From 0c198a7cc68d8c9989e82dc785112b6efaa74e87 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 18 Jan 2007 18:19:04 +0000
Subject: [PATCH] fixed last-residue bug and added sequence feature creation
 and transfer for resNum+insCode annotation for each
 sequence residue

---
 src/MCview/PDBChain.java |  571 ++++++++++++++++++++++++----------------------
 1 file changed, 302 insertions(+), 269 deletions(-)

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 0cb9f02..a9d2d3a 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,269 +1,302 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* 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
-* 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 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;
-    }
-
-    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);
-            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);
-        }
-    }
-
-    public void makeBond(Atom at1, Atom 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;
-        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()]);
-            }
-        }
-
-        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() {
-        for (int i = 0; i < bonds.size(); i++) {
-            try {
-                Bond b = (Bond) bonds.elementAt(i);
-
-                if (b.at1.resName.equalsIgnoreCase("ASP") ||
-                        b.at1.resName.equalsIgnoreCase("GLU")) {
-                    b.startCol = Color.red;
-                } else if (b.at1.resName.equalsIgnoreCase("LYS") ||
-                        b.at1.resName.equalsIgnoreCase("ARG")) {
-                    b.startCol = Color.blue;
-                } else if (b.at1.resName.equalsIgnoreCase("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.equalsIgnoreCase("ASP") ||
-                        b.at2.resName.equalsIgnoreCase("GLU")) {
-                    b.endCol = Color.red;
-                } else if (b.at2.resName.equalsIgnoreCase("LYS") ||
-                        b.at2.resName.equalsIgnoreCase("ARG")) {
-                    b.endCol = Color.blue;
-                } else if (b.at2.resName.equalsIgnoreCase("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;
-            }
-        }
-    }
-
-
-    public void setChainColours(jalview.schemes.ColourSchemeI cs)
-    {
-        Bond b;
-        for (int i = 0; i < bonds.size(); i++) {
-            try {
-              b = (Bond) bonds.elementAt(i);
-
-            /*  ( (Bond) bonds.elementAt(i)).startCol = cs.findColour(
-                  ResidueProperties.codonTranslate(
-                      ResidueProperties.aa3Hash.get(b.at1.resName).toString().charAt(0)
-                  );
-
-              b.endCol = cs.findColour(
-                  ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.
-                                         get(b.at2.resName)).intValue()]
-                  );*/
-
-            } catch (Exception e)
-            {
-                b = (Bond) bonds.elementAt(i);
-                b.startCol = Color.gray;
-                b.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;
-        }
-    }
-}
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* 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
+* 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 {
+    /**
+     * SequenceFeature group for PDB File features added to sequences
+     */
+    private static final String PDBFILEFEATURE = "PDBFile";
+    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 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;
+    }
+
+    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;
+                }
+            }
+        }
+    }
+    /**
+     * copy over the RESNUM seqfeatures from the internal chain sequence to the mapped sequence
+     * @param seq
+     */
+    public void transferRESNUMFeatures(SequenceI seq, String status) {
+        if (seq != sequence) {
+            /** SequenceFeature[] seqsfeatures=seq.getSequenceFeatures();
+            int totfeat=seqsfeatures.length;
+            // Remove any features for this exact chain ?
