X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBCanvas.java;h=17db1a0b26059f5fce1386a0c44c5609f84ba94b;hb=0712410094dece81fc8677d3a31fef6bac9d2b7d;hp=5ff0f1f5a8e1eafdc4cd9f5623e05509e06cbd61;hpb=9672f029a8731004f58fa3f1b78e4e0f62ad52c2;p=jalview.git

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 5ff0f1f..17db1a0 100755
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -66,33 +66,29 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
     int xmid;
     int ymid;
     Font font = new Font("Helvetica", Font.PLAIN, 10);
-    jalview.gui.SequenceRenderer sr;
-    jalview.gui.FeatureRenderer  fr;
     jalview.gui.SeqCanvas seqcanvas;
     public Sequence sequence;
     final StringBuffer mappingDetails = new StringBuffer();
     PDBChain mainchain;
+    Vector highlightRes;
+    boolean pdbAction = false;
 
     public PDBCanvas(jalview.gui.SeqCanvas seqcanvas, Sequence seq)
     {
       this.seqcanvas = seqcanvas;
       this.sequence = seq;
-      sr = seqcanvas.getSequenceRenderer();
-      fr = seqcanvas.getFeatureRenderer();
-
       seqcanvas.setPDBCanvas(this);
     }
 
   public void setPDBFile(PDBfile pdb)
    {
-        this.sr = sr;
-        this.fr = fr;
         int max = -10;
         int maxchain = -1;
         int pdbstart = 0;
         int pdbend = 0;
         int seqstart = 0;
         int seqend = 0;
+        AlignSeq maxAlignseq = null;
 
         for (int i = 0; i < pdb.chains.size(); i++)
         {
@@ -120,14 +116,17 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
             as.printAlignment(ps);
 
-            if (as.maxscore > max) {
+
+
+            if (as.maxscore > max)
+            {
                 max = as.maxscore;
                 maxchain = i;
-
                 pdbstart = as.seq2start;
                 pdbend = as.seq2end;
                 seqstart = as.seq1start + sequence.getStart()-1;
                 seqend = as.seq1end + sequence.getEnd()-1;
+                maxAlignseq = as;
             }
 
             mappingDetails.append("\nPDB start/end "  + pdbstart + " " + pdbend);
@@ -141,7 +140,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         mainchain.seqstart = seqstart;
         mainchain.seqend = seqend;
         mainchain.isVisible = true;
-        mainchain.sequence = sequence;
+        mainchain.makeExactMapping(maxAlignseq, sequence);
 
         this.pdb = pdb;
         this.prefsize = new Dimension(getWidth(), getHeight());
@@ -182,46 +181,45 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
           }
        });
 
-      /*
-       SequenceGroup sg = new SequenceGroup("PDB",
-                                            null, true,true,false,
-                                            sequence.findIndex(seqstart-1),
-                                            sequence.findIndex(seqend-1));
-       sg.addSequence(sequence, false);
-       sg.setOutlineColour(Color.black);
-       seqcanvas.getViewport().getAlignment().addGroup(sg);
-       */
 
         findCentre();
         findWidth();
 
-        scale = findScale();
+        setupBonds();
 
+        scale = findScale();
 
-        updateSeqColours();
         ToolTipManager.sharedInstance().registerComponent(this);
         ToolTipManager.sharedInstance().setInitialDelay(0);
         ToolTipManager.sharedInstance().setDismissDelay(10000);
-
     }
 
-    public void deleteBonds() {
-        scale = 0;
-        maxwidth = 0;
 
-        width[0] = 0;
-        width[1] = 0;
-        width[2] = 0;
+    Vector visiblebonds;
+    void setupBonds()
+    {
+      // Sort the bonds by z coord
+      visiblebonds = new Vector();
 
-        centre[0] = 0;
-        centre[1] = 0;
-        centre[2] = 0;
+      for (int ii = 0; ii < pdb.chains.size(); ii++)
+      {
+        if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+        {
+          Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
 
-        for (int i = 0; i < pdb.chains.size(); i++) {
-            ((PDBChain) pdb.chains.elementAt(i)).bonds = null;
+          for (int i = 0; i < tmp.size(); i++)
+          {
+            visiblebonds.addElement(tmp.elementAt(i));
+          }
         }
+      }
+
+      updateSeqColours();
+      redrawneeded = true;
+      repaint();
     }
 
+
     public void findWidth() {
         float[] max = new float[3];
         float[] min = new float[3];
@@ -367,11 +365,11 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         centre[2] = ztot / (2 * (float) bsize);
     }
 
