X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=f3e753226f2b5a9073703a25e5132bc8b6b04c01;hb=9be2898dd1635c87539a90de321975f043d005f3;hp=c33f3ed371da55393dac4948cb9c8679fd06c619;hpb=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index c33f3ed..f3e7532 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,25 +1,23 @@
 package jalview.gui;
 
 import java.awt.*;
+import java.awt.image.*;
 import javax.swing.*;
-import java.awt.event.*;
 import jalview.datamodel.*;
-import jalview.schemes.*;
 import jalview.analysis.*;
 
 
-public class SeqCanvas extends JPanel
+public class SeqCanvas extends JComponent
 {
      FeatureRenderer fr;
-    Image             img;
-    Graphics          gg;
+     SequenceRenderer sr;
+    BufferedImage             img;
+    Graphics2D          gg;
     int               imgWidth;
     int               imgHeight;
 
     AlignViewport     av;
 
-    public boolean paintFlag = false;
-
     boolean showScores = false;
     boolean displaySearch = false;
     int [] searchResults = null;
@@ -27,33 +25,142 @@ public class SeqCanvas extends JPanel
     int chunkHeight;
     int chunkWidth;
 
+    boolean fastPaint = false;
+
 
     public SeqCanvas(AlignViewport av)
     {
 	this.av         = av;
        fr = new FeatureRenderer(av);
+       sr = new SequenceRenderer(av);
        setLayout(new BorderLayout());
        PaintRefresher.Register(this);
 
     }
 
-  public void drawScale(Graphics g, int startx, int endx,int ypos) {
-      int scalestartx = startx - startx%10 + 10;
+  void drawNorthScale(Graphics g, int startx, int endx,int ypos) {
+    int scalestartx = startx - startx % 10 + 10;
 
-      g.setColor(Color.black);
+    g.setColor(Color.black);
+
+    // NORTH SCALE
+    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);
 
-      for (int i=scalestartx;i < endx;i+= 10)
+      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);
+
+    }
+  }
+
+  void drawWestScale(Graphics g, int startx, int endx, int ypos)
+  {
+    FontMetrics fm = getFontMetrics(av.getFont());
+    ypos+= av.charHeight;
+      // EAST SCALE
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      SequenceI seq = av.alignment.getSequenceAt(i);
+      int index = startx;
+      int value = -1;
+      while (index < endx)
       {
-          String string = String.valueOf(i);
-          g.drawString(string,(i-startx-1)*av.charWidth,ypos - av.charHeight/2);
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        {
+          index++;
+          continue;
+        }
 
-          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 );
+        value = av.alignment.getSequenceAt(i).findPosition(index);
+        break;
+      }
+      if(value!=-1)
+      {
+        int x = LABEL_WEST - fm.stringWidth(value+"");
+        g.drawString(value + "", x,  ypos +  i*av.charHeight - av.charHeight/5);
+      }
+    }
+  }
 
+  void drawEastScale(Graphics g, int startx, int endx, int ypos)
+{
+    ypos+= av.charHeight;
+    // EAST SCALE
+  for (int i = 0; i < av.alignment.getHeight(); i++)
+  {
+    SequenceI seq = av.alignment.getSequenceAt(i);
+    int index = endx;
+    int value = -1;
+    while (index > startx)
+    {
+      if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+      {
+        index--;
+        continue;
       }
 
+      value = av.alignment.getSequenceAt(i).findPosition(index);
+      break;
+    }
+    if(value!=-1)
+       g.drawString(value + "", 0,  ypos +  i*av.charHeight - av.charHeight/5);
   }
 
+}
+
+
+
+
+
+public void fastPaint(int horizontal, int vertical)
+{
+    if (horizontal == 0 && vertical == 0 || gg==null)
+      return;
+
+    gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
+                -vertical * av.charHeight);
+
+    int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,
+        transX = 0, transY = 0;
+    if (horizontal > 0) // scrollbar pulled right, image to the left
+    {
+      transX = (er - sr - horizontal) * av.charWidth;
+      sr = er - horizontal;
+    }
+    else if (horizontal < 0)
+      er = sr - horizontal;
+
+    else if (vertical > 0) // scroll down
+    {
+      ss = es - vertical;
+      if(ss<av.startSeq) // ie scrolling too fast, more than a page at a time
+        ss = av.startSeq;
+      else
+        transY = imgHeight - vertical * av.charHeight;
+    }
+    else if (vertical < 0)
+    {
+      es = ss - vertical;
+      if(es > av.endSeq)
+        es = av.endSeq;
+    }
+
+
+    gg.translate(transX, transY);
+
+    gg.setColor(Color.white);
+    gg.fillRect(0,0, (er-sr+1)*av.charWidth, (es-ss)*av.charHeight);
+    drawPanel(gg, sr, er, ss, es, sr, ss, 0);
+    gg.translate( -transX, -transY);
+
+    fastPaint = true;
+    repaint();
+
+}
 
