X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=dc3743e1bbf538fb868d2018971452b5d88a5072;hb=01a481ba71d1163cab48e586d4dca218f6323ff7;hp=a9d2d3a6e6251b431ddafcab79b004b0377de1cc;hpb=0c198a7cc68d8c9989e82dc785112b6efaa74e87;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index a9d2d3a..dc3743e 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,302 +1,362 @@
 /*
-* 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
+ * Copyright (C) 2007 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;
 
+import java.awt.*;
 
-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;
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+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 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 String pdbid = "";
+  public PDBChain(String pdbid, String id)
+  {
+    this.pdbid = pdbid.toLowerCase();
+    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";
     }
 
-    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;
+  }
 
-        return tmp;
-    }
+  void makeExactMapping(AlignSeq as, Sequence s1)
+  {
+    int pdbpos = as.getSeq2Start() - 2;
+    int alignpos = s1.getStart() + as.getSeq1Start() - 3;
 
-    void makeExactMapping(AlignSeq as, Sequence s1)
+    for (int i = 0; i < as.astr1.length(); i++)
     {
-        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())
         {
-            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;
-                }
-            }
+          Atom atom = (Atom) en.nextElement();
+          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)
+    {
+      if (sq == sequence)
+      {
+        return null;
+      }
+      sq = sq.getDatasetSequence();
     }
     /**
-     * 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);
-                }
-            }
-            
-        }
+     * 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++) {
+        } */
+    if (status == null)
+    {
+      status = PDBChain.IEASTATUS;
+    }
+    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.addSequenceFeature(tx);
+      }
     }
+    return features;
+  }
 
-    public void makeCaBondList()
+  public void makeCaBondList()
+  {
+    for (int i = 0; i < (residues.size() - 1); i++)
     {
-        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))
         {
-            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);
+          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 + " " +
+                              pdbid + id,
+                              "", 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++;
     }
 
-    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;
+    if (id.length() < 1 || id.equals(" "))
+    {
+      id = "_";
+    }
 
-        bonds.addElement(new Bond(start, end, at1, at2));
+    sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note: 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);
 
-    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++)
+        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
         {
-            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++;
+          b.startCol = Color.lightGray;
         }
 
-        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);
+        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;
         }
-   }
-
-    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;
-            }
+        else if (b.at2.resName.equalsIgnoreCase("CYS"))
+        {
+          b.endCol = Color.yellow;
+        }
+        else
+        {
+          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)
+  public void setChainColours(jalview.schemes.ColourSchemeI cs)
+  {
+    Bond b;
+    int index;
+    for (int i = 0; i < bonds.size(); i++)
     {
-        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;
-            }
-        }
+      try
+      {
+        b = (Bond) bonds.elementAt(i);
+
+        index = ( (Integer) ResidueProperties.aa3Hash.get(b.at1.
+            resName)).intValue();
+        b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+
+        index = ( (Integer) ResidueProperties.aa3Hash.get(b.at2.resName)).
+            intValue();
+        b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+
+      }
+      catch (Exception e)
+      {
+        b = (Bond) bonds.elementAt(i);
+        b.startCol = Color.gray;
+        b.endCol = Color.gray;
+      }
     }
+  }
 
-
-
-    public void setChainColours(Color col)
+  public void setChainColours(Color col)
+  {
+    for (int i = 0; i < bonds.size(); i++)
     {
-        for (int i = 0; i < bonds.size(); i++)
-        {
-            Bond tmp = (Bond) bonds.elementAt(i);
-            tmp.startCol = col;
-            tmp.endCol = col;
-        }
+      Bond tmp = (Bond) bonds.elementAt(i);
+      tmp.startCol = col;
+      tmp.endCol = col;
     }
+  }
 }