X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=a3505c70c981271351d7915b411aaf87cbf90682;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=a9d2d3a6e6251b431ddafcab79b004b0377de1cc;hpb=0c198a7cc68d8c9989e82dc785112b6efaa74e87;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index a9d2d3a..a3505c7 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,302 +1,595 @@
 /*
-* 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
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package MCview;
 
-import jalview.datamodel.*;
-
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureMapping;
 
-import java.awt.*;
+import java.awt.Color;
+import java.util.List;
+import java.util.Vector;
 
-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";
 
+  private static final String IEASTATUS = "IEA:jalview";
 
-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 id;
 
-    public String print() {
-        String tmp = "";
+  public Vector<Bond> bonds = new Vector<Bond>();
 
-        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 Vector<Atom> atoms = new Vector<Atom>();
 
-        return tmp;
-    }
+  public Vector<Residue> residues = new Vector<Residue>();
 
-    void makeExactMapping(AlignSeq as, Sequence s1)
-    {
-        int pdbpos =   as.getSeq2Start()-2;
-        int alignpos = s1.getStart() + as.getSeq1Start()-3;
+  public int offset;
 
-        for(int i=0; i<as.astr1.length(); i++)
-        {
-            if (as.astr1.charAt(i) != '-')
-            {
-              alignpos++;
-            }
+  /**
+   * sequence is the sequence extracted by the chain parsing code
+   */
+  public SequenceI sequence;
 
-            if (as.astr2.charAt(i) != '-')
-            {
-              pdbpos++;
-            }
+  /**
+   * shadow is the sequence created by any other parsing processes (e.g. Jmol,
+   * RNAview)
+   */
+  public SequenceI shadow = null;
 
-            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 boolean isNa = false;
+
+  public boolean isVisible = true;
+
+  public int pdbstart = 0;
+
+  public int pdbend = 0;
+
+  public int seqstart = 0;
+
+  public int seqend = 0;
+
+  public String pdbid = "";
+
+  public PDBChain(String pdbid, String id)
+  {
+    this.pdbid = pdbid.toLowerCase();
+    this.id = id;
+  }
+
+  /**
+   * character used to write newlines
+   */
+  protected String newline = System.getProperty("line.separator");
+
+  public Mapping shadowMap;
+
+  public void setNewlineString(String nl)
+  {
+    newline = nl;
+  }
+
+  public String getNewlineString()
+  {
+    return newline;
+  }
+
+  public String print()
+  {
+    StringBuilder tmp = new StringBuilder(256);
+
+    for (Bond b : bonds)
+    {
+      tmp.append(b.at1.resName).append(" ").append(b.at1.resNumber)
+              .append(" ").append(offset).append(newline);
+    }
+
+    return tmp.toString();
+  }
+
+  /**
+   * Annotate the residues with their corresponding positions in s1 using the
+   * alignment in as NOTE: This clears all atom.alignmentMapping values on the
+   * structure.
+   * 
+   * @param as
+   * @param s1
+   */
+  public void makeExactMapping(AlignSeq as, SequenceI s1)
+  {
+    int pdbpos = as.getSeq2Start() - 2;
+    int alignpos = s1.getStart() + as.getSeq1Start() - 3;
+    // first clear out any old alignmentMapping values:
+    for (Atom atom : atoms)
+    {
+      atom.alignmentMapping = -1;
+    }
+    // and now trace the alignment onto the atom set.
+    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 = residues.elementAt(pdbpos);
+        for (Atom atom : res.atoms)
+        {
+          atom.alignmentMapping = alignpos;
         }
+      }
+    }
+  }
+
+  /**
+   * copy over the RESNUM seqfeatures from the internal chain sequence to the
+   * mapped sequence
+   * 
+   * @param seq
+   * @param status
+   *          The Status of the transferred annotation
+   * @return the features added to sq (or its dataset)
+   */
+  public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
+          String status)
+  {
+    SequenceI sq = seq;
+    while (sq != null && sq.getDatasetSequence() != null)
+    {
+      sq = sq.getDatasetSequence();
+      if (sq == sequence)
+      {
+        return null;
+      }
     }
     /**
-     * copy over the RESNUM seqfeatures from the internal chain sequence to the mapped sequence
-     * @param seq
+     * Remove any existing features for this chain if they exist ?
+     * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
+     * totfeat=seqsfeatures.length; // Remove any features for this exact chain
+     * ? for (int i=0; i<seqsfeatures.length; i++) { }
      */
-    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);
-                }
-            }
-            
+    if (status == null)
+    {
+      status = PDBChain.IEASTATUS;
+    }
+    SequenceFeature[] features = sequence.getSequenceFeatures();
+    for (int i = 0; i < features.length; i++)
+    {
+      if (features[i].getFeatureGroup().equals(pdbid))
+      {
+        SequenceFeature tx = new SequenceFeature(features[i]);
+        tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
+                .elementAt(0).alignmentMapping);
+        tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms
+                .elementAt(0).alignmentMapping);
+        tx.setStatus(status
+                + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
+                        : ":" + tx.getStatus()));
+        if (tx.begin != 0 && tx.end != 0)
+        {
+          sq.addSequenceFeature(tx);
         }
+      }
     }
-
-    public void makeCaBondList()
+    return features;
+  }
+
+  /**
+   * Traverses the list of residues and constructs bonds where CA-to-CA atoms or
+   * P-to-P atoms are found. Also sets the 'isNa' flag if more than 99% of
+   * residues contain a P not a CA.
+   */
+  public void makeCaBondList()
+  {
+    boolean na = false;
+    int numNa = 0;
+    for (int i = 0; i < (residues.size() - 1); i++)
     {
-        for (int i = 0; i < (residues.size() - 1); i++)
+      Residue tmpres = residues.elementAt(i);
+      Residue tmpres2 = residues.elementAt(i + 1);
+      Atom at1 = tmpres.findAtom("CA");
+      Atom at2 = tmpres2.findAtom("CA");
+      na = false;
+      if ((at1 == null) && (at2 == null))
+      {
+        na = true;
+        at1 = tmpres.findAtom("P");
+        at2 = tmpres2.findAtom("P");
+      }
+      if ((at1 != null) && (at2 != null))
+      {
+        if (at1.chain.equals(at2.chain))
         {
-            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);
+          if (na)
+          {
+            numNa++;
+          }
+          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));
+    /*
+     * If > 99% 'P', flag as nucleotide; note the count doesn't include the last
+     * residue
+     */
+    if (residues.size() > 0 && (numNa / (residues.size() - 1) > 0.99))
+    {
+      isNa = true;
     }
-
-    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++)
+  }
+
+  /**
+   * Construct a bond from atom1 to atom2 and add it to the list of bonds for
+   * this chain
+   * 
+   * @param at1
+   * @param at2
+   */
+  public void makeBond(Atom at1, Atom at2)
+  {
+    bonds.addElement(new Bond(at1, at2));
+  }
+
+  /**
+   * Traverses the list of atoms and
+   * <ul>
+   * <li>constructs a list of Residues, each containing all the atoms that share
+   * the same residue number</li>
+   * <li>adds a RESNUM sequence feature for each position</li>
+   * <li>creates the sequence string</li>
+   * <li>determines if nucleotide</li>
+   * <li>saves the residue number of the first atom as 'offset'</li>
+   * <li>adds temp factor annotation if the flag is set to do so</li>
+   * </ul>
+   * 
+   * @param visibleChainAnnotation
+   */
+  public void makeResidueList(boolean visibleChainAnnotation)
+  {
+    int count = 0;
+    Object symbol;
+    boolean deoxyn = false;
+    boolean nucleotide = false;
+    StringBuilder seq = new StringBuilder(256);
+    Vector<SequenceFeature> resFeatures = new Vector<SequenceFeature>();
+    Vector<Annotation> resAnnotation = new Vector<Annotation>();
+    int i, iSize = atoms.size() - 1;
+    int resNumber = -1;
+    for (i = 0; i <= iSize; i++)
+    {
+      Atom tmp = atoms.elementAt(i);
+      resNumber = tmp.resNumber;
+      int res = resNumber;
+
+      if (i == 0)
+      {
+        offset = resNumber;
+      }
+
+      Vector<Atom> resAtoms = new Vector<Atom>();
+      // 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.add(atoms.elementAt(i));
+        i++;
+
+        if (i < atoms.size())
         {
-            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++;
+          resNumber = atoms.elementAt(i).resNumber;
         }
-
-        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);
+        else
+        {
+          resNumber++;
         }
-   }
-
-    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;
-            }
+      }
+
+      // 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 = residues.lastElement();
+      Atom tmpat = tmpres.atoms.get(0);
+      // Make A new SequenceFeature for the current residue numbering
+      SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
+              + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
+              + count, offset + count, pdbid);
+      // MCview.PDBChain.PDBFILEFEATURE);
+      resFeatures.addElement(sf);
+      resAnnotation.addElement(new Annotation(tmpat.tfactor));
+      // Keep totting up the sequence
+      if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
+      {
+        String nucname = tmpat.resName.trim();
+        // use the aaIndex rather than call 'toLower' - which would take a bit
+        // more time.
+        deoxyn = nucname.length() == 2
+                && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D'];
+        if (tmpat.name.equalsIgnoreCase("CA")
+                || ResidueProperties.nucleotideIndex[nucname
+                        .charAt((deoxyn ? 1 : 0))] == -1)
+        {
+          seq.append("X");
+          // System.err.println("PDBReader:Null aa3Hash for " +
+          // tmpat.resName);
         }
+        else
+        {
+          // nucleotide flag
+          nucleotide = true;
+          seq.append(nucname.charAt((deoxyn ? 1 : 0)));
+        }
+      }
+      else
+      {
+        if (nucleotide)
+        {
+          System.err
+                  .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
+        }
+        seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
+      }
+      count++;
     }
 
