/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+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.ResidueProperties;
+import jalview.structure.StructureMapping;
+
+import java.awt.Color;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
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;
+
+ /**
+ * sequence is the sequence extracted by the chain parsing code
+ */
+ public SequenceI sequence;
+
+ /**
+ * shadow is the sequence created by any other parsing processes (e.g. Jmol,
+ * RNAview)
+ */
+ public SequenceI shadow = null;
+
+ 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()
{
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";
+ tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " "
+ + ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset
+ + newline;
}
return tmp;
}
- void makeExactMapping(AlignSeq as, Sequence s1)
+ /**
+ * 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 : (Vector<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) != '-')
}
/**
- * copy over the RESNUM seqfeatures from the internal chain sequence to the mapped sequence
+ * copy over the RESNUM seqfeatures from the internal chain sequence to the
+ * mapped sequence
+ *
* @param seq
- * @param status The Status of the transferred annotation
+ * @param status
+ * The Status of the transferred annotation
* @return the features added to sq (or its dataset)
*/
- public SequenceFeature[] transferRESNUMFeatures(SequenceI seq, String status)
+ public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
+ String status)
{
SequenceI sq = seq;
- while (sq != null)
+ while (sq != null && sq.getDatasetSequence() != null)
{
+ sq = sq.getDatasetSequence();
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++) {
- } */
+ * 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))
+ 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()));
- seq.addSequenceFeature(tx);
+ 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()
{
+ boolean na = false;
+ int numNa = 0;
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))
+ 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))
{
+ if (na)
+ {
+ numNa++;
+ }
makeBond(at1, at2);
}
}
System.out.println("not found " + i);
}
}
+ if (numNa > 0 && ((numNa / residues.size()) > 0.99))
+ {
+ isNa = true;
+ }
}
public void makeBond(Atom at1, Atom at2)
bonds.addElement(new Bond(start, end, at1, at2));
}
- public void makeResidueList()
+ public void makeResidueList(boolean visibleChainAnnotation)
{
int count = 0;
+ Object symbol;
+ boolean deoxyn = false;
+ 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++)
}
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()))
+ // 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));
+ resAtoms.addElement(atoms.elementAt(i));
i++;
if (i < atoms.size())
{
- resNumber = ( (Atom) atoms.elementAt(i)).resNumber;
+ resNumber = ((Atom) atoms.elementAt(i)).resNumber;
}
else
{
}
}
- //We need this to keep in step with the outer for i = loop
+ // We need this to keep in step with the outer for i = loop
i--;
- //Make a new Residue object with the new atoms vector
+ // 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);
+ 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 (ResidueProperties.getAA3Hash().get(tmpat.resName) == null)
+ if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
{
- seq.append("X");
- // System.err.println("PDBReader:Null aa3Hash for " +
- // tmpat.resName);
+ 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
{
-
- seq.append(ResidueProperties.aa[ ( (Integer) ResidueProperties.
- getAA3Hash()
- .get(tmpat.resName)).intValue()]);
+ 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.equals(" "))
+ if (id.length() < 1)
{
- id = "_";
+ 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());
+ 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( (SequenceFeature) resFeatures.elementAt(i));
+ sequence.addSequenceFeature((SequenceFeature) 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] = (Annotation) 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);
+ }
}
public void setChargeColours()
{
Bond b = (Bond) bonds.elementAt(i);
- if (b.at1.resName.equalsIgnoreCase("ASP") ||
- b.at1.resName.equalsIgnoreCase("GLU"))
+ 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"))
+ else if (b.at1.resName.equalsIgnoreCase("LYS")
+ || b.at1.resName.equalsIgnoreCase("ARG"))
{
b.startCol = Color.blue;
}
b.startCol = Color.lightGray;
}
- if (b.at2.resName.equalsIgnoreCase("ASP") ||
- b.at2.resName.equalsIgnoreCase("GLU"))
+ 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"))
+ else if (b.at2.resName.equalsIgnoreCase("LYS")
+ || b.at2.resName.equalsIgnoreCase("ARG"))
{
b.endCol = Color.blue;
}
{
b.endCol = Color.lightGray;
}
- }
- catch (Exception e)
+ } catch (Exception e)
{
Bond b = (Bond) bonds.elementAt(i);
b.startCol = Color.gray;
{
b = (Bond) bonds.elementAt(i);
- index = ( (Integer) ResidueProperties.aa3Hash.get(b.at1.
- resName)).intValue();
+ 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();
+ index = ((Integer) ResidueProperties.aa3Hash.get(b.at2.resName))
+ .intValue();
b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
- }
- catch (Exception e)
+ } catch (Exception e)
{
b = (Bond) bonds.elementAt(i);
b.startCol = Color.gray;
tmp.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)
+ {
+ 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())
+ {
+ 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));
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff