X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=276525b34f4ca81bd610a15743da984675cc8299;hb=75d17bc3d8444203906499e651df6a69f6c2f518;hp=166e5374a2c6a0c7f235952a088a4c591e4e9b1f;hpb=65bf1cd0ea1526762e829059bf6ae0901db9731d;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 166e537..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 {
@@ -34,7 +35,7 @@ public class PDBChain {
     public Vector residues = new Vector();
     public int offset;
     public Sequence sequence;
-    public boolean isVisible = false;
+    public boolean isVisible = true;
     public int pdbstart = 0;
     public int pdbend = 0;
     public int seqstart = 0;
@@ -57,22 +58,58 @@ public class PDBChain {
         return tmp;
     }
 
-    public void makeCaBondList() {
-        for (int i = 0; i < (residues.size() - 1); i++) {
+    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++)
+        {
             Residue tmpres = (Residue) residues.elementAt(i);
             Residue tmpres2 = (Residue) residues.elementAt(i + 1);
-            myAtom at1 = tmpres.findAtom("CA");
-            myAtom at2 = tmpres2.findAtom("CA");
+            Atom at1 = tmpres.findAtom("CA");
+            Atom at2 = tmpres2.findAtom("CA");
 
-            if ((at1 != null) && (at2 != null)) {
-                if (at1.chain.equals(at2.chain)) {
+            if ((at1 != null) && (at2 != null))
+            {
+                if (at1.chain.equals(at2.chain))
+                {
                     makeBond(at1, at2);
                 }
             }
         }
     }
 
-    public void makeBond(myAtom at1, myAtom at2) {
+    public void makeBond(Atom at1, Atom at2) {
         float[] start = new float[3];
         float[] end = new float[3];
 
@@ -89,11 +126,12 @@ public class PDBChain {
 
     public void makeResidueList() {
         int count = 0;
-        String seq = "";
+        StringBuffer seq = new StringBuffer();
 
-        for (int i = 0; i < atoms.size(); i++) {
-            myAtom tmp = (myAtom) atoms.elementAt(i);
-            //String resName = tmp.resName;
+        int i, iSize = atoms.size()-1;
+        for (i = 0; i < iSize; i++)
+        {
+            Atom tmp = (Atom) atoms.elementAt(i);
             int resNumber = tmp.resNumber;
             int res = resNumber;
 
@@ -103,18 +141,18 @@ public class PDBChain {
 
             Vector resAtoms = new Vector();
 
-            resAtoms.addElement((myAtom) atoms.elementAt(i));
+            resAtoms.addElement((Atom) atoms.elementAt(i));
             i++;
-            resNumber = ((myAtom) atoms.elementAt(i)).resNumber;
+            resNumber = ((Atom) atoms.elementAt(i)).resNumber;
 
             //Add atoms to a vector while the residue number
             //remains the same
             while ((resNumber == res) && (i < atoms.size())) {
-                resAtoms.addElement((myAtom) atoms.elementAt(i));
+                resAtoms.addElement((Atom) atoms.elementAt(i));
                 i++;
 
                 if (i < atoms.size()) {
-                    resNumber = ((myAtom) atoms.elementAt(i)).resNumber;
+                    resNumber = ((Atom) atoms.elementAt(i)).resNumber;
                 } else {
                     resNumber++;
                 }
@@ -128,23 +166,27 @@ public class PDBChain {
             count++;
 
             Residue tmpres = (Residue) residues.lastElement();
-            myAtom tmpat = (myAtom) tmpres.atoms.elementAt(0);
+            Atom tmpat = (Atom) tmpres.atoms.elementAt(0);
 
             // Keep totting up the sequence
-            if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {
-                System.err.println("PDBReader:Null aa3Hash for " +
-                    tmpat.resName);
+            if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null)
+            {
+                seq.append("X") ;
+               //  System.err.println("PDBReader:Null aa3Hash for " +
+               //     tmpat.resName);
             } else {
-                String tmpres2 = ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()
-                                                                                  .get(tmpat.resName)).intValue()];
-                seq = seq + tmpres2;
-            }
 
+                seq.append(ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()
+                                                                                  .get(tmpat.resName)).intValue()]);
+            }
         }
 
-        sequence = new Sequence("PDB_seq", seq, 1, seq.length());
+        if(id.length()<1 || id.equals(" "))
+           id = "_";
+
+        sequence = new Sequence(id, seq.toString(), 1, seq.length());
       //  System.out.println("PDB Sequence is :\nSequence = " + seq);
-      //  System.out.println("No of residues = " + residues.size());
+     //   System.out.println("No of residues = " + residues.size());
     }
 
     public void setChargeColours() {
@@ -229,59 +271,15 @@ public class PDBChain {
         }
     }
 
-    public void colourBySequence(jalview.gui.SequenceRenderer sr,
-                                 jalview.gui.FeatureRenderer fr)
-    {
 
+
+    public void setChainColours(Color col)
+    {
         for (int i = 0; i < bonds.size(); i++)
         {
             Bond tmp = (Bond) bonds.elementAt(i);
-
-                if ((tmp.at1.resNumber >= ((offset + pdbstart) - 1)) &&
-                        (tmp.at1.resNumber <= ((offset + pdbend) - 1)))
-                    {
-                    int pos = seqstart +
-                        (tmp.at1.resNumber - pdbstart - offset);
-
-
-                    int index = sequence.findIndex(pos);
-
-                    tmp.startCol = sr.findSequenceColour(Color.gray, sequence,  index);
-
-                    tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);
-
-                } else
-                {
-                    tmp.startCol = Color.gray;
-                }
-
-                if ((tmp.at2.resNumber >= ((offset + pdbstart) - 1)) &&
-                        (tmp.at2.resNumber <= ((pdbend + offset) - 1))) {
-                    int pos = seqstart +
-                        (tmp.at2.resNumber - pdbstart - offset);
-                    int index = sequence.findIndex(pos);
-
-                   tmp.endCol = sr.findSequenceColour(Color.gray, sequence, index);
-                   tmp.endCol = fr.findFeatureColour( tmp.endCol, sequence, index);
-                }
-                else
-                {
-                    tmp.endCol = Color.gray;
-                }
-        }
-    }
-
-    public void setChainColours() {
-        for (int i = 0; i < bonds.size(); i++) {
-            Bond tmp = (Bond) bonds.elementAt(i);
-
-            try {
-                tmp.startCol = (Color) ResidueProperties.getChainColours().get(id);
-                tmp.endCol = (Color) ResidueProperties.getChainColours().get(id);
-            } catch (Exception e) {
-                tmp.startCol = Color.lightGray;
-                tmp.endCol = Color.lightGray;
-            }
+            tmp.startCol = col;
+            tmp.endCol = col;
         }
     }
 }