-
-    public void setChainColours(jalview.schemes.ColourSchemeI cs)
+    if (id.length() < 1)
     {
-        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;
-            }
+      id = " ";
+    }
+    isNa = nucleotide;
+    sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
+    // resNumber-offset
+    // ~=
+    // seq.size()
+    // Add normalised feature scores to RESNUM indicating start/end of sequence
+    // sf.setScore(offset+count);
+
+    // 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(resFeatures.elementAt(i));
+      resFeatures.setElementAt(null, i);
+    }
+    if (visibleChainAnnotation)
+    {
+      Annotation[] annots = new Annotation[resAnnotation.size()];
+      float max = 0;
+      for (i = 0, iSize = annots.length; i < iSize; i++)
+      {
+        annots[i] = resAnnotation.elementAt(i);
+        if (annots[i].value > max)
+        {
+          max = annots[i].value;
         }
+        resAnnotation.setElementAt(null, i);
+      }
+
+      AlignmentAnnotation tfactorann = new AlignmentAnnotation(
+              "Temperature Factor", "Temperature Factor for " + pdbid + id,
+              annots, 0, max, AlignmentAnnotation.LINE_GRAPH);
+      tfactorann.setSequenceRef(sequence);
+      sequence.addAlignmentAnnotation(tfactorann);
     }
+  }
+
+  /**
+   * Colour start/end of bonds by charge
+   * <ul>
+   * <li>ASP and GLU red</li>
+   * <li>LYS and ARG blue</li>
+   * <li>CYS yellow</li>
+   * <li>others light gray</li>
+   * </ul>
+   */
+  public void setChargeColours()
+  {
+    for (Bond b : bonds)
+    {
+      if (b.at1 != null && b.at2 != null)
+      {
+        b.startCol = getChargeColour(b.at1.resName);
+        b.endCol = getChargeColour(b.at2.resName);
+      }
+      else
+      {
+        b.startCol = Color.gray;
+        b.endCol = Color.gray;
+      }
+    }
+  }
 