-    public void paintComponent(Graphics g) {
-
+    public void paintComponent(Graphics g)
+    {
       super.paintComponent(g);
 
-      if(pdb==null)
+      if(visiblebonds==null)
       {
         g.setColor(Color.black);
         g.setFont(new Font("Verdana", Font.BOLD, 14));
@@ -382,8 +380,11 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
         //Only create the image at the beginning -
         //this saves much memory usage
-        if ((img == null) || (prefsize.width != getWidth()) ||
-                (prefsize.height != getHeight())) {
+        if ((img == null)
+            || (prefsize.width != getWidth())
+            || (prefsize.height != getHeight()))
+
+      {
             prefsize.width = getWidth();
             prefsize.height = getHeight();
 
@@ -395,7 +396,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
             ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
                                  RenderingHints.VALUE_ANTIALIAS_ON);
 
-
             redrawneeded = true;
         }
 
@@ -407,6 +407,8 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         }
 
         g.drawImage(img, 0, 0, this);
+
+        pdbAction = false;
     }
 
     public void drawAll(Graphics g, int width, int height)
@@ -420,87 +422,115 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
     public void updateSeqColours()
     {
+      if(pdbAction)
+      {
+        return;
+      }
+
+     // System.out.println("update seq colours");
       if(bysequence && pdb!=null)
       {
         for (int ii = 0; ii < pdb.chains.size(); ii++)
         {
-          colourBySequence( (PDBChain) pdb.chains.elementAt(ii) );
+          colourBySequence( (PDBChain) pdb.chains.elementAt(ii));
         }
       }
 
       redrawneeded=true;
       repaint();
+    }
+
+    int findTrueIndex(int pos)
+    {
+      // returns the alignment position for a residue
+      int j = sequence.getStart();
+      int i = 0;
 
+      while ( (i < sequence.getLength()) && (j <= sequence.getEnd()) && (j <= pos+1))
+      {
+        if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))
+        {
+          j++;
+        }
+
+        i++;
+      }
+
+      if(i>1)
+         i--;
+
+      if ( (j == sequence.getEnd()) && (j < pos))
+      {
+        return sequence.getEnd() + 1;
+      }
+      else
+      {
+        return i;
+      }
     }
 
     // This method has been taken out of PDBChain to allow
     // Applet and Application specific sequence renderers to be used
     void colourBySequence(PDBChain chain)
     {
+     // System.out.println("colour by seq");
       for (int i = 0; i < chain.bonds.size(); i++)
       {
         Bond tmp = (Bond) chain.bonds.elementAt(i);
+        tmp.startCol = Color.lightGray;
+        tmp.endCol = Color.lightGray;
+
+        if(chain!=mainchain)
+          continue;
 
         if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
             (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))
         {
-          int pos = chain.seqstart +
-              (tmp.at1.resNumber - chain.pdbstart - chain.offset);
-
-          int index = sequence.findIndex(pos);
-
-          tmp.startCol = sr.findSequenceColour(Color.lightGray, sequence, index);
-
-          tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);
+            int index = findTrueIndex(tmp.at1.alignmentMapping);
+                //sequence.findIndex(tmp.at1.alignmentMapping);
+            if (index != -1)
+            {
+              tmp.startCol = seqcanvas.getSequenceRenderer().
+                  getResidueBoxColour( sequence, index);
+              if(tmp.startCol==null)
+                tmp.startCol = Color.white;
 
-        }
-        else
-        {
-          tmp.startCol = Color.gray;
+              tmp.startCol = seqcanvas.getFeatureRenderer().
+                  findFeatureColour(tmp.startCol, sequence, index);
+            }
         }
 
         if ( (tmp.at2.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
             (tmp.at2.resNumber <= ( (chain.pdbend + chain.offset) - 1)))
         {
-          int pos = chain.seqstart +
-              (tmp.at2.resNumber - chain.pdbstart - chain.offset);
-          int index = sequence.findIndex(pos);
 
-          tmp.endCol = sr.findSequenceColour(tmp.endCol, sequence, index);
-          tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index);
-        }
-        else
-        {
-          tmp.endCol = Color.gray;
+            int index =  findTrueIndex(tmp.at2.alignmentMapping);
+                //sequence.findIndex( tmp.at2.alignmentMapping );
+            if (index != -1)
+            {
+              tmp.endCol = seqcanvas.getSequenceRenderer().
+                  getResidueBoxColour( sequence, index);
+              if(tmp.endCol==null)
+                tmp.endCol = Color.white;
+              tmp.endCol = seqcanvas.getFeatureRenderer().
+                  findFeatureColour(tmp.endCol, sequence, index);
+            }
         }
       }
     }
 
