Exact mapping for applet as well

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 7a6a368..bdef555 100755 (executable)
--- 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\r
 {\r
 \r
-  MCMatrix idmat = new MCMatrix(3, 3);\r
+    MCMatrix idmat = new MCMatrix(3, 3);\r
     MCMatrix objmat = new MCMatrix(3, 3);\r
     boolean redrawneeded = true;\r
     int omx = 0;\r
@@ -66,21 +66,20 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     int xmid;\r
     int ymid;\r
     Font font = new Font("Helvetica", Font.PLAIN, 10);\r
-    jalview.appletgui.SequenceRenderer sr;\r
-    jalview.appletgui.FeatureRenderer  fr;\r
     jalview.appletgui.SeqCanvas seqcanvas;\r
     public Sequence sequence;\r
     final StringBuffer mappingDetails = new StringBuffer();\r
     String appletToolTip = null;\r
     int toolx, tooly;\r
     PDBChain mainchain;\r
+    Vector highlightRes;\r
+    boolean pdbAction = false;\r
+    Bond highlightBond1, highlightBond2;\r
 \r
     public AppletPDBCanvas(jalview.appletgui.SeqCanvas seqcanvas, Sequence seq)\r
     {\r
       this.seqcanvas = seqcanvas;\r
       this.sequence = seq;\r
-      sr = seqcanvas.getSequenceRenderer();\r
-      fr = seqcanvas.getFeatureRenderer();\r
 \r
       seqcanvas.setPDBCanvas(this);\r
       addKeyListener(new KeyAdapter()\r
@@ -93,45 +92,16 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       });\r
     }\r
 \r
-    Bond highlightBond1, highlightBond2;\r
-    public void highlightRes(int ii)\r
-   {\r
-     highlightBond1 = null;\r
-     highlightBond2 = null;\r
-\r
-     int index = ii - mainchain.seqstart;\r
-\r
-     System.out.println(ii+" "+mainchain.seqstart+" "+index);\r
-\r
-     if(index <0 )\r
-       return;\r
-\r
-     if(index<=mainchain.bonds.size())\r
-     {\r
-       if(index>0)\r
-       {\r
-         highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);\r
-       }\r
-\r
-       if(index!=mainchain.bonds.size())\r
-         highlightBond2 = (Bond) mainchain.bonds.elementAt(index);\r
-     }\r
-\r
-     redrawneeded = true;\r
-     repaint();\r
-  }\r
-\r
 \r
   public void setPDBFile(PDBfile pdb)\r
    {\r
-        this.sr = sr;\r
-        this.fr = fr;\r
         int max = -10;\r
         int maxchain = -1;\r
         int pdbstart = 0;\r
         int pdbend = 0;\r
         int seqstart = 0;\r
         int seqend = 0;\r
+        AlignSeq maxAlignseq = null;;\r
 \r
         for (int i = 0; i < pdb.chains.size(); i++)\r
         {\r
@@ -167,6 +137,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
                 pdbend = as.seq2end;\r
                 seqstart = as.seq1start + sequence.getStart()-1;\r
                 seqend = as.seq1end + sequence.getEnd()-1;\r
+                maxAlignseq = as;\r
             }\r
 \r
             mappingDetails.append("\nPDB start/end "  + pdbstart + " " + pdbend);\r
@@ -180,7 +151,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
         mainchain.seqstart = seqstart;\r
         mainchain.seqend = seqend;\r
         mainchain.isVisible = true;\r
-        mainchain.sequence = sequence;\r
+        mainchain.makeExactMapping(maxAlignseq, sequence);\r
 \r
         this.pdb = pdb;\r
         this.prefsize = new Dimension(getSize().width, getSize().height);\r
@@ -201,41 +172,39 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
         addMouseMotionListener(this);\r
         addMouseListener(this);\r
 \r
-      /*\r
-       SequenceGroup sg = new SequenceGroup("PDB",\r
-                                            null, true,true,false,\r
-                                            sequence.findIndex(seqstart-1),\r
-                                            sequence.findIndex(seqend-1));\r
-       sg.addSequence(sequence, false);\r
-       sg.setOutlineColour(Color.black);\r
-       seqcanvas.getViewport().getAlignment().addGroup(sg);\r
-       */\r
 \r
         findCentre();\r
         findWidth();\r
 \r
+        setupBonds();\r
