X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=698489e717589fb504aceb3f31b092f2707d443a;hb=1340920fd1b15c9bc8cd2284def7ec176a4989d5;hp=663977421e2242eb9a04b3140bf61b9eb23fb8f2;hpb=c6e2247dff4ec4158d0d234a22390fae4baff178;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 6639774..698489e 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -2,23 +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
 {
+     FeatureRenderer fr;
     Image             img;
-    Graphics          gg;
+    Graphics2D          gg;
     int               imgWidth;
     int               imgHeight;
 
     AlignViewport     av;
 
-    public boolean paintFlag = false;
-
     boolean showScores = false;
     boolean displaySearch = false;
     int [] searchResults = null;
@@ -26,26 +23,133 @@ public class SeqCanvas extends JPanel
     int chunkHeight;
     int chunkWidth;
 
+    boolean fastPaint = false;
+
 
     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) {
-      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);
+
+    // 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);
+
+      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);
 
-      gg.setColor(Color.black);
+    }
+  }
 
-      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));
+  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)
+      {
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        {
+          index++;
+          continue;
+        }
+
+        value = av.alignment.getSequenceAt(i).findPosition(index);
+        break;
+      }
+      if(value!=-1)
+      {
+        int x = fm.stringWidth("000") - 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)
+      return;
+
+    gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
+                -vertical * av.charHeight);
+
+    int sr = av.startRes, er = av.endRes + 1, 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
+    {
+      transY = imgHeight - vertical * av.charHeight;
+      ss = es - vertical;
+    }
+    else if (vertical < 0)
+      es = ss - vertical;
+
+    gg.translate(transX, transY);
+
+    gg.setColor(Color.white);
+    gg.fillRect(0,0, (er-sr)*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):
@@ -58,127 +162,122 @@ 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)
+  {
+    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();
+      if(imgWidth==0 || imgHeight==0)
+        return;
 
-      img = createImage(imgWidth,imgHeight);
-      gg  = img.getGraphics();
+      imgWidth -= imgWidth%av.charWidth;
+      imgHeight-= imgHeight%av.charHeight;
 
+      img = createImage(imgWidth,imgHeight);
+      gg  = (Graphics2D)img.getGraphics();
       gg.setFont(av.getFont());
+      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
 
-      paintFlag = false;
-    }
+      gg.setColor(Color.white);
+      gg.fillRect(0,0,imgWidth,imgHeight);
 
-    chunkWidth  =   getWidth()/av.charWidth;
-    chunkHeight =  (da.getHeight() + 2)*av.charHeight;
+    chunkWidth  =   getWrappedCanvasWidth( getWidth() );
+    chunkHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
 
     av.setChunkHeight(chunkHeight);
     av.setChunkWidth(chunkWidth);
 
 
+    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);
 
-    fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);
+    g.drawImage(img, 0, 0, this);
 
-    /* if (av.getWrapAlignment()) {
-        int offy = av.getStartSeq();
-	  startx = (int)(offy/chunkWidth)*chunkWidth;
-	  endx   = startx + chunkWidth;
-	  starty = offy%chunkHeight;
-	  endy   = starty + da.getHeight();
+  }
 
-	  int ypos     = 0;
-	  int rowstart = starty;
+  public int getWrappedCanvasWidth(int cwidth)
+  {
+    FontMetrics fm = getFontMetrics(av.getFont());
 
-	  if (starty == 0) {
-	      ypos = 2*charHeight;
-	  } else if (starty == 1) {
-	      starty = 0;
-	      ypos = charHeight;
-	  }
+    int LABEL_EAST = 0;
+    if(av.scaleRightWrapped)
+      LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" );
+    int LABEL_WEST = 0;
+    if(av.scaleLeftWrapped)
+      LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"0" );
 
-	  if (endy > da.getHeight()) {
-	      endy = da.getHeight();
-	  }
+    return  (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
+  }
 
-	  if (endx > da.getWidth()) {
-	      endx = da.getWidth();
-	  }
+  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)
+  {
+      AlignmentI al = av.getAlignment();
 
