady = 2;
-    int oldstartx;
-    int oldstarty;
-    int oldendx;
-    int oldendy;
+
     public boolean paintFlag = false;
 
     boolean showScores = false;
@@ -35,19 +29,27 @@ public class SeqCanvas extends JPanel
     public SeqCanvas(AlignViewport av)
     {
 	this.av         = av;
+       fr = new FeatureRenderer(av);
        setLayout(new BorderLayout());
+       PaintRefresher.Register(this);
 
     }
 
-  public void drawScale(int startx, int endx,int charWidth, int charHeight,int ypos) {
+  public void drawScale(Graphics g, int startx, int endx,int ypos) {
       int scalestartx = startx - startx%10 + 10;
 
-      gg.setColor(Color.black);
+      g.setColor(Color.black);
+
+      for (int i=scalestartx;i < endx;i+= 10)
+      {
+          String string = String.valueOf(i);
+          g.drawString(string,(i-startx-1)*av.charWidth,ypos - av.charHeight/2);
+
+          g.drawLine( (i-startx-1)*av.charWidth +av.charWidth/2, ypos+2 - av.charHeight/2,
+                    (i-startx-1)*av.charWidth +av.charWidth/2, ypos-2 );
 
-      for (int i=scalestartx;i < endx;i+= 10) {
-	  String string = String.valueOf(i);
-	  gg.drawString(string,(int)((i-startx-1)*charWidth),ypos+15 - charHeight*(2));
       }
+
   }
 
 
@@ -62,244 +64,70 @@ public class SeqCanvas extends JPanel
  * in the adjustment listener in SeqPanel when the scrollbars move.
  */
 
-  public void paintComponent(Graphics g) {
-
-    AlignmentI da = av.getAlignment();
+  public void paintComponent(Graphics g)
+  {
 
-    if (img == null ||
-        imgWidth  !=  getWidth()  ||
-        imgHeight !=  getHeight()
-        || paintFlag)
+    if (img==null ||  imgWidth!=getWidth() || imgHeight!=getHeight() || paintFlag)
     {
-
-      imgWidth  = (getWidth() > 0 ? getWidth() : 1);
-      imgHeight = (getHeight() > 0 ? getHeight() : 1);
-
+      imgWidth  = getWidth();
+      imgHeight = getHeight();
       img = createImage(imgWidth,imgHeight);
       gg  = img.getGraphics();
-
       gg.setFont(av.getFont());
-
-      oldstartx = -1;
-      oldendx   = -1;
-      oldstarty = -1;
-      oldendy   = -1;
       paintFlag = false;
     }
 
-    int startx = av.getStartRes();
-    int starty = av.getStartSeq();
-
-    int endx   = av.getEndRes();
-    int endy   = av.getEndSeq();
-
-    int charWidth  = av.getCharWidth();
-    int charHeight = av.getCharHeight();
 
-    chunkWidth  =   getWidth()/charWidth;
-    chunkHeight =  (da.getHeight() + 2)*charHeight;
+    chunkWidth  =   getWidth()/av.charWidth;
+    chunkHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
 
     av.setChunkHeight(chunkHeight);
     av.setChunkWidth(chunkWidth);
 
-    int offy = av.getStartSeq();
+    fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);
 
-    if (oldendx == -1) {
-      fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);
-
-     if (av.getWrapAlignment()) {
-	  startx = (int)(offy/chunkWidth)*chunkWidth;
-	  endx   = startx + chunkWidth;
-	  starty = offy%chunkHeight;
-	  endy   = starty + da.getHeight();
-
-	  int ypos     = 0;
-	  int rowstart = starty;
-
-	  if (starty == 0) {
-	      ypos = 2*charHeight;
-	  } else if (starty == 1) {
-	      starty = 0;
-	      ypos = charHeight;
-	  }
-
-	  if (endy > da.getHeight()) {
-	      endy = da.getHeight();
-	  }
-
-	  if (endx > da.getWidth()) {
-	      endx = da.getWidth();
-	  }
-
-	  if (rowstart < 2) {
-	      drawScale(startx,endx,charWidth,charHeight,ypos);
-	  }
-
-	  drawPanel(gg,startx,endx,starty,endy,startx,starty,ypos);
-
-	  if (rowstart == 0) {
-	      ypos = ypos + chunkHeight;
-	  } else if (rowstart == 1) {
-	      ypos = ypos + chunkHeight;
-	  } else {
-	      ypos   = ypos + chunkHeight - rowstart*charHeight;
-	  }
+    if (av.getWrapAlignment())
+      drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
+    else
+      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);
 