 
-    public void drawScene(Graphics g) {
-        // Sort the bonds by z coord
-        Vector bonds = new Vector();
-
-        for (int ii = 0; ii < pdb.chains.size(); ii++)
+    public void drawScene(Graphics g)
+    {
+        if (zbuffer)
         {
-          if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
-          {
-            Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
-
-            for (int i = 0; i < tmp.size(); i++)
-            {
-              bonds.addElement(tmp.elementAt(i));
-            }
-          }
-        }
-
-        if (zbuffer) {
-            Zsort.Zsort(bonds);
+            Zsort.Zsort(visiblebonds);
         }
 
         Bond tmpBond=null;
-        for (int i = 0; i < bonds.size(); i++) {
-            tmpBond = (Bond) bonds.elementAt(i);
+        for (int i = 0; i < visiblebonds.size(); i++)
+        {
+            tmpBond = (Bond) visiblebonds.elementAt(i);
 
             xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +
                 (getWidth() / 2));
@@ -515,11 +545,11 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
             xmid = (xend + xstart) / 2;
             ymid = (yend + ystart) / 2;
 
-            if (depthcue && !bymolecule) {
+            if (depthcue && !bymolecule)
+            {
                 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
                     g.setColor(tmpBond.startCol.darker().darker());
                     drawLine(g, xstart, ystart, xmid, ymid);
-
                     g.setColor(tmpBond.endCol.darker().darker());
                     drawLine(g, xmid, ymid, xend, yend);
                 } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
@@ -613,13 +643,34 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       }
     }
 
-    public void mousePressed(MouseEvent e) {
+    public void mousePressed(MouseEvent e)
+    {
+        pdbAction = true;
         Atom fatom = findAtom(e.getX(), e.getY());
         if(fatom!=null)
         {
           fatom.isSelected = !fatom.isSelected;
+
           redrawneeded = true;
           repaint();
+          if (foundchain != -1)
+          {
+            PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
+            if (chain == mainchain)
+            {
+              if (fatom.alignmentMapping != -1)
+              {
+                if (highlightRes == null)
+                  highlightRes = new Vector();
+
+                if (highlightRes.contains(fatom.alignmentMapping+"" + ""))
+                  highlightRes.remove(fatom.alignmentMapping + "");
+                else
+                  highlightRes.add(fatom.alignmentMapping + "");
+              }
+            }
+          }
+
         }
         mx = e.getX();
         my = e.getY();
@@ -628,7 +679,16 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         dragging = false;
     }
 
-    public void mouseMoved(MouseEvent e) {
+    public void mouseMoved(MouseEvent e)
+    {
+      pdbAction = true;
+      if(highlightBond1!=null)
+      {
+        highlightBond1.at2.isSelected = false;
+        highlightBond2.at1.isSelected = false;
+        highlightBond1 = null;
+        highlightBond2 = null;
+      }
 
         Atom fatom = findAtom(e.getX(), e.getY());
 
@@ -638,43 +698,69 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
           chain = (PDBChain) pdb.chains.elementAt(foundchain);
           if(chain == mainchain)
           {
-            int pos = chain.seqstart +
-                (fatom.resNumber - chain.pdbstart - chain.offset) + 1;
-
-            int index = seqcanvas.getViewport().getAlignment().findIndex(
-                sequence);
-
-            seqcanvas.highlightSearchResults(new int[]
-                                             {index, pos, pos});
+            highlightSeqcanvas( fatom.alignmentMapping );
           }
         }
-        else
-          seqcanvas.highlightSearchResults(null);
 
         if (fatom != null)
         {
             this.setToolTipText(chain.id+":"+ fatom.resNumber+" "+ fatom.resName);
         } else
         {
-            this.setToolTipText("");
+            highlightSeqcanvas( -1);
+            this.setToolTipText(null);
         }
     }
 
-    public void mouseClicked(MouseEvent e) {
-    }
 
-    public void mouseEntered(MouseEvent e) {
-    }
+    void highlightSeqcanvas(int pos)
+    {
+      int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);
+
+      int size = pos==-1?0:3;
 
