X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=2eaf8a3d8ffe210147491569cd8b2d724fad5fec;hb=d423f22792e47dbc800ae220a58677f988971d06;hp=0715b6abd2e8ac892fbd166856e9256b31631e2f;hpb=dbbe146185027d9cb041a83645985a6b1a26cb75;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 0715b6a..2eaf8a3 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,286 +1,468 @@
-/*
-* 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 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 setHydrophobicityColours() {
-        float hydmin = (float) ResidueProperties.getHydmin();
-        float hydmax = (float) ResidueProperties.getHydmax();
-        double[] hyd = ResidueProperties.getHyd();
-
-        Hashtable AA3Hash = ResidueProperties.getAA3Hash();
-
-        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);
-
-                if (red > (float) 1.0) {
-                    red = (float) 1.0;
-                }
-
-                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();
-
-                red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);
-
-                if (red > (float) 1.0) {
-                    red = (float) 1.0;
-                }
-
-                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 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 (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+package MCview;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.structure.StructureMapping;
+
+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";
+    }
+
+    return tmp;
+  }
+
+  public void makeExactMapping(AlignSeq as, SequenceI 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
+   * @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;
+      }
+    }
+    /**
+     * 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(pdbid))
+      {
+        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()));
+        if (tx.begin != 0 && tx.end != 0)
+          sq.addSequenceFeature(tx);
+      }
+    }
+    return features;
+  }
+
+  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;
+    Object symbol;
+    boolean nucleotide = false;
+    StringBuffer seq = new StringBuffer();
+    Vector resFeatures = new Vector();
+    Vector resAnnotation = 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, 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)
+      {
+        if (ResidueProperties.nucleotideIndex[tmpat.resName.charAt(0)] == -1)
+        {
+          seq.append("X");
+          // System.err.println("PDBReader:Null aa3Hash for " +
+          // tmpat.resName);
+        }
+        else
+        {
+          // nucleotide flag
+          nucleotide = true;
+          seq.append(tmpat.resName.charAt(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++;
+    }
+
+    if (id.length() < 1)
+    {
+      id = " ";
+    }
+
+    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((SequenceFeature) resFeatures
+              .elementAt(i));
+      resFeatures.setElementAt(null, i);
+    }
+    Annotation[] annots = new Annotation[resAnnotation.size()];
+    float max = 0;
+    for (i = 0, iSize = annots.length; i < iSize; i++)
+    {
+      annots[i] = (Annotation) resAnnotation.elementAt(i);
+      if (annots[i].value > max)
+        max = annots[i].value;
+      resAnnotation.setElementAt(null, i);
+    }
+    AlignmentAnnotation tfactorann = new AlignmentAnnotation(
+            "PDB.TempFactor", "Temperature Factor for "
+                    + sequence.getName(), annots, 0, max,
+            AlignmentAnnotation.LINE_GRAPH);
+    tfactorann.setSequenceRef(sequence);
+    sequence.addAlignmentAnnotation(tfactorann);
+  }
+
+  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
+        {
+          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
+        {
+          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;
+    int index;
+    for (int i = 0; i < bonds.size(); i++)
+    {
+      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)
+  {
+    for (int i = 0; i < bonds.size(); i++)
+    {
+      Bond tmp = (Bond) bonds.elementAt(i);
+      tmp.startCol = col;
+      tmp.endCol = col;
+    }
+  }
+
+  public AlignmentAnnotation[] transferResidueAnnotation(SequenceI seq,
+          String status)
+  {
+    AlignmentAnnotation[] transferred = null;
+
+    return transferred;
+
+  }
+
+  /**
+   * copy any sequence annotation onto the sequence mapped using the provided
+   * StructureMapping
+   * 
+   * @param mapping
+   */
+  public void transferResidueAnnotation(StructureMapping mapping)
+  {
+    SequenceI sq = mapping.getSequence();
+    if (sq != null)
+    {
+      if (sequence != null && sequence.getAnnotation() != null)
+      {
+
+      }
+      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((float) 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, (float) min, (float) max,
+                      AlignmentAnnotation.LINE_GRAPH));
+    }
+  }
+}