X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=ddf05e1320e827b35ea4d32d8aef973135ad335f;hb=f1bef1a257c565ebf63ff5f55e62f48329f5bf81;hp=4bfe2559558fc7d7c75ca3c99a10c58a6b524b23;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 4bfe255..ddf05e1 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -25,6 +25,7 @@ import jalview.schemes.ResidueProperties;
 import java.awt.*;
 
 import java.util.*;
+import jalview.analysis.AlignSeq;
 
 
 public class PDBChain {
@@ -34,13 +35,12 @@ 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;
     public int seqend = 0;
 
-    //public DrawableSequence ds;
     public PDBChain(String id) {
         this.id = id;
     }
@@ -57,22 +57,60 @@ 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);
                 }
             }
+            else
+              System.out.println("not found "+i);
         }
     }
 
-    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 +127,12 @@ 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 +142,18 @@ 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++;
                 }
@@ -128,24 +167,27 @@ 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;
-            }
 
-            //      System.out.println(tmpat.resName + " " + tmpres2);
+                seq.append(ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()
+                                                                                  .get(tmpat.resName)).intValue()]);
+            }
         }
 
-        sequence = new Sequence("PDB_seq", seq, 1, seq.length());
-        System.out.println("PDB Sequence is :\nSequence = " + seq);
-        System.out.println("No of residues = " + residues.size());
+        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());
     }
 
     public void setChargeColours() {
@@ -153,29 +195,29 @@ public class PDBChain {
             try {
                 Bond b = (Bond) bonds.elementAt(i);
 
-                if (b.at1.resName.toUpperCase().equals("ASP") ||
-                        b.at1.resName.toUpperCase().equals("GLU")) {
+                if (b.at1.resName.equalsIgnoreCase("ASP") ||
+                        b.at1.resName.equalsIgnoreCase("GLU")) {
                     b.startCol = Color.red;
-                } else if (b.at1.resName.toUpperCase().equals("LYS") ||
-                        b.at1.resName.toUpperCase().equals("ARG")) {
+                } else if (b.at1.resName.equalsIgnoreCase("LYS") ||
+                        b.at1.resName.equalsIgnoreCase("ARG")) {
                     b.startCol = Color.blue;
-                } else if (b.at1.resName.toUpperCase().equals("CYS")) {
+                } else if (b.at1.resName.equalsIgnoreCase("CYS")) {
                     b.startCol = Color.yellow;
                 } else {
-                    int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();
+                    //int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();
                     b.startCol = Color.lightGray;
                 }
 
-                if (b.at2.resName.toUpperCase().equals("ASP") ||
-                        b.at2.resName.toUpperCase().equals("GLU")) {
+                if (b.at2.resName.equalsIgnoreCase("ASP") ||
+                        b.at2.resName.equalsIgnoreCase("GLU")) {
                     b.endCol = Color.red;
-                } else if (b.at2.resName.toUpperCase().equals("LYS") ||
-                        b.at2.resName.toUpperCase().equals("ARG")) {
+                } else if (b.at2.resName.equalsIgnoreCase("LYS") ||
+                        b.at2.resName.equalsIgnoreCase("ARG")) {
                     b.endCol = Color.blue;
-                } else if (b.at2.resName.toUpperCase().equals("CYS")) {
+                } else if (b.at2.resName.equalsIgnoreCase("CYS")) {
                     b.endCol = Color.yellow;
                 } else {
-                    int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();
+                    //int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();
                     b.endCol = Color.lightGray;
                 }
             } catch (Exception e) {
@@ -186,98 +228,42 @@ public class PDBChain {
         }
     }
 
-    public void setHydrophobicityColours() {
-        float hydmin = (float) ResidueProperties.getHydmin();
-        float hydmax = (float) ResidueProperties.getHydmax();
-        double[] hyd = ResidueProperties.getHyd();
-
-        Hashtable AA3Hash = ResidueProperties.getAA3Hash();
 
+    public void setChainColours(jalview.schemes.ColourSchemeI cs)
+    {
+        Bond b;
         for (int i = 0; i < bonds.size(); i++) {
             try {
-                Bond b = (Bond) bonds.elementAt(i);
-
-                int atno = ((Integer) AA3Hash.get(b.at1.resName.toUpperCase())).intValue();
-                float red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);
+              b = (Bond) bonds.elementAt(i);
 
-                if (red > (float) 1.0) {
-                    red = (float) 1.0;
-                }
-
-                if (red < (float) 0.0) {
-                    red = (float) 0.0;
-                }
+              ( (Bond) bonds.elementAt(i)).startCol = cs.findColour(
+                  ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.
+                                         get(b.at1.resName)).intValue()]
+                  );
 
-                b.startCol = new Color(red, (float) 0.0, (float) 1.0 - red);
-                atno = ((Integer) AA3Hash.get(b.at2.resName.toUpperCase())).intValue();
-
-                red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);
-
-                if (red > (float) 1.0) {
-                    red = (float) 1.0;
-                }
+              b.endCol = cs.findColour(
+                  ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.
+                                         get(b.at2.resName)).intValue()]
+                  );
 
-                if (red < (float) 0.0) {
-                    red = (float) 0.0;
-                }
-
-                b.endCol = new Color(red, (float) 0.2, (float) 1.0 - red);
-            } catch (Exception e) {
-                Bond b = (Bond) bonds.elementAt(i);
+            } catch (Exception e)
+            {
+                b = (Bond) bonds.elementAt(i);
                 b.startCol = Color.gray;
                 b.endCol = Color.gray;
             }
         }
     }
 
-    public void colourBySequence(jalview.gui.AlignViewport av, Sequence seq) {
-        jalview.gui.SequenceRenderer sr = new jalview.gui.SequenceRenderer(av);
-
-        for (int i = 0; i < bonds.size(); i++) {
-            Bond tmp = (Bond) bonds.elementAt(i);
-
-            try {
-                if ((tmp.at1.resNumber >= ((offset + pdbstart) - 1)) &&
-                        (tmp.at1.resNumber <= ((offset + pdbend) - 1))) {
-                    int pos = seqstart +
-                        (tmp.at1.resNumber - pdbstart - offset);
-                    int index = seq.findIndex(pos);
-
-                    tmp.startCol = sr.getResidueBoxColour(av.getGlobalColourScheme(),
-                            seq, 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 = seq.findIndex(pos);
 
-                    tmp.endCol = sr.getResidueBoxColour(av.getGlobalColourScheme(),
-                            seq, index);
-                } else {
-                    tmp.endCol = Color.gray;
-                }
-            } catch (Exception e) {
-                tmp.startCol = Color.lightGray;
-                tmp.endCol = Color.lightGray;
-            }
-        }
-    }
-
-    public void setChainColours() {
-        for (int i = 0; i < bonds.size(); i++) {
+    public void setChainColours(Color col)
+    {
+        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;
         }
     }
 }