+\r
         scale = findScale();\r
 \r
         updateSeqColours();\r
     }\r
 \r
-    public void deleteBonds() {\r
-        scale = 0;\r
-        maxwidth = 0;\r
 \r
-        width[0] = 0;\r
-        width[1] = 0;\r
-        width[2] = 0;\r
+    Vector visiblebonds;\r
+    void setupBonds()\r
+    {\r
+      // Sort the bonds by z coord\r
+      visiblebonds = new Vector();\r
 \r
-        centre[0] = 0;\r
-        centre[1] = 0;\r
-        centre[2] = 0;\r
+      for (int ii = 0; ii < pdb.chains.size(); ii++)\r
+      {\r
+        if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)\r
+        {\r
+          Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
 \r
-        for (int i = 0; i < pdb.chains.size(); i++) {\r
-            ((PDBChain) pdb.chains.elementAt(i)).bonds = null;\r
+          for (int i = 0; i < tmp.size(); i++)\r
+          {\r
+            visiblebonds.addElement(tmp.elementAt(i));\r
+          }\r
         }\r
+      }\r
     }\r
 \r
+\r
     public void findWidth() {\r
         float[] max = new float[3];\r
         float[] min = new float[3];\r
@@ -380,7 +349,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     public void paint(Graphics g)\r
     {\r
 \r
-      if(pdb==null)\r
+      if(visiblebonds==null)\r
       {\r
         g.setColor(Color.black);\r
         g.setFont(new Font("Verdana", Font.BOLD, 14));\r
@@ -423,7 +392,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
 \r
         g.drawImage(img, 0, 0, this);\r
 \r
-\r
+        pdbAction = false;\r
     }\r
 \r
     public void drawAll(Graphics g, int width, int height)\r
@@ -437,6 +406,11 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
 \r
     public void updateSeqColours()\r
     {\r
+      if (pdbAction)\r
+      {\r
+        return;\r
+      }\r
+\r
       if(bysequence && pdb!=null)\r
       {\r
         for (int ii = 0; ii < pdb.chains.size(); ii++)\r
@@ -449,6 +423,37 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       repaint();\r
     }\r
 \r
+\r
+    int findTrueIndex(int pos)\r
+    {\r
+      // returns the alignment position for a residue\r
+      int j = sequence.getStart();\r
+      int i = 0;\r
+\r
+      while ( (i < sequence.getLength()) && (j <= sequence.getEnd()) && (j <= pos+1))\r
+      {\r
+        if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))\r
+        {\r
+          j++;\r
+        }\r
+\r
+        i++;\r
+      }\r
+\r
+      if(i>1)\r
+         i--;\r
+\r
+      if ( (j == sequence.getEnd()) && (j < pos))\r
+      {\r
+        return sequence.getEnd() + 1;\r
+      }\r
+      else\r
+      {\r
+        return i;\r
+      }\r
+    }\r
+\r
+\r
     // This method has been taken out of PDBChain to allow\r
     // Applet and Application specific sequence renderers to be used\r
     void colourBySequence(PDBChain chain)\r
@@ -456,76 +461,52 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       for (int i = 0; i < chain.bonds.size(); i++)\r
       {\r
         Bond tmp = (Bond) chain.bonds.elementAt(i);\r
+        tmp.startCol = Color.lightGray;\r
+        tmp.endCol = Color.lightGray;\r
+        if(chain!=mainchain)\r
+          continue;\r
+\r
         if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&\r
             (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))\r
         {\r
 \r
-          int pos = chain.seqstart +\r
-              (tmp.at1.resNumber - chain.pdbstart - chain.offset);\r
-\r
-          int index = sequence.findIndex(pos);\r
-\r
-          if(jalview.util.Comparison.isGap((sequence.getCharAt(index))))\r
-           {\r
-             index--;\r
-           }\r
-\r
-           tmp.startCol = sr.findSequenceColour(sequence, index);\r
-\r
-        //  tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);\r
+          int index = findTrueIndex(tmp.at1.alignmentMapping);\r
+                //sequence.findIndex(tmp.at1.alignmentMapping);\r
+            if (index != -1)\r
