X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=5f23a266bd21902c84b9ed881177e07bc9ccbf6b;hb=dfc5d2b04210799f956df7824eba3693eca592c8;hp=2e0ce30bd721ed429e6ae06227f2a2f4cfbd2d3f;hpb=e5127e5f27f02c8f328539eaac68eabfbee1d135;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 2e0ce30..5f23a26 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,265 +1,286 @@
-/* Copyright (C) 1998  Michele Clamp
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
- */
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 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
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
 package MCview;
 
 import jalview.datamodel.*;
+
 import jalview.schemes.ResidueProperties;
 
 import java.awt.*;
+
 import java.util.*;
+import jalview.analysis.AlignSeq;
 
 
 public class PDBChain {
+    public String id;
+    public Vector bonds = new Vector();
+    public Vector atoms = new Vector();
+    public Vector residues = new Vector();
+    public int offset;
+    public Sequence sequence;
+    public boolean isVisible = true;
+    public int pdbstart = 0;
+    public int pdbend = 0;
+    public int seqstart = 0;
+    public int seqend = 0;
+
+    public PDBChain(String id) {
+        this.id = id;
+    }
 
-  public String id;
-  public Vector bonds = new Vector();
-  public Vector atoms = new Vector();
-  public Vector residues = new Vector();
-  public int offset;
+    public String print() {
+        String tmp = "";
 
-  public Sequence sequence;
-  public boolean isVisible = false;
+        for (int i = 0; i < bonds.size(); i++) {
+            tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " " +
+                ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset +
+                "\n";
+        }
 
-  public int pdbstart=0, pdbend=0, seqstart=0, seqend=0;
+        return tmp;
+    }
 
-  //public DrawableSequence ds;
+    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 PDBChain(String id) {
-    this.id = id;
-  }
+    }
 
 
-  public String print() {
-    String tmp = "";
-    for (int i=0; i < bonds.size() ;i++) {
-      tmp = tmp + ((Bond)bonds.elementAt(i)).at1.resName + " " + ((Bond)bonds.elementAt(i)).at1.resNumber +" " + offset+ "\n";
-    }
-    return tmp;
-  }
-  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");
-      if ((at1 != null) && (at2 != null)) {
-        if (at1.chain.equals(at2.chain)) {
-          makeBond(at1,at2);
-        }
-      }
-    }
-  }
-
-  public void makeBond(myAtom at1, myAtom at2) {
-    float[] start = new float[3];
-    float[] end = new float[3];
-
-    start[0] = at1.x;
-    start[1] = at1.y;
-    start[2] = at1.z;
-
-    end[0] = at2.x;
-    end[1] = at2.y;
-    end[2] = at2.z;
-
-    bonds.addElement(new Bond(start, end, at1,at2));
-  }
-
-  public void makeResidueList() {
-    int count = 0;
-    String seq = "";
-    for (int i = 0; i < atoms.size(); i++) {
-
-      myAtom tmp = (myAtom)atoms.elementAt(i);
-      String resName = tmp.resName;
-      int resNumber = tmp.resNumber;
-      int res = resNumber;
-
-      if (i ==0) {
-        offset = resNumber;
-      }
-      Vector resAtoms = new Vector();
-
-      resAtoms.addElement((myAtom)atoms.elementAt(i));
-      i++;
-      resNumber = ((myAtom)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));
-        i++;
-        if (i < atoms.size()) {
-          resNumber = ((myAtom)atoms.elementAt(i)).resNumber;
-        } else {
-          resNumber++;
-        }
-      }
-
-      //We need this to keep in step with the outer for i = loop
-      i--;
-
-      //Make a new Residue object with the new atoms vector
-      residues.addElement(new Residue(resAtoms, resNumber - 1,count));
-      count++;
-      Residue tmpres = (Residue)residues.lastElement();
-      myAtom tmpat = (myAtom)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);
-      } else {
-        String tmpres2 =
-          ResidueProperties.aa[((Integer)ResidueProperties.getAA3Hash().get(tmpat.resName)).intValue()];
-        seq = seq + tmpres2;
-      }
-      //      System.out.println(tmpat.resName + " " + tmpres2);
-    }
-    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());
-  }
-
-  public void setChargeColours() {
-    for (int i = 0; i < bonds.size(); i++) {
-      try {
-        Bond b = (Bond)bonds.elementAt(i);
-
-        if (b.at1.resName.toUpperCase().equals("ASP") || b.at1.resName.toUpperCase().equals("GLU")) {
-          b.startCol = Color.red;
-        } else if (b.at1.resName.toUpperCase().equals("LYS") || b.at1.resName.toUpperCase().equals("ARG")) {
-          b.startCol = Color.blue;
-        } else if (b.at1.resName.toUpperCase().equals("CYS")) {
-          b.startCol = Color.yellow;
-        } else {
-          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")) {
-          b.endCol = Color.red;
-        } else if (b.at2.resName.toUpperCase().equals("LYS") || b.at2.resName.toUpperCase().equals("ARG")) {
-          b.endCol = Color.blue;
-        } else if (b.at2.resName.toUpperCase().equals("CYS")) {
-          b.endCol = Color.yellow;
-        } else {
-          int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();
-          b.endCol = Color.lightGray;
+    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);
+            Atom at1 = tmpres.findAtom("CA");
+            Atom at2 = tmpres2.findAtom("CA");
+
+            if ((at1 != null) && (at2 != null))
+            {
+                if (at1.chain.equals(at2.chain))
+                {
+                    makeBond(at1, at2);
+                }
+            }
+            else
+              System.out.println("not found "+i);
         }
-      } catch (Exception e) {
-        Bond b = (Bond)bonds.elementAt(i);
-        b.startCol = Color.gray;
-        b.endCol = Color.gray;
-      }
     }
-  }
 