 /**
  * Definitions of startx and endx (hopefully):
@@ -66,204 +173,276 @@ public class SeqCanvas extends JPanel
  * in the adjustment listener in SeqPanel when the scrollbars move.
  */
 
-  public void paintComponent(Graphics g)
+  public void paint(Graphics g)
   {
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getWidth(), getHeight());
 
-    if (img==null ||  imgWidth!=getWidth() || imgHeight!=getHeight() || paintFlag)
+    if (fastPaint)
     {
+      g.drawImage(img, 0, 0, this);
+      fastPaint = false;
+      return;
+    }
+
+    // this draws the whole of the alignment
       imgWidth  = getWidth();
       imgHeight = getHeight();
-      img = createImage(imgWidth,imgHeight);
-      gg  = img.getGraphics();
+      if(imgWidth==0 || imgHeight==0)
+        return;
+
+      imgWidth -= imgWidth%av.charWidth;
+      imgHeight-= imgHeight%av.charHeight;
+
+      img = new BufferedImage(imgWidth,imgHeight,BufferedImage.TYPE_INT_RGB);
+      gg  = (Graphics2D)img.getGraphics();
       gg.setFont(av.getFont());
-      paintFlag = false;
-    }
+      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
 
+      gg.setColor(Color.white);
+      gg.fillRect(0,0,imgWidth,imgHeight);
 
-    chunkWidth  =   getWidth()/av.charWidth;
+    chunkWidth  =   getWrappedCanvasWidth( getWidth() );
     chunkHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
 
     av.setChunkHeight(chunkHeight);
     av.setChunkWidth(chunkWidth);
 
-    fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);
 
     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);
 
+    g.drawImage(img, 0, 0, this);
+
+  }
+
+  int LABEL_WEST, LABEL_EAST;
+  public int getWrappedCanvasWidth(int cwidth)
+  {
+    FontMetrics fm = getFontMetrics(av.getFont());
+
+    LABEL_EAST = 0;
+    LABEL_WEST = 0;
+
+    if(av.scaleRightWrapped)
+      LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" );
 
-    g.drawImage(img,0,0,this);
+    if(av.scaleLeftWrapped)
+      LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" );
 
+    return  (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
   }
 
   public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)
   {
-      AlignmentI da = av.getAlignment();
+      AlignmentI al = av.getAlignment();
 
-      int cWidth  =   canvasWidth/av.charWidth;
+      FontMetrics fm = getFontMetrics(av.getFont());
+
+      int LABEL_EAST = 0;
+      if(av.scaleRightWrapped)
+        LABEL_EAST = fm.stringWidth( al.getWidth()+"000" );
+      int LABEL_WEST = 0;
+      if(av.scaleLeftWrapped)
+        LABEL_WEST = fm.stringWidth(al.getWidth()+"0");
+
+
+      int cWidth  =   (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
       int cHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
 
       int  endx   = startRes+cWidth-1;
-      int ypos  = 2*av.charHeight;
+      int  ypos  = 2*av.charHeight;
 
-      while (ypos <= canvasHeight)
+      while (ypos <= canvasHeight && startRes<av.alignment.getWidth() )
       {
-        drawScale(g, startRes, endx, ypos);
-        drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos);
+        g.setColor(Color.black);
+
+        if(av.scaleLeftWrapped)
+          drawWestScale(g, startRes, endx, ypos);
+
+        if(av.scaleRightWrapped)
+        {
+          g.translate(canvasWidth - LABEL_EAST +av.charWidth, 0);
+          drawEastScale(g, startRes, endx, ypos);
+          g.translate( - (canvasWidth - LABEL_EAST+av.charWidth), 0);
+        }
+
+        g.translate(LABEL_WEST,0);
+        if(av.scaleAboveWrapped)
+          drawNorthScale(g, startRes, endx, ypos);
+
+
+        // When printing we have an extra clipped region,
+        // the Printable page which we need to account for here
+        Shape clip = g.getClip();
+        if(clip==null)
+          g.setClip(0, 0, cWidth*av.charWidth, canvasHeight);
+        else
+          g.setClip(0,
+                    (int)clip.getBounds().getY(),
+                    cWidth*av.charWidth,
+                    (int)clip.getBounds().getHeight()
+                    );
+
+        drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
+        g.setClip(clip);
+        g.translate(-LABEL_WEST,0);
 
         ypos += cHeight;
         startRes += cWidth;
         endx = startRes + cWidth - 1;
 
-        if (endx > da.getWidth())
-          endx = da.getWidth();
+        if (endx > al.getWidth())
+          endx = al.getWidth();
       }
 
   }
 
 
-  public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
-
+  synchronized public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
 