+            {\r
+              tmp.startCol = seqcanvas.getSequenceRenderer().\r
+                  getResidueBoxColour( sequence, index);\r
 \r
+          //    tmp.startCol = seqcanvas.getFeatureRenderer().\r
+         //         findFeatureColour(tmp.startCol, sequence, index);\r
+            }\r
         }\r
-        else\r
-        {\r
-          tmp.startCol = Color.gray;\r
-        }\r
-\r
-        if ( (tmp.at2.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&\r
-            (tmp.at2.resNumber <= ( (chain.pdbend + chain.offset) - 1)))\r
-        {\r
-          int pos = chain.seqstart +\r
-              (tmp.at2.resNumber - chain.pdbstart - chain.offset);\r
-          int index = sequence.findIndex(pos);\r
-          if (jalview.util.Comparison.isGap( (sequence.getCharAt(index))))\r
-          {\r
-            index--;\r
-          }\r
-\r
 \r
-            tmp.endCol = sr.findSequenceColour(sequence, index);\r
-      //    tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index);\r
-        }\r
-        else\r
+        int index =  findTrueIndex(tmp.at2.alignmentMapping);\r
+            //sequence.findIndex( tmp.at2.alignmentMapping );\r
+        if (index != -1)\r
         {\r
-          tmp.endCol = Color.gray;\r
+          tmp.endCol = seqcanvas.getSequenceRenderer().\r
+              getResidueBoxColour( sequence, index);\r
+        //  tmp.endCol = seqcanvas.getFeatureRenderer().\r
+        //      findFeatureColour(tmp.endCol, sequence, index);\r
         }\r
       }\r
     }\r
 \r
 \r
-    public void drawScene(Graphics g) {\r
-        // Sort the bonds by z coord\r
-        Vector bonds = new Vector();\r
-\r
-        for (int ii = 0; ii < pdb.chains.size(); ii++)\r
-        {\r
-          if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)\r
-          {\r
-            Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
-\r
-            for (int i = 0; i < tmp.size(); i++)\r
-            {\r
-                bonds.addElement(tmp.elementAt(i));\r
-            }\r
-          }\r
-        }\r
+    public void drawScene(Graphics g)\r
+    {\r
 \r
         if (zbuffer) {\r
-            Zsort.Zsort(bonds);\r
+            Zsort.Zsort(visiblebonds);\r
         }\r
 \r
-        for (int i = 0; i < bonds.size(); i++) {\r
-            Bond tmpBond = (Bond) bonds.elementAt(i);\r
+\r
+        Bond tmpBond=null;\r
+        for (int i = 0; i < visiblebonds.size(); i++)\r
+        {\r
+            tmpBond = (Bond) visiblebonds.elementAt(i);\r
 \r
 \r
             xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +\r
@@ -639,12 +620,32 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     }\r
 \r
     public void mousePressed(MouseEvent e) {\r
-        Atom fatom = findAtom(e.getX(), e.getY());\r
-        if(fatom!=null)\r
+      pdbAction = true;\r
+      Atom fatom = findAtom(e.getX(), e.getY());\r
+      if(fatom!=null)\r
+      {\r
+        fatom.isSelected = !fatom.isSelected;\r
+\r
+        redrawneeded = true;\r
+        repaint();\r
+        if (foundchain != -1)\r
         {\r
-          fatom.isSelected = !fatom.isSelected;\r
-          redrawneeded = true;\r
-          repaint();\r
+          PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);\r
+          if (chain == mainchain)\r
+          {\r
+            if (fatom.alignmentMapping != -1)\r
+            {\r
+              if (highlightRes == null)\r
+                highlightRes = new Vector();\r
+\r
+              if (highlightRes.contains(fatom.alignmentMapping+"" + ""))\r
+                highlightRes.removeElement(fatom.alignmentMapping + "");\r
+              else\r
+                highlightRes.addElement(fatom.alignmentMapping + "");\r
+            }\r
+          }\r
+        }\r
+\r
         }\r
         mx = e.getX();\r
         my = e.getY();\r
@@ -654,6 +655,14 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     }\r
 \r
     public void mouseMoved(MouseEvent e) {\r
