/*
-* 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";
- 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;
+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";
}
- 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;
- }
+ public void makeExactMapping(AlignSeq as, SequenceI 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 && 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
- * @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();
- }
- /**
- * 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;
+ * 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()));
+ if (tx.begin!=0 && tx.end!=0)
+ sq.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();
+ 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,
+ MCview.PDBChain.PDBFILEFEATURE);
+ resFeatures.addElement(sf);
+ resAnnotation.addElement(new Annotation(tmpat.tfactor));
+ // 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 = " ";
+ }
- 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);
+ }
+ 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.CATempFactor","CA 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);
- 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"))
{
- 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++;
+ 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(id.length()<1 || id.equals(" "))
- id = "_";
-
- 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);
+ if (b.at2.resName.equalsIgnoreCase("ASP") ||
+ b.at2.resName.equalsIgnoreCase("GLU"))
+ {
+ b.endCol = Color.red;
}
- }
-
- 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("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)
+ 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;
+ }
+ }
+
+ 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)
{
- Bond tmp = (Bond) bonds.elementAt(i);
- tmp.startCol = col;
- tmp.endCol = col;
+ 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));
}
+ }
}
git://source.jalview.org / jalview.git / blobdiff