-	  if (rowstart < 2) {
-	      drawScale(startx,endx,charWidth,charHeight,ypos);
-	  }
+      FontMetrics fm = getFontMetrics(av.getFont());
 
-	  drawPanel(gg,startx,endx,starty,endy,startx,starty,ypos);
+      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" );
 
-	  if (rowstart == 0) {
-	      ypos = ypos + chunkHeight;
-	  } else if (rowstart == 1) {
-	      ypos = ypos + chunkHeight;
-	  } else {
-	      ypos   = ypos + chunkHeight - rowstart*charHeight;
-	  }
+      int cWidth  =   (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
+      int cHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
 
-	  startx += chunkWidth;
-	  endx   = startx + chunkWidth;
-	  starty = 0;
+      int  endx   = startRes+cWidth-1;
+      int  ypos  = 2*av.charHeight;
 
-	  if (endx > da.getWidth()) {
-	      endx = da.getWidth();
-	  }
-	  // Draw the rest of the panels
 
-	  while (ypos <= getHeight()) {
-	      drawScale(startx,endx,charWidth,charHeight,ypos);
-	      drawPanel(gg,startx,endx,0,da.getHeight(),startx,starty,ypos);
+      while (ypos <= canvasHeight && endx <al.getWidth())
+      {
+        g.setColor(Color.black);
 
-	      ypos   += chunkHeight;
-	      startx += chunkWidth;
-	      endx   = startx + chunkWidth;
+        if(av.scaleLeftWrapped)
+          drawWestScale(g, startRes, endx, ypos);
 
-	      if (endy > da.getHeight()) {
-		  endy = da.getHeight();
-	      }
+        if(av.scaleRightWrapped)
+        {
+          g.translate(canvasWidth - LABEL_EAST +av.charWidth, 0);
+          drawEastScale(g, startRes, endx, ypos);
+          g.translate( - (canvasWidth - LABEL_EAST+av.charWidth), 0);
+        }
 
-	      if (endx > da.getWidth()) {
-		  endx = da.getWidth();
-	      }
 
-	  }
-      }
-      else*/
-      {
-	  drawPanel(gg,av.startRes,av.endRes,av.startSeq,av.endSeq,av.startRes,av.startSeq,0);
-      }
+        g.translate(LABEL_WEST,0);
+        if(av.scaleAboveWrapped)
+          drawNorthScale(g, startRes, endx, ypos);
 
+        drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
+        g.translate(-LABEL_WEST,0);
 
-  /*  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());
-    }*/
+        ypos += cHeight;
+        startRes += cWidth;
+        endx = startRes + cWidth - 1;
 
-    g.drawImage(img,0,0,this);
+        if (endx > al.getWidth())
+          endx = al.getWidth();
+      }
 
   }
 
 
+  public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
 
-
-  public void drawPanel(Graphics g,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();
 
     /*Vector    pid    = av.getConsensus(false);
@@ -208,98 +307,156 @@ public class SeqCanvas extends JPanel
     }*/
 
     SequenceI nextSeq;
-    SequenceGroup group=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 );
-
-     sr.drawSequence(g, nextSeq, group,x1,x2,
-                 (x1 - startx) * charWidth,
-                 offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),
-                 charWidth,charHeight,null, i);
+     nextSeq = av.alignment.getSequenceAt(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.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());
+    // 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 (!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;
+
+          if (av.getWrapAlignment())
+          {
+            if (sx < 0)
+              sx = 0;
+
+            if (ex > getWidth())
+            {
+              if (av.getWrapAlignment())
+                ex = getWrappedCanvasWidth(getWidth()) * av.charWidth;
+
+            }
+          }
+          else if(ex>getWidth())
+            ex -= av.charWidth;
+
+
+          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)
@@ -308,32 +465,29 @@ 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;
+          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)
   {
@@ -345,7 +499,6 @@ public class SeqCanvas extends JPanel
 
     searchResults = results;
 
-    paintFlag = true;
     repaint();
   }