-    public void mouseExited(MouseEvent e) {
+      if(highlightRes!=null)
+        size += highlightRes.size()*3;
+
+      int [] array = new int[size];
+      int i=0;
+      if(highlightRes!=null)
+      {
+        for (i = 0; i < highlightRes.size(); i++)
+        {
+          int a = Integer.parseInt(highlightRes.elementAt(
+              i).toString())+1;
+          array[i * 3] = index;
+          array[ (i * 3) + 1] = a;
+          array[ (i * 3) + 2] = a;
+        }
+      }
+
+      if(pos!=-1)
+      {
+        array[i * 3] = index;
+        array[i * 3 + 1] = pos+1;
+        array[i * 3 + 2] = pos+1;
+      }
+
+      seqcanvas.highlightSearchResults(array);
     }
 
-    public void mouseDragged(MouseEvent evt) {
+
+    public void mouseClicked(MouseEvent e)  { }
+
+    public void mouseEntered(MouseEvent e) {  }
+
+    public void mouseExited(MouseEvent e) { }
+
+    public void mouseDragged(MouseEvent evt)
+    {
         int x = evt.getX();
         int y = evt.getY();
         mx = x;
         my = y;
 
+
         MCMatrix objmat = new MCMatrix(3, 3);
         objmat.setIdentity();
 
@@ -716,7 +802,8 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         repaint();
     }
 
-    public void mouseReleased(MouseEvent evt) {
+    public void mouseReleased(MouseEvent evt)
+    {
         dragging = false;
         return;
     }
@@ -729,22 +816,22 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
             if (chain.isVisible)
             {
-                Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+              Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
-                for (int i = 0; i < bonds.size(); i++)
-                {
-                    Bond tmpBond = (Bond) bonds.elementAt(i);
+              for (int i = 0; i < bonds.size(); i++)
+              {
+                  Bond tmpBond = (Bond) bonds.elementAt(i);
 
-                    if (tmpBond.at1.isSelected)
-                    {
-                        labelAtom(g, tmpBond, 1);
-                    }
+                  if (tmpBond.at1.isSelected)
+                  {
+                      labelAtom(g, tmpBond, 1);
+                  }
 
-                    if (tmpBond.at2.isSelected)
-                    {
+                  if (tmpBond.at2.isSelected)
+                  {
 
-                        labelAtom(g, tmpBond, 2);
-                    }
+                      labelAtom(g, tmpBond, 2);
+                  }
                 }
             }
         }
@@ -752,14 +839,14 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
     public void labelAtom(Graphics g, Bond b, int n) {
         g.setFont(font);
-
-        if (n == 1) {
+        g.setColor(Color.red);
+        if (n == 1)
+        {
             int xstart = (int) (((b.start[0] - centre[0]) * scale) +
                 (getWidth() / 2));
             int ystart = (int) (((b.start[1] - centre[1]) * scale) +
                 (getHeight() / 2));
 
-            g.setColor(Color.red);
             g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
         }
 
@@ -769,7 +856,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
             int ystart = (int) (((b.end[1] - centre[1]) * scale) +
                 (getHeight() / 2));
 
-            g.setColor(Color.red);
             g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
         }
     }
@@ -843,23 +929,43 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
    Bond highlightBond1, highlightBond2;
    public void highlightRes(int ii)
   {
-    highlightBond1 = null;
-    highlightBond2 = null;
 
-    int index = ii - mainchain.seqstart;
-
-    if(index <0 )
+    if (highlightRes != null
+        && highlightRes.contains((ii-1) + ""))
+    {
       return;
+    }
 
-    if(index<=mainchain.bonds.size())
+    int index = -1;
+    Bond tmpBond;
+    for(index=0; index<mainchain.bonds.size(); index++)
     {
-      if(index>0)
+      tmpBond = (Bond) mainchain.bonds.elementAt(index);
+      if (tmpBond.at1.alignmentMapping == ii - 1)
       {
-        highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
-      }
+        if (highlightBond1 != null)
+          highlightBond1.at2.isSelected = false;
+
+        if (highlightBond2 != null)
+          highlightBond2.at1.isSelected = false;
+
+        highlightBond1 = null;
+        highlightBond2 = null;
 
-      if(index!=mainchain.bonds.size())
-        highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+        if (index > 0)
+        {
+          highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
+          highlightBond1.at2.isSelected = true;
+        }
+
+        if (index != mainchain.bonds.size())
+        {
+          highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+          highlightBond2.at1.isSelected = true;
+        }
+
+        break;
+      }
     }
 
     redrawneeded = true;
@@ -875,5 +981,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       }
       mainchain.isVisible = true;
       findCentre();
+      setupBonds();
     }
 }