/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * 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.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
+import java.awt.Color;
+import java.util.List;
+import java.util.Vector;
+
public class PDBChain
{
/**
public String id;
- public Vector bonds = new Vector();
+ public Vector<Bond> bonds = new Vector<Bond>();
- public Vector atoms = new Vector();
+ public Vector<Atom> atoms = new Vector<Atom>();
- public Vector residues = new Vector();
+ public Vector<Residue> residues = new Vector<Residue>();
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;
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 = "";
+ StringBuilder tmp = new StringBuilder(256);
- for (int i = 0; i < bonds.size(); i++)
+ for (Bond b : bonds)
{
- tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " "
- + ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset
- + "\n";
+ tmp.append(b.at1.resName).append(" ").append(b.at1.resNumber)
+ .append(" ").append(offset).append(newline);
}
- return tmp;
+ return tmp.toString();
}
+ /**
+ * 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 : 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) != '-')
if (as.astr1.charAt(i) == as.astr2.charAt(i))
{
- Residue res = (Residue) residues.elementAt(pdbpos);
- Enumeration en = res.atoms.elements();
- while (en.hasMoreElements())
+ Residue res = residues.elementAt(pdbpos);
+ for (Atom atom : res.atoms)
{
- Atom atom = (Atom) en.nextElement();
atom.alignmentMapping = alignpos;
}
}
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.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
+ .elementAt(0).alignmentMapping);
+ tx.setEnd(1 + 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;
}
+ /**
+ * Traverses the list of residues and constructs bonds where CA-to-CA atoms or
+ * P-to-P atoms are found. Also sets the 'isNa' flag if more than 99% of
+ * residues contain a P not a CA.
+ */
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);
+ Residue tmpres = residues.elementAt(i);
+ Residue tmpres2 = residues.elementAt(i + 1);
Atom at1 = tmpres.findAtom("CA");
Atom at2 = tmpres2.findAtom("CA");
na = false;
System.out.println("not found " + i);
}
}
- if (numNa > 0 && ((numNa / residues.size()) > 0.99))
+
+ /*
+ * If > 99% 'P', flag as nucleotide; note the count doesn't include the last
+ * residue
+ */
+ if (residues.size() > 0 && (numNa / (residues.size() - 1) > 0.99))
{
isNa = true;
}
}
+ /**
+ * Construct a bond from atom1 to atom2 and add it to the list of bonds for
+ * this chain
+ *
+ * @param at1
+ * @param at2
+ */
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));
+ bonds.addElement(new Bond(at1, at2));
}
- public void makeResidueList()
+ /**
+ * Traverses the list of atoms and
+ * <ul>
+ * <li>constructs a list of Residues, each containing all the atoms that share
+ * the same residue number</li>
+ * <li>adds a RESNUM sequence feature for each position</li>
+ * <li>creates the sequence string</li>
+ * <li>determines if nucleotide</li>
+ * <li>saves the residue number of the first atom as 'offset'</li>
+ * <li>adds temp factor annotation if the flag is set to do so</li>
+ * </ul>
+ *
+ * @param visibleChainAnnotation
+ */
+ 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();
+ StringBuilder seq = new StringBuilder(256);
+ Vector<SequenceFeature> resFeatures = new Vector<SequenceFeature>();
+ Vector<Annotation> resAnnotation = new Vector<Annotation>();
int i, iSize = atoms.size() - 1;
int resNumber = -1;
for (i = 0; i <= iSize; i++)
{
- Atom tmp = (Atom) atoms.elementAt(i);
+ Atom tmp = atoms.elementAt(i);
resNumber = tmp.resNumber;
int res = resNumber;
offset = resNumber;
}
- Vector resAtoms = new Vector();
+ Vector<Atom> resAtoms = new Vector<Atom>();
// 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.add(atoms.elementAt(i));
i++;
if (i < atoms.size())
{
- resNumber = ((Atom) atoms.elementAt(i)).resNumber;
+ resNumber = atoms.elementAt(i).resNumber;
}
else
{
// 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);
+ Residue tmpres = residues.lastElement();
+ Atom tmpat = tmpres.atoms.get(0);
// Make A new SequenceFeature for the current residue numbering
SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
+ ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
{
String nucname = tmpat.resName.trim();
- if (tmpat.name.equalsIgnoreCase("CA") || ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
+ // 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 " +
{
// nucleotide flag
nucleotide = true;
- seq.append(nucname.charAt(0));
+ seq.append(nucname.charAt((deoxyn ? 1 : 0)));
}
}
else
// 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(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++)
+ 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] = 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.TempFactor", "Temperature Factor for "
- + sequence.getName(), annots, 0, max,
- AlignmentAnnotation.LINE_GRAPH);
- tfactorann.setSequenceRef(sequence);
- sequence.addAlignmentAnnotation(tfactorann);
}
+ /**
+ * Colour start/end of bonds by charge
+ * <ul>
+ * <li>ASP and GLU red</li>
+ * <li>LYS and ARG blue</li>
+ * <li>CYS yellow</li>
+ * <li>others light gray</li>
+ * </ul>
+ */
public void setChargeColours()
{
- for (int i = 0; i < bonds.size(); i++)
+ for (Bond b : bonds)
{
- try
+ if (b.at1 != null && b.at2 != null)
{
- 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)
+ b.startCol = getChargeColour(b.at1.resName);
+ b.endCol = getChargeColour(b.at2.resName);
+ }
+ else
{
- Bond b = (Bond) bonds.elementAt(i);
b.startCol = Color.gray;
b.endCol = Color.gray;
}
}
}
- public void setChainColours(jalview.schemes.ColourSchemeI cs)
+ public static Color getChargeColour(String resName)
+ {
+ Color result = Color.lightGray;
+ if ("ASP".equals(resName) || "GLU".equals(resName))
+ {
+ result = Color.red;
+ }
+ else if ("LYS".equals(resName) || "ARG".equals(resName))
+ {
+ result = Color.blue;
+ }
+ else if ("CYS".equals(resName))
+ {
+ result = Color.yellow;
+ }
+ return result;
+ }
+
+ /**
+ * Sets the start/end colours of bonds to those of the start/end atoms
+ * according to the specified colour scheme. Note: currently only works for
+ * peptide residues.
+ *
+ * @param cs
+ */
+ public void setChainColours(ColourSchemeI cs)
{
- Bond b;
int index;
- for (int i = 0; i < bonds.size(); i++)
+ for (Bond b : bonds)
{
try
{
- b = (Bond) bonds.elementAt(i);
-
- index = ((Integer) ResidueProperties.aa3Hash.get(b.at1.resName))
- .intValue();
+ index = 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 = 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++)
+ for (Bond b : bonds)
{
- Bond tmp = (Bond) bonds.elementAt(i);
- tmp.startCol = col;
- tmp.endCol = col;
+ b.startCol = col;
+ b.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
+ * - 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