-  public void setHydrophobicityColours() {
-    float hydmin = (float)ResidueProperties.getHydmin();
-    float hydmax = (float)ResidueProperties.getHydmax();
-    double[] hyd  = ResidueProperties.getHyd();
+    public void makeBond(Atom at1, Atom at2) {
+        float[] start = new float[3];
+        float[] end = new float[3];
 
-    Hashtable AA3Hash = ResidueProperties.getAA3Hash();
+        start[0] = at1.x;
+        start[1] = at1.y;
+        start[2] = at1.z;
 
-    for (int i = 0; i < bonds.size(); i++) {
-      try {
-        Bond b = (Bond)bonds.elementAt(i);
+        end[0] = at2.x;
+        end[1] = at2.y;
+        end[2] = at2.z;
 
-        int   atno = ((Integer)AA3Hash.get(b.at1.resName.toUpperCase())).intValue();
-        float red  = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);
+        bonds.addElement(new Bond(start, end, at1, at2));
+    }
 
-        if (red > (float)1.0) {
-          red = (float)1.0;
-        }
-        if (red < (float)0.0) {
-          red = (float)0.0;
+    public void makeResidueList() {
+        int count = 0;
+        StringBuffer seq = new StringBuffer();
+
+        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;
+
+            if (i == 0) {
+                offset = resNumber;
+            }
+
+            Vector resAtoms = new Vector();
+
+            resAtoms.addElement((Atom) atoms.elementAt(i));
+            i++;
+            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((Atom) atoms.elementAt(i));
+                i++;
+
+                if (i < atoms.size()) {
+                    resNumber = ((Atom) atoms.elementAt(i)).resNumber;
+                } else {
+                    resNumber++;
+                }
+            }
+
+            //We need this to keep in step with the outer for i = loop
+            i--;
+
+            //Make a new Residue object with the new atoms vector
+            residues.addElement(new Residue(resAtoms, resNumber - 1, count));
+            count++;
+
+            Residue tmpres = (Residue) residues.lastElement();
+            Atom tmpat = (Atom) tmpres.atoms.elementAt(0);
+
+            // Keep totting up the sequence
+            if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null)
+            {
+                seq.append("X") ;
+               //  System.err.println("PDBReader:Null aa3Hash for " +
+               //     tmpat.resName);
+            } else {
+
+                seq.append(ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()
+                                                                                  .get(tmpat.resName)).intValue()]);
+            }
         }
 
-        b.startCol = new Color(red,(float)0.0,(float)1.0-red);
-        atno = ((Integer)AA3Hash.get(b.at2.resName.toUpperCase())).intValue();
+        if(id.length()<1 || id.equals(" "))
+           id = "_";
 