-	  startx += chunkWidth;
-	  endx   = startx + chunkWidth;
-	  starty = 0;
 
-	  if (endx > da.getWidth()) {
-	      endx = da.getWidth();
-	  }
-	  // Draw the rest of the panels
+    g.drawImage(img,0,0,this);
 
-	  while (ypos <= getHeight()) {
-	      drawScale(startx,endx,charWidth,charHeight,ypos);
-	      drawPanel(gg,startx,endx,0,da.getHeight(),startx,starty,ypos);
+  }
 
-	      ypos   += chunkHeight;
-	      startx += chunkWidth;
-	      endx   = startx + chunkWidth;
+  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)
+  {
+      AlignmentI da = av.getAlignment();
 
-	      if (endy > da.getHeight()) {
-		  endy = da.getHeight();
-	      }
+      int cWidth  =   canvasWidth/av.charWidth;
+      int cHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
 
-	      if (endx > da.getWidth()) {
-		  endx = da.getWidth();
-	      }
+      int  endx   = startRes+cWidth-1;
+      int ypos  = 2*av.charHeight;
 
-	  }
-      }
-      else
+      while (ypos <= canvasHeight)
       {
-	  drawPanel(gg,startx,endx,starty,endy,startx,starty,0);
-
-	  oldstartx = startx;
-	  oldendx   = endx;
-	  oldstarty = starty;
-	  oldendy   = endy;
-
-      }
-    }
-
-    else if (oldstartx < startx)
-    {
-      // This is dragging horizontal scrollbar to the right
-
-      int delx  = (startx - oldstartx)   * charWidth;
-      int delx2 = (oldendx - startx + 1) * charWidth;
-
-      gg.copyArea(delx,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),-delx,0);
-
-      if (startx > oldendx)
-	drawPanel(gg,startx,endx,starty,endy,startx,starty,0);
-      else
-	drawPanel(gg,oldendx+1,endx,starty,endy,startx,starty,0);
-
-
-      oldstartx = startx;
-      oldendx   = endx;
-
-    } else if (oldstartx > startx)
-    {
-     // Horizontal scrollbar pulled to the left
-
-      int delx  = (oldstartx - startx)    * charWidth;
-      int delx2 = (endx - oldstartx +1)   * charWidth;
-
-      gg.copyArea(0,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),delx,0);
-
-      if (oldstartx > endx) {
-	drawPanel(gg,startx,endx,starty,endy,startx,starty,0);
-      } else {
-	drawPanel(gg,startx,oldstartx-1,starty,endy,startx,starty,0);
-      }
-
-      oldstartx = startx;
-      oldendx   = endx;
-
-    }  else if (oldstarty < starty) {
-      // Vertical scrollbar down
-      int dely  = AlignmentUtil.getPixelHeight(oldstarty,starty,charHeight);
-      int dely2 = AlignmentUtil.getPixelHeight(starty,oldendy,charHeight);
-
-      gg.copyArea(0,dely,(endx-startx+1)*charWidth,dely2,0,-dely);
-
-      if (starty > oldendy) {
-	drawPanel(gg,startx,endx,starty,endy,startx,starty,0);
-      } else {
-	drawPanel(gg,startx,endx,oldendy,endy,startx,starty,0);
-      }
-
-      oldstarty = starty;
-      oldendy   = endy;
-
-    } else if (oldstarty > starty) {
-
-      // Vertical scrollbar up
-      int dely  = AlignmentUtil.getPixelHeight(endy,oldendy,charHeight);
-      int dely2 = AlignmentUtil.getPixelHeight(oldstarty,endy,charHeight);
+        drawScale(g, startRes, endx, ypos);
+        drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos);
 
-      gg.copyArea(0,0,(endx-startx+1)*charWidth,dely2,0,dely);
+        ypos += cHeight;
+        startRes += cWidth;
+        endx = startRes + cWidth - 1;
 