+      pdbAction = true;\r
+      if(highlightBond1!=null)\r
+      {\r
+        highlightBond1.at2.isSelected = false;\r
+        highlightBond2.at1.isSelected = false;\r
+        highlightBond1 = null;\r
+        highlightBond2 = null;\r
+      }\r
 \r
         Atom fatom = findAtom(e.getX(), e.getY());\r
 \r
@@ -663,18 +672,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
           chain = (PDBChain) pdb.chains.elementAt(foundchain);\r
           if(chain == mainchain)\r
           {\r
-            int pos = chain.seqstart +\r
-                (fatom.resNumber - chain.pdbstart - chain.offset) + 1;\r
-\r
-            int index = seqcanvas.getViewport().getAlignment().findIndex(\r
-                sequence);\r
-\r
-            seqcanvas.highlightSearchResults(new int[]\r
-                                             {index, pos, pos});\r
+            highlightSeqcanvas( fatom.alignmentMapping );\r
           }\r
         }\r
-        else\r
-          seqcanvas.highlightSearchResults(null);\r
 \r
         if (fatom != null) {\r
             toolx = e.getX();\r
@@ -684,12 +684,48 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
             redrawneeded = true;\r
             repaint();\r
         } else {\r
+            highlightSeqcanvas( -1);\r
             appletToolTip = null;\r
             redrawneeded = true;\r
             repaint();\r
         }\r
     }\r
 \r
+\r
+    void highlightSeqcanvas(int pos)\r
+    {\r
+      int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);\r
+\r
+      int size = pos==-1?0:3;\r
+\r
+      if(highlightRes!=null)\r
+        size += highlightRes.size()*3;\r
+\r
+      int [] array = new int[size];\r
+      int i=0;\r
+      if(highlightRes!=null)\r
+      {\r
+        for (i = 0; i < highlightRes.size(); i++)\r
+        {\r
+          int a = Integer.parseInt(highlightRes.elementAt(\r
+              i).toString())+1;\r
+          array[i * 3] = index;\r
+          array[ (i * 3) + 1] = a;\r
+          array[ (i * 3) + 2] = a;\r
+        }\r
+      }\r
+\r
+      if(pos!=-1)\r
+      {\r
+        array[i * 3] = index;\r
+        array[i * 3 + 1] = pos+1;\r
+        array[i * 3 + 2] = pos+1;\r
+      }\r
+\r
+      seqcanvas.highlightSearchResults(array);\r
+    }\r
+\r
+\r
     public void mouseClicked(MouseEvent e) {\r
     }\r
 \r
@@ -810,19 +846,25 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
 \r
         foundchain = -1;\r
 \r
-        for (int ii = 0; ii < pdb.chains.size(); ii++) {\r
+        for (int ii = 0; ii < pdb.chains.size(); ii++)\r
+        {\r
             PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);\r
+            int truex;\r
+            Bond tmpBond=null;\r
 \r
-            if (chain.isVisible) {\r
+            if (chain.isVisible)\r
+            {\r
                 Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;\r
 \r
-                for (int i = 0; i < bonds.size(); i++) {\r
-                    Bond tmpBond = (Bond) bonds.elementAt(i);\r
+                for (int i = 0; i < bonds.size(); i++)\r
+                {\r
+                    tmpBond = (Bond) bonds.elementAt(i);\r
 \r
-                    int truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +\r
+                    truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +\r
                         (getSize().width / 2));\r
 \r
-                    if (Math.abs(truex - x) <= 2) {\r
+                    if (Math.abs(truex - x) <= 2)\r
+                    {\r
                         int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +\r
                             (getSize().height / 2));\r
 \r
@@ -834,6 +876,25 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
                         }\r
                     }\r
                 }\r
+\r
+                // Still here? Maybe its the last bond\r
+\r
+                truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +\r