-        red = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);
+        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());
+    }
 
-        if (red > (float)1.0) {
-          red = (float)1.0;
+    public void setChargeColours() {
+        for (int i = 0; i < bonds.size(); i++) {
+            try {
+                Bond b = (Bond) bonds.elementAt(i);
+
+                if (b.at1.resName.toUpperCase().equals("ASP") ||
+                        b.at1.resName.toUpperCase().equals("GLU")) {
+                    b.startCol = Color.red;
+                } else if (b.at1.resName.toUpperCase().equals("LYS") ||
+                        b.at1.resName.toUpperCase().equals("ARG")) {
+                    b.startCol = Color.blue;
+                } else if (b.at1.resName.toUpperCase().equals("CYS")) {
+                    b.startCol = Color.yellow;
+                } else {
+                    //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")) {
+                    b.endCol = Color.red;
+                } else if (b.at2.resName.toUpperCase().equals("LYS") ||
+                        b.at2.resName.toUpperCase().equals("ARG")) {
+                    b.endCol = Color.blue;
+                } else if (b.at2.resName.toUpperCase().equals("CYS")) {
+                    b.endCol = Color.yellow;
+                } else {
+                    //int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();
+                    b.endCol = Color.lightGray;
+                }
+            } catch (Exception e) {
+                Bond b = (Bond) bonds.elementAt(i);
+                b.startCol = Color.gray;
+                b.endCol = Color.gray;
+            }
         }
-        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);
-        b.startCol = Color.gray;
-        b.endCol = Color.gray;
-      }
     }
-  }
 
+    public void setHydrophobicityColours() {
+        float hydmin = (float) ResidueProperties.getHydmin();
+        float hydmax = (float) ResidueProperties.getHydmax();
+        double[] hyd = ResidueProperties.getHyd();
 
-  public void colourBySequence(jalview.gui.AlignViewport av, Sequence seq) {
-jalview.gui.SequenceRenderer sr = new jalview.gui.SequenceRenderer(av);
+        Hashtable AA3Hash = ResidueProperties.getAA3Hash();
 
+        for (int i = 0; i < bonds.size(); i++) {
+            try {
+                Bond b = (Bond) bonds.elementAt(i);
 
-    for (int i = 0; i < bonds.size(); i++) {
-      Bond tmp = (Bond)bonds.elementAt(i);
-      try {
+                int atno = ((Integer) AA3Hash.get(b.at1.resName.toUpperCase())).intValue();
+                float red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);
 
-        if (tmp.at1.resNumber >= (offset + pdbstart - 1) && tmp.at1.resNumber <= (offset + pdbend - 1)) {
+                if (red > (float) 1.0) {
+                    red = (float) 1.0;
+                }
 
-          int pos   = seqstart + (tmp.at1.resNumber - pdbstart - offset) ;
-          int index = seq.findIndex(pos);
+                if (red < (float) 0.0) {
+                    red = (float) 0.0;
+                }
 
+                b.startCol = new Color(red, (float) 0.0, (float) 1.0 - red);
+                atno = ((Integer) AA3Hash.get(b.at2.resName.toUpperCase())).intValue();
 
-          tmp.startCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);
+                red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);
 
-        } else {
-          tmp.startCol = Color.gray;
-        }
+                if (red > (float) 1.0) {
+                    red = (float) 1.0;
+                }
 
-        if (tmp.at2.resNumber >= (offset + pdbstart -1) && tmp.at2.resNumber <= (pdbend+offset-1)) {
+                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);
+                b.startCol = Color.gray;
+                b.endCol = Color.gray;
+            }
+        }
+    }
 
-          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;
+    public void setChainColours(Color col)
+    {
+        for (int i = 0; i < bonds.size(); i++)
+        {
+            Bond tmp = (Bond) bonds.elementAt(i);
+            tmp.startCol = col;
+            tmp.endCol = col;
         }
-      } catch (Exception e) {
-        tmp.startCol = Color.lightGray;
-        tmp.endCol = Color.lightGray;
-      }
     }
-  }
-
-  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;
-      }
-    }
-  }
 }
-
-