-      if (oldstarty > endy) {
-	drawPanel(gg,startx,endx,starty,endy,startx,starty,0);
-      } else {
-	drawPanel(gg,startx,endx,starty,oldstarty,startx,starty,0);
+        if (endx > da.getWidth())
+          endx = da.getWidth();
       }
 
-      oldstarty = starty;
-      oldendy   = endy;
-    }
-
-    if ((oldendy -oldstarty) > (getWidth() / av.getCharWidth())) {
-      System.out.println("LIMITS ERROR LIMITS ERROR");
-      System.out.println("Corrds " + (oldendy-oldstarty) + " " + (getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth());
-    }
-
-
-  //  gg.setColor(Color.red);
-  //  gg.drawRect( groupX, groupY, groupendX-groupX, groupendY-groupY );
-   // gg.drawRect( groupX+1, groupY+1, groupendX-groupX-2, groupendY-groupY-2 );
-
-
-    g.drawImage(img,0,0,this);
-
   }
 
 
-
-
   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);
-    System.out.println("                      y1     = " + y1);
-    System.out.println("                      y2     = " + y2);
-    System.out.println("                      startx = " + startx);
-    System.out.println("                      starty = " + starty);
-*/
 
     g.setFont(av.getFont());
-    int            charWidth  = av.getCharWidth();
-    int            charHeight = av.getCharHeight();
     RendererI sr = av.getRenderer();
 
-
     /*Vector    pid    = av.getConsensus(false);
     Vector tmpseq = new Vector();
     for (int i = 0; i < av.getAlignment().getHeight(); i++)
@@ -316,68 +144,108 @@ public class SeqCanvas extends JPanel
 
 */
 
-    if (y2 > starty && y1 < av.getEndSeq())
+   /* if (y2 > starty && y1 < av.getEndSeq())
     {
        fillBackground(g,
-                   Color.WHITE,
+                   Color.red,
                    (x1-startx)*charWidth,
                    offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()),
                    (x2-x1+1)*charWidth,
                    offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight()));
-    }
+    }*/
 
     SequenceI nextSeq;
-    SequenceGroup group=null;
-    boolean newGroup=false;
-    int sx, sy, ex, ey;
-    int oldStartX=0,oldEndX=0,oldY=0;
+
+    /// First draw the sequences
+    /////////////////////////////
     for (int i = y1 ; i < y2 ;i++)
     {
      nextSeq = av.getAlignment().getSequenceAt(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);
+     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( group!=null )
+     if(av.showSequenceFeatures)
      {
+       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);
+     }
+    }
+    //
+    /////////////////////////////////////
 
-        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());
+    // 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 (newGroup)
+    if (group != null)
+      do
+      {
+        int oldY = -1;
+        int i = 0;
+        boolean inGroup = false;
+        for (i = y1; i < y2; i++)
+        {
+          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)
         {
-          g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box
-          g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box
+          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
+        groupIndex++;
+        if (groupIndex >= groups.size())
+          break;
 
-        oldStartX = sx;
-        oldEndX = ex;
-        oldY = ey;
+        group = (SequenceGroup) groups.elementAt(groupIndex);
 
-     }
+      }
+      while (groupIndex < groups.size());
 
-    }
 
     /// Highlight search Results once all sequences have been drawn
+    //////////////////////////////////////////////////////////
     if(displaySearch)
     {
       for(int r=0; r<searchResults.length; r+=3)
@@ -386,71 +254,24 @@ public class SeqCanvas extends JPanel
         int searchStart = searchResults[r+1];
         int searchEnd = searchResults[r+2];
 
-        if (searchSeq >= y1 && searchSeq <= y2)
+        if (searchSeq >= y1 && searchSeq < y2)
         {
           SequenceRenderer ssr = (SequenceRenderer) sr;
-          ssr.drawHighlightedText(g, av.getAlignment().getSequenceAt(searchSeq),
+          ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),
                                   searchStart,
                                   searchEnd,
-                                  (searchStart - startx) * charWidth,
+                                  (searchStart - startx) * av.charWidth,
                                   offset +
                                   AlignmentUtil.getPixelHeight(starty, searchSeq,
-              charHeight),
-                                  charWidth,
-                                  charHeight);
+              av.charHeight),
+                                  av.charWidth,
+                                  av.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;
-
   public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) {
     g.setColor(c);
     g.fillRect(x1,y1,width,height);