+            for (int i=0; i<seqsfeatures.length; i++) {
+                
+            } */
+            if (status==null)
+                status = "IEA:jalview";
+            SequenceFeature[] features = sequence.getSequenceFeatures();
+            for (int i=0; i<features.length; i++) {
+                if (features[i].getFeatureGroup().equals(PDBChain.PDBFILEFEATURE)) {
+                    SequenceFeature tx = new SequenceFeature(features[i]);
+                    tx.setBegin(1+((Atom)((Residue)residues.elementAt(tx.getBegin()-offset)).atoms.elementAt(0)).alignmentMapping);
+                    tx.setEnd(1+((Atom)((Residue)residues.elementAt(tx.getEnd()-offset)).atoms.elementAt(0)).alignmentMapping);
+                    tx.setStatus(status+((tx.getStatus()==null || tx.getStatus().length()==0) ? "" : ":"+tx.getStatus()));
+                    seq.getDatasetSequence().addSequenceFeature(tx);
+                }
+            }
+            
+        }
+    }
+
+    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);
+        }
+    }
+
+    public void makeBond(Atom at1, Atom 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;
+        StringBuffer seq = new StringBuffer();
+        Vector resFeatures=new Vector();
+        int i, iSize = atoms.size()-1;
+        int resNumber=-1;
+        for (i = 0; i <= iSize; i++)
+        {
+            Atom tmp = (Atom) atoms.elementAt(i);
+            resNumber = tmp.resNumber;
+            int res = resNumber;
+
+            if (i == 0) {
+                offset = resNumber;
+            }
+
+            Vector resAtoms = new Vector();
+            //Add atoms to a vector while the residue number
+            //remains the same as the first atom's resNumber (res)
+            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));
+            
+            Residue tmpres = (Residue) residues.lastElement();
+            Atom tmpat = (Atom) tmpres.atoms.elementAt(0);
+            // Make A new SequenceFeature for the current residue numbering
+            SequenceFeature sf = 
+                new SequenceFeature("RESNUM",tmpat.resName+":"+tmpat.resNumIns,
+                        "",offset+count,offset+count,MCview.PDBChain.PDBFILEFEATURE);
+            resFeatures.addElement(sf);
+            // 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()]);
+            }
+            count++;
+        }
+
+        if(id.length()<1 || id.equals(" "))
+           id = "_";
+        
+        sequence = new Sequence(id, seq.toString(), offset, resNumber); // resNumber-offset ~= seq.size() 
+      //  System.out.println("PDB Sequence is :\nSequence = " + seq);
+     //   System.out.println("No of residues = " + residues.size());
+        for (i=0,iSize=resFeatures.size(); i<iSize; i++) {
+            sequence.addSequenceFeature((SequenceFeature) resFeatures.elementAt(i));
+            resFeatures.setElementAt(null, i);
+        }
+   }
+
+    public void setChargeColours() {
+        for (int i = 0; i < bonds.size(); i++) {
+            try {
+                Bond b = (Bond) bonds.elementAt(i);
+
+                if (b.at1.resName.equalsIgnoreCase("ASP") ||
+                        b.at1.resName.equalsIgnoreCase("GLU")) {
+                    b.startCol = Color.red;
+                } else if (b.at1.resName.equalsIgnoreCase("LYS") ||
+                        b.at1.resName.equalsIgnoreCase("ARG")) {
+                    b.startCol = Color.blue;
+                } else if (b.at1.resName.equalsIgnoreCase("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.equalsIgnoreCase("ASP") ||
+                        b.at2.resName.equalsIgnoreCase("GLU")) {
+                    b.endCol = Color.red;
+                } else if (b.at2.resName.equalsIgnoreCase("LYS") ||
+                        b.at2.resName.equalsIgnoreCase("ARG")) {
+                    b.endCol = Color.blue;
+                } else if (b.at2.resName.equalsIgnoreCase("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;
+            }
+        }
+    }
+
+
+    public void setChainColours(jalview.schemes.ColourSchemeI cs)
+    {
+        Bond b;
+        for (int i = 0; i < bonds.size(); i++) {
+            try {
+              b = (Bond) bonds.elementAt(i);
+
+            /*  ( (Bond) bonds.elementAt(i)).startCol = cs.findColour(
+                  ResidueProperties.codonTranslate(
+                      ResidueProperties.aa3Hash.get(b.at1.resName).toString().charAt(0)
+                  );
+
+              b.endCol = cs.findColour(
+                  ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.
+                                         get(b.at2.resName)).intValue()]
+                  );*/
+
+            } catch (Exception e)
+            {
+                b = (Bond) bonds.elementAt(i);
+                b.startCol = Color.gray;
+                b.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;
+        }
+    }
+}
-- 
1.7.10.2