X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=ba93046f0a3467e670725a67398d6d8e7b48b656;hb=1810df9d010000e434975a8a4e68dcbda238f7f1;hp=1b65c48237e5c0c00d46efebbd546d397def2020;hpb=a8e0f82df5adb89da02647b3f37db93966996fea;p=jalview.git
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 1b65c48..ba93046 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,311 +1,642 @@
/*
-* 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 ($$Version-Rel$$)
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package MCview;
-import jalview.datamodel.*;
-
+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.StructureImportSettings;
+import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
-import java.awt.*;
+import java.awt.Color;
+import java.util.List;
+import java.util.Vector;
-import java.util.*;
-import jalview.analysis.AlignSeq;
+public class PDBChain
+{
+ public static final String RESNUM_FEATURE = "RESNUM";
+ /**
+ * SequenceFeature group for PDB File features added to sequences
+ */
+ private static final String PDBFILEFEATURE = "PDBFile";
-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;
- }
+ private static final String IEASTATUS = "IEA:jalview";
- public String print() {
- String tmp = "";
+ public String id;
- 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 Vector bonds = new Vector();
- return tmp;
- }
+ public Vector atoms = new Vector();
- void makeExactMapping(AlignSeq as, Sequence s1)
- {
- int pdbpos = as.getSeq2Start()-2;
- int alignpos = s1.getStart() + as.getSeq1Start()-3;
+ public Vector residues = new Vector();
- for(int i=0; i= residues.size())
+ {
+ continue;
+ }
+ Residue res = residues.elementAt(pdbpos);
+ for (Atom atom : res.atoms)
+ {
+ 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)
+ * 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 99% 'P', flag as nucleotide; note the count doesn't include the last
+ * residue
+ */
+ if (residues.size() > 1 && (numNa / (residues.size() - 1) > 0.99))
+ {
+ isNa = true;
}
-
- 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++)
+ }
+
+ /**
+ * 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)
+ {
+ bonds.addElement(new Bond(at1, at2));
+ }
+
+ /**
+ * Traverses the list of atoms and
+ *
+ * - constructs a list of Residues, each containing all the atoms that share
+ * the same residue number
+ * - adds a RESNUM sequence feature for each position
+ * - creates the sequence string
+ * - determines if nucleotide
+ * - saves the residue number of the first atom as 'offset'
+ * - adds temp factor annotation if the flag is set to do so
+ *
+ *
+ * @param visibleChainAnnotation
+ */
+ public void makeResidueList(boolean visibleChainAnnotation)
+ {
+ int count = 0;
+ Object symbol;
+ boolean deoxyn = false;
+ boolean nucleotide = false;
+ StringBuilder seq = new StringBuilder(256);
+ Vector resFeatures = new Vector();
+ Vector resAnnotation = new Vector();
+ int i, iSize = atoms.size() - 1;
+ int resNumber = -1;
+ char insCode = ' ';
+ for (i = 0; i <= iSize; i++)
+ {
+ Atom tmp = atoms.elementAt(i);
+ resNumber = tmp.resNumber;
+ insCode = tmp.insCode;
+
+ int res = resNumber;
+ char ins = insCode;
+
+ 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) && (ins == insCode) && (i < atoms.size()))
+ {
+ resAtoms.add(atoms.elementAt(i));
+ i++;
+
+ if (i < atoms.size())
{
- 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++;
+ resNumber = atoms.elementAt(i).resNumber;
+ insCode = atoms.elementAt(i).insCode;
}
-
- 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
+ * ASP and GLU red
+ * LYS and ARG blue
+ * CYS yellow
+ * others light gray
+ *
+ */
+ public void setChargeColours()
+ {
+ for (Bond b : bonds)
+ {
+ if (b.at1 != null && b.at2 != null)
+ {
+ b.startCol = getChargeColour(b.at1.resName);
+ b.endCol = getChargeColour(b.at2.resName);
+ }
+ else
+ {
+ b.startCol = Color.gray;
+ b.endCol = Color.gray;
+ }
+ }
+ }
+ 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)
+ {
+ int index;
+ for (Bond b : bonds)
+ {
+ try
+ {
+ index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
+ b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0),
+ 0, null, null, 0f);
+
+ index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
+ b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
+ null, null, 0f);
+
+ } catch (Exception e)
+ {
+ b.startCol = Color.gray;
+ b.endCol = Color.gray;
+ }
+ }
+ }
-
- public void setChainColours(Color col)
+ public void setChainColours(Color col)
+ {
+ for (Bond b : bonds)
{
- for (int i = 0; i < bonds.size(); i++)
+ b.startCol = col;
+ b.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())
{
- Bond tmp = (Bond) bonds.elementAt(i);
- tmp.startCol = col;
- tmp.endCol = col;
+ List 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 transfer = dsq
+ .getAlignmentAnnotations(ana.getCalcId(), ana.label);
+ if (transfer == null || transfer.size() == 0)
+ {
+ ana = new AlignmentAnnotation(ana);
+ ana.liftOver(dsq, sqmpping);
+ dsq.addAlignmentAnnotation(ana);
+ // 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));
+ }
}
+ }
}