From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 28 Nov 2005 17:13:54 +0000 (+0000)
Subject: Mapping for alignment added to residue
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=59349f26c3a53e4fb5da3ad1a506560124d62700;p=jalview.git

Mapping for alignment added to residue
---

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 6ae2baa..51c4f01 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -32,6 +32,7 @@ public class Atom {
     int type;
     Color color;
     String chain;
+    int alignmentMapping=-1;
 
     public boolean isSelected = false;
 
diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index b3eb23f..4672271 100755
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -88,7 +88,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         int pdbend = 0;
         int seqstart = 0;
         int seqend = 0;
-        int [] mapping = null;
+        AlignSeq maxAlignseq = null;;
 
         for (int i = 0; i < pdb.chains.size(); i++)
         {
@@ -126,7 +126,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
                 pdbend = as.seq2end;
                 seqstart = as.seq1start + sequence.getStart()-1;
                 seqend = as.seq1end + sequence.getEnd()-1;
-                mapping = as.getExactMapping();
+                maxAlignseq = as;
             }
 
             mappingDetails.append("\nPDB start/end "  + pdbstart + " " + pdbend);
@@ -140,7 +140,8 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         mainchain.seqstart = seqstart;
         mainchain.seqend = seqend;
         mainchain.isVisible = true;
-        mainchain.seqMapping = mapping;
+        mainchain.makeExactMapping(maxAlignseq, sequence);
+
       //  mainchain.sequence = sequence;
 
       this.pdb = pdb;
@@ -182,15 +183,6 @@ 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();
@@ -206,6 +198,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         ToolTipManager.sharedInstance().setDismissDelay(10000);
     }
 
+
     Vector visiblebonds;
     void setupBonds()
     {
@@ -463,6 +456,35 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       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)
@@ -477,34 +499,30 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
             (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))
         {
-
-          int pos = // chain.seqstart + Don't include seqstart here, start from 0
-              (tmp.at1.resNumber - chain.pdbstart - chain.offset)+1;
-
-            int index = chain.seqMapping[pos];
+            int index = findTrueIndex(tmp.at1.alignmentMapping);
+                //sequence.findIndex(tmp.at1.alignmentMapping);
             if (index != -1)
             {
-              tmp.startCol = seqcanvas.getSequenceRenderer().findSequenceColour(
-                  Color.lightGray, sequence, index);
+              tmp.startCol = seqcanvas.getSequenceRenderer().
+                  getResidueBoxColour( sequence, index);
 
-              tmp.startCol = seqcanvas.getFeatureRenderer().findFeatureColour(tmp.
-                  startCol, sequence, index);
+              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 + Don't include seqstart here, start from 0
-              (tmp.at2.resNumber - chain.pdbstart - chain.offset)+1;
 
-            int index = chain.seqMapping[pos];
+            int index =  findTrueIndex(tmp.at2.alignmentMapping);
+                //sequence.findIndex( tmp.at2.alignmentMapping );
             if (index != -1)
             {
-              tmp.endCol = seqcanvas.getSequenceRenderer().findSequenceColour(
-                  tmp.endCol, sequence, index);
-              tmp.endCol = seqcanvas.getFeatureRenderer().findFeatureColour(tmp.
-                  endCol, sequence, index);
+              tmp.endCol = seqcanvas.getSequenceRenderer().
+                  getResidueBoxColour( sequence, index);
+              tmp.endCol = seqcanvas.getFeatureRenderer().
+                  findFeatureColour(tmp.endCol, sequence, index);
             }
         }
       }
@@ -652,18 +670,15 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
             PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
             if (chain == mainchain)
             {
-              int pos = // chain.seqstart + Don't include seqstart here, start from 0
-                  (fatom.resNumber - chain.pdbstart - chain.offset) +1 ;
-
-              if (chain.seqMapping[pos] != -1)
+              if (fatom.alignmentMapping != -1)
               {
                 if (highlightRes == null)
                   highlightRes = new Vector();
 
