/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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 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 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
{
/**
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;
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 = "";
{
tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " "
+ ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset
- + "\n";
+ + newline;
}
return tmp;
}
+ /**
+ * 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) != '-')
*
* @param seq
* @param status
- * The Status of the transferred annotation
+ * The Status of the transferred annotation
* @return the features added to sq (or its dataset)
*/
public SequenceFeature[] transferRESNUMFeatures(SequenceI 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++) { }
+ * totfeat=seqsfeatures.length; // Remove any features for this exact chain
+ * ? for (int i=0; i<seqsfeatures.length; i++) { }
*/
if (status == null)
{
- 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()));
+ 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");
-
+ 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();
// 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())
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++;
}
{
id = " ";
}
-
+ isNa = nucleotide;
sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
- // resNumber-offset
- // ~=
- // seq.size()
+ // 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++)
.elementAt(i));
resFeatures.setElementAt(null, i);
}
- Annotation[] annots = new Annotation[resAnnotation.size()];
- float max = 0;
- for (i = 0, iSize = annots.length; i < iSize; i++)
+ if (visibleChainAnnotation)
{
- annots[i] = (Annotation) resAnnotation.elementAt(i);
- if (annots[i].value > max)
- max = annots[i].value;
- resAnnotation.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(
+ "Temperature Factor", "Temperature Factor for " + pdbid + id,
+ annots, 0, max,
+ AlignmentAnnotation.LINE_GRAPH);
+ tfactorann.setSequenceRef(sequence);
+ sequence.addAlignmentAnnotation(tfactorann);
}
- 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()
}
}
- 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
+ * - positional mapping between destination sequence and pdb resnum
+ * @param sqmpping
+ * - mapping between destination sequence and local chain
*/
- public void transferResidueAnnotation(StructureMapping mapping)
+ public void transferResidueAnnotation(
+ StructureMapping mapping, jalview.datamodel.Mapping sqmpping)
{
SequenceI sq = mapping.getSequence();
+ SequenceI dsq = sq;
if (sq != null)
{
- if (sequence != null && sequence.getAnnotation() != null)
+ while (dsq.getDatasetSequence() != null)
{
-
+ dsq = dsq.getDatasetSequence();
}
- 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++)
+ // any annotation will be transferred onto the dataset sequence
+
+ if (shadow != null && shadow.getAnnotation() != null)
{
- int prn = mapping.getPDBResNum(k + 1);
- an[k] = new Annotation((float) prn);
- if (min == -1)
+ for (AlignmentAnnotation ana : shadow.getAnnotation())
{
- min = k;
- max = k;
+ 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
+ }
+ else
+ {
+ if (sequence != null && sequence.getAnnotation() != null)
{
- if (min > k)
+ for (AlignmentAnnotation ana : sequence.getAnnotation())
{
- min = k;
+ 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;
+ }
}
- else if (max < k)
+ }
+ }
+ 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));
}
- 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