From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 30 Nov 2005 15:06:14 +0000 (+0000)
Subject: Exact mapping for applet as well
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=19609f31cb839e3e86de561283fa1cdb508c6eae;p=jalview.git

Exact mapping for applet as well
---

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 7a6a368..bdef555 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -35,7 +35,7 @@ import java.util.*;
 public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotionListener
 {
 
-  MCMatrix idmat = new MCMatrix(3, 3);
+    MCMatrix idmat = new MCMatrix(3, 3);
     MCMatrix objmat = new MCMatrix(3, 3);
     boolean redrawneeded = true;
     int omx = 0;
@@ -66,21 +66,20 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     int xmid;
     int ymid;
     Font font = new Font("Helvetica", Font.PLAIN, 10);
-    jalview.appletgui.SequenceRenderer sr;
-    jalview.appletgui.FeatureRenderer  fr;
     jalview.appletgui.SeqCanvas seqcanvas;
     public Sequence sequence;
     final StringBuffer mappingDetails = new StringBuffer();
     String appletToolTip = null;
     int toolx, tooly;
     PDBChain mainchain;
+    Vector highlightRes;
+    boolean pdbAction = false;
+    Bond highlightBond1, highlightBond2;
 
     public AppletPDBCanvas(jalview.appletgui.SeqCanvas seqcanvas, Sequence seq)
     {
       this.seqcanvas = seqcanvas;
       this.sequence = seq;
-      sr = seqcanvas.getSequenceRenderer();
-      fr = seqcanvas.getFeatureRenderer();
 
       seqcanvas.setPDBCanvas(this);
       addKeyListener(new KeyAdapter()
@@ -93,45 +92,16 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       });
     }
 
-    Bond highlightBond1, highlightBond2;
-    public void highlightRes(int ii)
-   {
-     highlightBond1 = null;
-     highlightBond2 = null;
-
-     int index = ii - mainchain.seqstart;
-
-     System.out.println(ii+" "+mainchain.seqstart+" "+index);
-
-     if(index <0 )
-       return;
-
-     if(index<=mainchain.bonds.size())
-     {
-       if(index>0)
-       {
-         highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
-       }
-
-       if(index!=mainchain.bonds.size())
-         highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
-     }
-
-     redrawneeded = true;
-     repaint();
-  }
-
 
   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++)
         {
@@ -167,6 +137,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
                 pdbend = as.seq2end;
                 seqstart = as.seq1start + sequence.getStart()-1;
                 seqend = as.seq1end + sequence.getEnd()-1;
+                maxAlignseq = as;
             }
 
             mappingDetails.append("\nPDB start/end "  + pdbstart + " " + pdbend);
@@ -180,7 +151,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
         mainchain.seqstart = seqstart;
         mainchain.seqend = seqend;
         mainchain.isVisible = true;
-        mainchain.sequence = sequence;
+        mainchain.makeExactMapping(maxAlignseq, sequence);
 
         this.pdb = pdb;
         this.prefsize = new Dimension(getSize().width, getSize().height);
@@ -201,41 +172,39 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
         addMouseMotionListener(this);
         addMouseListener(this);
 
-      /*
-       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();
 
+        setupBonds();
+
         scale = findScale();
 
         updateSeqColours();
     }
 
-    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));
+          }
         }
+      }
     }
 
+
     public void findWidth() {
         float[] max = new float[3];
         float[] min = new float[3];
@@ -380,7 +349,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     public void paint(Graphics g)
     {
 
-      if(pdb==null)
+      if(visiblebonds==null)
       {
         g.setColor(Color.black);
         g.setFont(new Font("Verdana", Font.BOLD, 14));
@@ -423,7 +392,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
 
         g.drawImage(img, 0, 0, this);
 
-
+        pdbAction = false;
     }
 
     public void drawAll(Graphics g, int width, int height)
@@ -437,6 +406,11 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
 
     public void updateSeqColours()
     {
+      if (pdbAction)
+      {
+        return;
+      }
+
       if(bysequence && pdb!=null)
       {
         for (int ii = 0; ii < pdb.chains.size(); ii++)
@@ -449,6 +423,37 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       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)
@@ -456,76 +461,52 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       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);
-
-          if(jalview.util.Comparison.isGap((sequence.getCharAt(index))))
-           {
-             index--;
-           }
-
-           tmp.startCol = sr.findSequenceColour(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);
 
+          //    tmp.startCol = seqcanvas.getFeatureRenderer().
+         //         findFeatureColour(tmp.startCol, sequence, index);
+            }
         }
-        else
-        {
-          tmp.startCol = Color.gray;
-        }
-
-        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);
-          if (jalview.util.Comparison.isGap( (sequence.getCharAt(index))))
-          {
-            index--;
-          }
-
 
-            tmp.endCol = sr.findSequenceColour(sequence, index);
-      //    tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index);
-        }
-        else
+        int index =  findTrueIndex(tmp.at2.alignmentMapping);
+            //sequence.findIndex( tmp.at2.alignmentMapping );
+        if (index != -1)
         {
-          tmp.endCol = Color.gray;
+          tmp.endCol = seqcanvas.getSequenceRenderer().
+              getResidueBoxColour( sequence, index);
+        //  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++)
-        {
-          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));
-            }
-          }
-        }
+    public void drawScene(Graphics g)
+    {
 
         if (zbuffer) {
-            Zsort.Zsort(bonds);
+            Zsort.Zsort(visiblebonds);
         }
 
