X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=c33f3ed371da55393dac4948cb9c8679fd06c619;hb=c87b480e692410c150592b48beb8b1e234450717;hp=4e287b150cdb3e65a168b2775fa566c338f94a03;hpb=412265975277586d03ec183fce0f6e18a022b240;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 4e287b1..c33f3ed 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.*;
@@ -10,46 +10,48 @@ import jalview.analysis.*;
 
 public class SeqCanvas extends JPanel
 {
+     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;
+    boolean displaySearch = false;
+    int [] searchResults = null;
 
     int chunkHeight;
     int chunkWidth;
 
-    Graphics debugG;
-   // FeatureRenderer fr = new FeatureRenderer();
-  //  BlockRenderer   br = new BlockRenderer();
-  //  CpGRenderer     cgr = new CpGRenderer();
-
-    ColourSchemeI    cs = new ZappoColourScheme();
 
     public SeqCanvas(AlignViewport av)
     {
 	this.av         = av;
+       fr = new FeatureRenderer(av);
        setLayout(new BorderLayout());
+       PaintRefresher.Register(this);
+
     }
 
-  public void drawScale(int startx, int endx,double 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));
       }
+
   }
 
 
@@ -64,239 +66,72 @@ public class SeqCanvas extends JPanel
  * in the adjustment listener in SeqPanel when the scrollbars move.
  */
 
-  public void paintComponent(Graphics g) {
-    debugG = g;
-
-    AlignmentI da = av.getAlignment();
-
-    if (img == null ||
-        imgWidth  !=  getWidth()  ||
-        imgHeight !=  getHeight() ||
-        paintFlag == true) {
-
-      imgWidth  = (getWidth() > 0 ? getWidth() : 1);
-      imgHeight = (getHeight() > 0 ? getHeight() : 1);
+  public void paintComponent(Graphics g)
+  {
 
+    if (img==null ||  imgWidth!=getWidth() || imgHeight!=getHeight() || paintFlag)
+    {
+      imgWidth  = getWidth();
+      imgHeight = getHeight();
       img = createImage(imgWidth,imgHeight);
       gg  = img.getGraphics();
-
-     // SMJS I added this in to update the AV when the size changes
-      //      until I figure out how this should be done
-      setFont(av.getFont());
-
       gg.setFont(av.getFont());
-
       paintFlag = false;
-
-      oldstartx = -1;
-      oldendx   = -1;
-      oldstarty = -1;
-      oldendy   = -1;
     }
 
-    int startx = av.getStartRes();
-    int starty = av.getStartSeq();
-
-    int endx   = av.getEndRes();
-    int endy   = av.getEndSeq();
-
-    double charWidth  = av.getCharWidth();
-    int charHeight    = av.getCharHeight();
 
-    chunkWidth = (int)(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();
-
-    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;
+    fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);
 
-	  if (starty == 0) {
-	      ypos = 2*charHeight;
-	  } else if (starty == 1) {
-	      starty = 0;
-	      ypos = 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);
 
-	  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;
-	  }
-
-	  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  = (int)((startx - oldstartx) * charWidth);
-      int delx2 = (int)((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;
+        drawScale(g, startRes, endx, ypos);
+        drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos);
 
-    } else if (oldstartx > startx)
-    {
-     // Horizontal scrollbar pulled to the left
-
-      int delx  = (int)((oldstartx - startx) * charWidth);
-      int delx2 = (int)((endx - oldstartx +1)   * charWidth);
+        ypos += cHeight;
+        startRes += cWidth;
+        endx = startRes + cWidth - 1;
 
-      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);
+        if (endx > da.getWidth())
+          endx = da.getWidth();
       }
 
-      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,(int)((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);
-
-      gg.copyArea(0,0,(int)((endx-startx+1)*charWidth),dely2,0,dely);
-
-      if (oldstarty > endy) {
-	drawPanel(gg,startx,endx,starty,endy,startx,starty,0);
-      } else {
-	drawPanel(gg,startx,endx,starty,oldstarty,startx,starty,0);
-      }
-
-      oldstarty = starty;
-      oldendy   = endy;
-    }
-
-    if ((oldendy -oldstarty) > (int)((getWidth() / av.getCharWidth()))) {
-      System.out.println("LIMITS ERROR LIMITS ERROR");
-      System.out.println("Corrds " + (oldendy-oldstarty) + " " + (int)(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) {
 
-/*
-    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());
-    double            charWidth  = av.getCharWidth();
-    int               charHeight = av.getCharHeight();
+    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++)
@@ -313,65 +148,148 @@ public class SeqCanvas extends JPanel
 
 */
 
-    if (y2 > starty && y1 < av.getEndSeq())
+   /* if (y2 > starty && y1 < av.getEndSeq())
     {
        fillBackground(g,
-                   Color.WHITE,
-                   (int)((x1-startx)*charWidth),
+                   Color.red,
+                   (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;
+    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;
     for (int i = y1 ; i < y2 ;i++)
     {
-      RendererI r = sr;
-    /*  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 );
+     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);
+
+     if(av.showSequenceFeatures)
+     {
+       fr.drawSequence(g, nextSeq, groups, x1, x2,
+                       (x1 - startx) * charWidth,
+                       offset +
+                       AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),
+                       charWidth, charHeight, null, i);
+     }
+
+
+
+
      if( group!=null )
      {
-       r.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);
+
+        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)
+        {
+          g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box
+          inGroup=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
+
+        oldStartX = sx;
+        oldEndX = ex;
+        oldY = ey;
+
      }
-     else
+     else if(inGroup)
      {
-       r.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.lightGray);
+       g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box
+     }
+     else
+       inGroup = false;
 
+     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;
 
+    }
 
+    /// Highlight search Results once all sequences have been drawn
+    if(displaySearch)
+    {
+      for(int r=0; r<searchResults.length; r+=3)
+      {
+        int searchSeq = searchResults[r];
+        int searchStart = searchResults[r+1];
+        int searchEnd = searchResults[r+2];
+
+        if (searchSeq >= y1 && searchSeq < y2)
+        {
+          SequenceRenderer ssr = (SequenceRenderer) sr;
+          ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),
+                                  searchStart,
+                                  searchEnd,
+                                  (searchStart - startx) * charWidth,
+                                  offset +
+                                  AlignmentUtil.getPixelHeight(starty, searchSeq,
+              charHeight),
+                                  charWidth,
+                                  charHeight);
+        }
+      }
     }
 
   }
 
-  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);
@@ -381,4 +299,19 @@ public class SeqCanvas extends JPanel
     return chunkWidth;
   }
 
+  public void highlightSearchResults(int [] results)
+  {
+    // results are in the order sequence, startRes, endRes
+    if(results==null)
+      displaySearch = false;
+    else
+      displaySearch = true;
+
+    searchResults = results;
+
+    paintFlag = true;
+    repaint();
+  }
+
+
 }