+  public static Color getChargeColour(String resName)
+  {
+    Color result = Color.lightGray;
+    if ("ASP".equals(resName) || "GLU".equals(resName))
+    {
+      result = Color.red;
+    }
+    else if ("LYS".equals(resName) || "ARG".equals(resName))
+    {
+      result = Color.blue;
+    }
+    else if ("CYS".equals(resName))
+    {
+      result = Color.yellow;
+    }
+    return result;
+  }
+
+  /**
+   * Sets the start/end colours of bonds to those of the start/end atoms
+   * according to the specified colour scheme. Note: currently only works for
+   * peptide residues.
+   * 
+   * @param cs
+   */
+  public void setChainColours(ColourSchemeI cs)
+  {
+    int index;
+    for (Bond b : bonds)
+    {
+      try
+      {
+        index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
+        b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+
+        index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
+        b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+
+      } catch (Exception e)
+      {
+        b.startCol = Color.gray;
+        b.endCol = Color.gray;
+      }
+    }
+  }
 
-
-    public void setChainColours(Color col)
+  public void setChainColours(Color col)
+  {
+    for (Bond b : bonds)
+    {
+      b.startCol = col;
+      b.endCol = col;
+    }
+  }
+
+  /**
+   * copy any sequence annotation onto the sequence mapped using the provided
+   * StructureMapping
+   * 
+   * @param mapping
+   *          - positional mapping between destination sequence and pdb resnum
+   * @param sqmpping
+   *          - mapping between destination sequence and local chain
+   */
+  public void transferResidueAnnotation(StructureMapping mapping,
+          jalview.datamodel.Mapping sqmpping)
+  {
+    SequenceI sq = mapping.getSequence();
+    SequenceI dsq = sq;
+    if (sq != null)
     {
-        for (int i = 0; i < bonds.size(); i++)
+      while (dsq.getDatasetSequence() != null)
+      {
+        dsq = dsq.getDatasetSequence();
+      }
+      // any annotation will be transferred onto the dataset sequence
+
+      if (shadow != null && shadow.getAnnotation() != null)
+      {
+
+        for (AlignmentAnnotation ana : shadow.getAnnotation())
         {
-            Bond tmp = (Bond) bonds.elementAt(i);
-            tmp.startCol = col;
-            tmp.endCol = col;
+          List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
+                  ana.getCalcId(), ana.label);
+          if (transfer == null || transfer.size() == 0)
+          {
+            ana = new AlignmentAnnotation(ana);
+            ana.liftOver(sequence, shadowMap);
+            ana.liftOver(dsq, sqmpping);
+            dsq.addAlignmentAnnotation(ana);
+          }
+          else
+          {
+            continue;
+          }
+        }
+      }
+      else
+      {
+        if (sequence != null && sequence.getAnnotation() != null)
+        {
+          for (AlignmentAnnotation ana : sequence.getAnnotation())
+          {
+            List<AlignmentAnnotation> transfer = sq
+                    .getAlignmentAnnotations(ana.getCalcId(), ana.label);
+            if (transfer == null || transfer.size() == 0)
+            {
+              ana = new AlignmentAnnotation(ana);
+              ana.liftOver(dsq, sqmpping);
+              // mapping.transfer(ana);
+            }
+            else
+            {
+              continue;
+            }
+          }
+        }
+      }
+      if (false)
+      {
+        // Useful for debugging mappings - adds annotation for mapped position
+        float min = -1, max = 0;
+        Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
+        for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)
+        {
+          int prn = mapping.getPDBResNum(k + 1);
+
+          an[k] = new Annotation(prn);
+          if (min == -1)
+          {
+            min = k;
+            max = k;
+          }
+          else
+          {
+            if (min > k)
+            {
+              min = k;
+            }
+            else if (max < k)
+            {
+              max = k;
+            }
+          }
         }
+        sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
+                "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
+                an, min, max, AlignmentAnnotation.LINE_GRAPH));
+      }
     }
+  }
 }