-                if (highlightRes.contains((chain.seqMapping[pos]) + ""))
-                  highlightRes.remove((chain.seqMapping[pos]) + "");
+                if (highlightRes.contains(fatom.alignmentMapping+"" + ""))
+                  highlightRes.remove(fatom.alignmentMapping + "");
                 else
-                  highlightRes.add((chain.seqMapping[pos]) + "");
+                  highlightRes.add(fatom.alignmentMapping + "");
               }
             }
           }
@@ -695,10 +710,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
           chain = (PDBChain) pdb.chains.elementAt(foundchain);
           if(chain == mainchain)
           {
-           int pos = // chain.seqstart + Don't include seqstart here, start from 0
-               (fatom.resNumber - chain.pdbstart - chain.offset) +1 ;
-
-            highlightSeqcanvas( chain.seqMapping[pos] );
+            highlightSeqcanvas( fatom.alignmentMapping );
           }
         }
 
@@ -928,42 +940,41 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
    public void highlightRes(int ii)
   {
 
-    int index = ii - mainchain.seqstart;
-
-    if (highlightRes!=null
-        && highlightRes.contains( mainchain.seqMapping[index]+ ""))
+    if (highlightRes != null
+        && highlightRes.contains((ii-1) + ""))
     {
-       return;
+      return;
     }
 
-    if(highlightBond1!=null)
-      highlightBond1.at2.isSelected = false;
-
-    if(highlightBond2!=null)
-      highlightBond2.at1.isSelected = false;
-
-    highlightBond1 = null;
-    highlightBond2 = null;
+    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 )
-      return;
+        if (index > 0)
+        {
+          highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
+          highlightBond1.at2.isSelected = true;
+        }
 
-    if(index<=mainchain.bonds.size())
-    {
-      if(index>0)
-      {
-        highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
-        highlightBond1.at2.isSelected = true;
-       // highlightBond1.at2.isSelected = true;
-      }
+        if (index != mainchain.bonds.size())
+        {
+          highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+          highlightBond2.at1.isSelected = true;
+        }
 
-      if(index!=mainchain.bonds.size())
-      {
-        highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
-        highlightBond2.at1.isSelected = true;
-     //   highlightBond2.at2.isSelected = true;
+        break;
       }
     }
 
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 3cf73d1..276525b 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -25,6 +25,7 @@ import jalview.schemes.ResidueProperties;
 import java.awt.*;
 
 import java.util.*;
+import jalview.analysis.AlignSeq;
 
 
 public class PDBChain {
@@ -39,7 +40,6 @@ public class PDBChain {
     public int pdbend = 0;
     public int seqstart = 0;
     public int seqend = 0;
-    public int [] seqMapping;
 
     //public DrawableSequence ds;
     public PDBChain(String id) {
@@ -58,6 +58,38 @@ public class PDBChain {
         return tmp;
     }
 
+    void makeExactMapping(AlignSeq as, Sequence s1)
+    {
+        int pdbpos =   as.getSeq2Start()-2;
+        int alignpos = s1.getStart() + as.getSeq1Start()-3;
+
+        for(int i=0; i<as.astr1.length(); i++)
+        {
+            if (as.astr1.charAt(i) != '-')
+            {
+              alignpos++;
+            }
+
+            if (as.astr2.charAt(i) != '-')
+            {
+              pdbpos++;
+            }
+
+            if (as.astr1.charAt(i) == as.astr2.charAt(i))
+            {
+                Residue res = (Residue) residues.elementAt(pdbpos);
+                Enumeration en = res.atoms.elements();
+                while (en.hasMoreElements())
+                {
+                  Atom atom = (Atom) en.nextElement();
+                  atom.alignmentMapping = alignpos;
+                }
+            }
+        }
+
+    }
+
+
     public void makeCaBondList()
     {
         for (int i = 0; i < (residues.size() - 1); i++)