+                               (getSize().width / 2));\r
+\r
+                if (Math.abs(truex - x) <= 2)\r
+                {\r
+                  int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +\r
+                                     (getSize().height / 2));\r
+\r
+                  if (Math.abs(truey - y) <= 2)\r
+                  {\r
+                    fatom = tmpBond.at2;\r
+                    foundchain = ii;\r
+                    break;\r
+                  }\r
+                }\r
+\r
             }\r
 \r
             if (fatom != null) //)&& chain.ds != null)\r
@@ -850,6 +911,52 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       paint(g);\r
     }\r
 \r
+    public void highlightRes(int ii)\r
+   {\r
+\r
+     if (highlightRes != null\r
+         && highlightRes.contains((ii-1) + ""))\r
+     {\r
+       return;\r
+     }\r
+\r
+     int index = -1;\r
+     Bond tmpBond;\r
+     for(index=0; index<mainchain.bonds.size(); index++)\r
+     {\r
+       tmpBond = (Bond) mainchain.bonds.elementAt(index);\r
+       if (tmpBond.at1.alignmentMapping == ii - 1)\r
+       {\r
+         if (highlightBond1 != null)\r
+           highlightBond1.at2.isSelected = false;\r
+\r
+         if (highlightBond2 != null)\r
+           highlightBond2.at1.isSelected = false;\r
+\r
+         highlightBond1 = null;\r
+         highlightBond2 = null;\r
+\r
+         if (index > 0)\r
+         {\r
+           highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);\r
+           highlightBond1.at2.isSelected = true;\r
+         }\r
+\r
+         if (index != mainchain.bonds.size())\r
+         {\r
+           highlightBond2 = (Bond) mainchain.bonds.elementAt(index);\r
+           highlightBond2.at1.isSelected = true;\r
+         }\r
+\r
+         break;\r
+       }\r
+     }\r
+\r
+     redrawneeded = true;\r
+     repaint();\r
+   }\r
+\r
+\r
     public void setAllchainsVisible(boolean b)\r
     {\r
       for (int ii = 0; ii < pdb.chains.size(); ii++)\r
@@ -859,6 +966,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       }\r
       mainchain.isVisible = true;\r
       findCentre();\r
+      setupBonds();\r
+      redrawneeded = true;\r
+      repaint();\r
+\r
     }\r
 \r
 }\r

diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index 1ed4d10..3f4e42c 100755 (executable)
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -117,14 +117,6 @@ public class AppletPDBViewer extends Frame
             seqButton_actionPerformed();\r
           }\r
         });\r
-        molecule.setLabel("By Molecule");\r
-        molecule.addItemListener(new ItemListener()\r
-        {\r
-          public void itemStateChanged(ItemEvent e)\r
-          {\r
-            molecule_actionPerformed();\r
-          }\r
-        });\r
     allchains.setLabel("All Chains Visible");\r
     allchains.addItemListener(new ItemListener()\r
     {\r
@@ -141,7 +133,6 @@ public class AppletPDBViewer extends Frame
         coloursMenu.add(chain);\r
     coloursMenu.add(hydro);\r
     coloursMenu.add(charge);\r
-    coloursMenu.add(molecule);\r
     coloursMenu.addSeparator();\r
         coloursMenu.add(wire);\r
         coloursMenu.add(depth);\r
@@ -164,7 +155,6 @@ public class AppletPDBViewer extends Frame
       MenuItem chain = new MenuItem();\r
       MenuItem seqButton = new MenuItem();\r
 \r
-      CheckboxMenuItem molecule = new CheckboxMenuItem();\r
      CheckboxMenuItem allchains = new CheckboxMenuItem();\r
 \r
   public void charge_actionPerformed()\r
@@ -198,13 +188,6 @@ public class AppletPDBViewer extends Frame
         pdbcanvas.repaint();\r
       }\r
 \r
-      public void molecule_actionPerformed()\r
-      {\r
-        pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;\r
-        pdbcanvas.redrawneeded=true;\r
-        pdbcanvas.repaint();\r
-      }\r
-\r
       public void depth_actionPerformed()\r
       {\r
       pdbcanvas.depthcue = ! pdbcanvas.depthcue;\r