-        for (int i = 0; i < bonds.size(); i++) {
-            Bond tmpBond = (Bond) bonds.elementAt(i);
+
+        Bond tmpBond=null;
+        for (int i = 0; i < visiblebonds.size(); i++)
+        {
+            tmpBond = (Bond) visiblebonds.elementAt(i);
 
 
             xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +
@@ -639,12 +620,32 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     }
 
     public void mousePressed(MouseEvent e) {
-        Atom fatom = findAtom(e.getX(), e.getY());
-        if(fatom!=null)
+      pdbAction = true;
+      Atom fatom = findAtom(e.getX(), e.getY());
+      if(fatom!=null)
+      {
+        fatom.isSelected = !fatom.isSelected;
+
+        redrawneeded = true;
+        repaint();
+        if (foundchain != -1)
         {
-          fatom.isSelected = !fatom.isSelected;
-          redrawneeded = true;
-          repaint();
+          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.removeElement(fatom.alignmentMapping + "");
+              else
+                highlightRes.addElement(fatom.alignmentMapping + "");
+            }
+          }
+        }
+
         }
         mx = e.getX();
         my = e.getY();
@@ -654,6 +655,14 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     }
 
     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());
 
@@ -663,18 +672,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
           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) {
             toolx = e.getX();
@@ -684,12 +684,48 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
             redrawneeded = true;
             repaint();
         } else {
+            highlightSeqcanvas( -1);
             appletToolTip = null;
             redrawneeded = true;
             repaint();
         }
     }
 
+
+    void highlightSeqcanvas(int pos)
+    {
+      int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);
+
+      int size = pos==-1?0:3;
+
+      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 mouseClicked(MouseEvent e) {
     }
 
@@ -810,19 +846,25 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
 
         foundchain = -1;
 
-        for (int ii = 0; ii < pdb.chains.size(); ii++) {
+        for (int ii = 0; ii < pdb.chains.size(); ii++)
+        {
             PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+            int truex;
+            Bond tmpBond=null;
 
-            if (chain.isVisible) {
+            if (chain.isVisible)
+            {
                 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++)
+                {
+                    tmpBond = (Bond) bonds.elementAt(i);
 
-                    int truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +
+                    truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +
                         (getSize().width / 2));
 
-                    if (Math.abs(truex - x) <= 2) {
+                    if (Math.abs(truex - x) <= 2)
+                    {
                         int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +
                             (getSize().height / 2));
 
@@ -834,6 +876,25 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
                         }
                     }
                 }
+
+                // Still here? Maybe its the last bond
+
+                truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
+                               (getSize().width / 2));
+
+                if (Math.abs(truex - x) <= 2)
+                {
+                  int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
+                                     (getSize().height / 2));
+
+                  if (Math.abs(truey - y) <= 2)
+                  {
+                    fatom = tmpBond.at2;
+                    foundchain = ii;
+                    break;
+                  }
+                }
+
             }
 
             if (fatom != null) //)&& chain.ds != null)
@@ -850,6 +911,52 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       paint(g);
     }
 
+    public void highlightRes(int ii)
+   {
+
+     if (highlightRes != null
+         && highlightRes.contains((ii-1) + ""))
+     {
+       return;
+     }
+
+     int index = -1;
+     Bond tmpBond;
+     for(index=0; index<mainchain.bonds.size(); index++)
+     {
+       tmpBond = (Bond) mainchain.bonds.elementAt(index);
+       if (tmpBond.at1.alignmentMapping == ii - 1)
+       {
+         if (highlightBond1 != null)
+           highlightBond1.at2.isSelected = false;
+
+         if (highlightBond2 != null)
+           highlightBond2.at1.isSelected = false;
+
+         highlightBond1 = null;
+         highlightBond2 = null;
+
+         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;
+     repaint();
+   }
+
+
     public void setAllchainsVisible(boolean b)
     {
       for (int ii = 0; ii < pdb.chains.size(); ii++)
@@ -859,6 +966,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       }
       mainchain.isVisible = true;
       findCentre();
+      setupBonds();
+      redrawneeded = true;
+      repaint();
+
     }
 
 }
diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index 1ed4d10..3f4e42c 100755
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -117,14 +117,6 @@ public class AppletPDBViewer extends Frame
             seqButton_actionPerformed();
           }
         });
-        molecule.setLabel("By Molecule");
-        molecule.addItemListener(new ItemListener()
-        {
-          public void itemStateChanged(ItemEvent e)
-          {
-            molecule_actionPerformed();
-          }
-        });
     allchains.setLabel("All Chains Visible");
     allchains.addItemListener(new ItemListener()
     {
@@ -141,7 +133,6 @@ public class AppletPDBViewer extends Frame
         coloursMenu.add(chain);
     coloursMenu.add(hydro);
     coloursMenu.add(charge);
-    coloursMenu.add(molecule);
     coloursMenu.addSeparator();
         coloursMenu.add(wire);
         coloursMenu.add(depth);
@@ -164,7 +155,6 @@ public class AppletPDBViewer extends Frame
       MenuItem chain = new MenuItem();
       MenuItem seqButton = new MenuItem();
 
-      CheckboxMenuItem molecule = new CheckboxMenuItem();
      CheckboxMenuItem allchains = new CheckboxMenuItem();
 
   public void charge_actionPerformed()
@@ -198,13 +188,6 @@ public class AppletPDBViewer extends Frame
         pdbcanvas.repaint();
       }
 
-      public void molecule_actionPerformed()
-      {
-        pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
-        pdbcanvas.redrawneeded=true;
-        pdbcanvas.repaint();
-      }
-
       public void depth_actionPerformed()
       {
       pdbcanvas.depthcue = ! pdbcanvas.depthcue;