+    Graphics2D g = (Graphics2D)g1;
     g.setFont(av.getFont());
-    int            charWidth  = av.getCharWidth();
-    int            charHeight = av.getCharHeight();
-    RendererI sr = av.getRenderer();
+    sr.renderGaps(av.renderGaps);
 
-    /*Vector    pid    = av.getConsensus(false);
-    Vector tmpseq = new Vector();
-    for (int i = 0; i < av.getAlignment().getHeight(); i++)
-	if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
-	    tmpseq.addElement(av.getAlignment().getSequenceAt(i));
-
-    if (sr instanceof SequenceRenderer)
-	pid    = AAFrequency.calculate(tmpseq,x1,x2);
-
-    else if (sr instanceof GraphRenderer)
-	pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),
-				       av.getAlignment().getSequences(),
-				       av.getPIDWindow(),x1,x2);
-
-*/
-
-   /* if (y2 > starty && y1 < av.getEndSeq())
-    {
-       fillBackground(g,
-                   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;
-    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);
+     nextSeq = av.alignment.getSequenceAt(i);
 
-     group = av.alignment.findGroup( nextSeq );
-     groups = av.alignment.findAllGroups( nextSeq );
-
-     sr.drawSequence(g, nextSeq, groups,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);
 
      if(av.showSequenceFeatures)
      {
-       fr.drawSequence(g, nextSeq, groups, x1, x2,
-                       (x1 - startx) * charWidth,
+       fr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ), x1, x2,
+                       (x1 - startx) * av.charWidth,
                        offset +
-                       AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),
-                       charWidth, charHeight, null, i);
+                       AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
+                       av.charWidth, av.charHeight);
      }
+    }
+    //
+    /////////////////////////////////////
 
+    // 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)*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 (!inGroup)
+    if (group != null)
+      do
+      {
+        int oldY = -1;
+        int i = 0;
+        boolean inGroup = false;
+        int top=-1, bottom =-1;
+        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 -1;
+
+          if (sx < getWidth()
+              && ex > 0
+              && group.sequences.contains(av.alignment.getSequenceAt(i)))
+          {
+            if (bottom == -1 &&
+                !group.sequences.contains(av.alignment.getSequenceAt(i + 1)))
+              bottom = sy + av.charHeight ;
+
+            if (!inGroup)
+            {
+              if (top == -1 && i==0 ||
+                  !group.sequences.contains(av.alignment.getSequenceAt(i - 1)))
+                top = sy;
+
+
+              oldY = sy;
+              inGroup = true;
+              if (group == av.getSelectionGroup())
+              {
+                g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[]{5f,3f}, 0f ));
+                g.setColor(Color.RED);
+              }
+              else
+              {
+                g.setStroke(new BasicStroke());
+                g.setColor(group.getOutlineColour());
+              }
+            }
+          }
+          else
+          {
+            if (inGroup)
+            {
+              g.drawLine(sx, oldY, sx, sy );
+              g.drawLine(sx+ex, oldY, sx+ex, sy );
+
+              if (top != -1)
+              {
+                g.drawLine(sx, top, sx + ex, top);
+                top =-1;
+              }
+              if (bottom != -1)
+              {
+                g.drawLine(sx, bottom, sx + ex, bottom);
+                bottom = -1;
+              }
+
+
+              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
+        if (inGroup)
+        {
 
-        oldStartX = sx;
-        oldEndX = ex;
-        oldY = ey;
+          if(top!=-1)
+          {
+            g.drawLine(sx, top, sx + ex, top);
+            top =-1;
+          }
+          if(bottom!=-1)
+           {
+             g.drawLine(sx, bottom-1, sx + ex, bottom-1);
+             bottom = -1;
+
+           }
+          sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
+          g.drawLine(sx, oldY, sx, sy );
+          g.drawLine(sx+ex, oldY, sx+ex, sy );
+          inGroup = false;
+        }
+        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.getRubberbandGroup();
-     if( group != null && group.sequences.contains(nextSeq) )
-     {
-         g.setColor(Color.RED.brighter());
-         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 (!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)
@@ -275,29 +454,26 @@ public class SeqCanvas extends JPanel
         if (searchSeq >= y1 && searchSeq < y2)
         {
           SequenceRenderer ssr = (SequenceRenderer) sr;
+          if(searchStart<x1)
+            searchStart = x1;
+          if(searchEnd > x2)
+            searchEnd = x2;
           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);
         }
       }
     }
 
   }
 
-  public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) {
-    g.setColor(c);
-    g.fillRect(x1,y1,width,height);
-  }
 
-  public int getChunkWidth() {
-    return chunkWidth;
-  }
 
   public void highlightSearchResults(int [] results)
   {
@@ -309,7 +485,6 @@ public class SeqCanvas extends JPanel
 
     searchResults = results;
 
-    paintFlag = true;
     repaint();
   }