X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=7774dac96936327b49508ff203e98a6c9d3c9e71;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=c1c586a3e4c0dff15e4d31f8f2bd02dead1b924b;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index c1c586a..7774dac 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,32 +1,41 @@
/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * 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.StructureImportSettings;
import jalview.structure.StructureMapping;
+import java.awt.Color;
+import java.util.List;
+import java.util.Vector;
+
public class PDBChain
{
/**
@@ -38,15 +47,26 @@ public class PDBChain
public String id;
- public Vector bonds = new Vector();
+ public Vector bonds = new Vector();
- public Vector atoms = new Vector();
+ public Vector atoms = new Vector();
- public Vector residues = 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;
@@ -62,29 +82,58 @@ public class PDBChain
public PDBChain(String pdbid, String id)
{
- this.pdbid = pdbid.toLowerCase();
+ this.pdbid = pdbid == null ? 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 = "";
+ 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) != '-')
@@ -99,11 +148,13 @@ public class PDBChain
if (as.astr1.charAt(i) == as.astr2.charAt(i))
{
- Residue res = (Residue) residues.elementAt(pdbpos);
- Enumeration en = res.atoms.elements();
- while (en.hasMoreElements())
+ if (pdbpos >= residues.size())
+ {
+ continue;
+ }
+ Residue res = residues.elementAt(pdbpos);
+ for (Atom atom : res.atoms)
{
- Atom atom = (Atom) en.nextElement();
atom.alignmentMapping = alignpos;
}
}
@@ -116,7 +167,7 @@ public class PDBChain
*
* @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,
@@ -134,47 +185,70 @@ public class PDBChain
/**
* 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;
+ }
}
+ /**
+ * 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
+ *
+ * - 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;
- StringBuffer seq = new StringBuffer();
- Vector resFeatures = new Vector();
- Vector resAnnotation = new Vector();
+ 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 = (Atom) atoms.elementAt(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();
+ 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()))
+ while ((resNumber == res) && (ins == insCode) && (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;
+ insCode = atoms.elementAt(i).insCode;
}
else
{
@@ -241,144 +342,184 @@ public class PDBChain
// 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, 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)
+ // Add inserted residues as features to the base residue
+ Atom currAtom = resAtoms.get(0);
+ if (currAtom.insCode != ' '
+ && !residues.isEmpty()
+ && residues.lastElement().atoms.get(0).resNumber == currAtom.resNumber)
{
- seq.append("X");
- // System.err.println("PDBReader:Null aa3Hash for " +
- // tmpat.resName);
+ SequenceFeature sf = new SequenceFeature("INSERTION",
+ currAtom.resName + ":" + currAtom.resNumIns + " " + pdbid
+ + id, "", offset + count - 1, offset + count - 1,
+ "PDB_INS");
+ resFeatures.addElement(sf);
+ residues.lastElement().atoms.addAll(resAtoms);
}
else
{
- seq.append(ResidueProperties.aa[((Integer) ResidueProperties
- .getAA3Hash().get(tmpat.resName)).intValue()]);
+ // Make a new Residue object with the new atoms vector
+ residues.addElement(new Residue(resAtoms, resNumber - 1, count));
+
+ 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
+ + count, offset + count, pdbid);
+ resFeatures.addElement(sf);
+ resAnnotation.addElement(new Annotation(tmpat.tfactor));
+ // Keep totting up the sequence
+
+ if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
+ {
+ 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)
+ {
+ char r = ResidueProperties
+ .getSingleCharacterCode(ResidueProperties
+ .getCanonicalAminoAcid(tmpat.resName));
+ seq.append(r == '0' ? 'X' : r);
+ // System.err.println("PDBReader:Null aa3Hash for " +
+ // tmpat.resName);
+ }
+ else
+ {
+ // nucleotide flag
+ nucleotide = true;
+ seq.append(nucname.charAt((deoxyn ? 1 : 0)));
+ }
+ }
+ else
+ {
+ 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++;
}
- count++;
}
if (id.length() < 1)
{
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++)
+
+ if (StructureImportSettings.isShowSeqFeatures())
{
- sequence.addSequenceFeature((SequenceFeature) resFeatures
- .elementAt(i));
- resFeatures.setElementAt(null, i);
+ for (i = 0, iSize = resFeatures.size(); i < iSize; 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.CATempFactor", "CA Temperature Factor for "
- + sequence.getName(), annots, 0, max,
- AlignmentAnnotation.LINE_GRAPH);
- tfactorann.setSequenceRef(sequence);
- sequence.addAlignmentAnnotation(tfactorann);
}
+ /**
+ * Colour start/end of bonds by charge
+ *
+ * - ASP and GLU red
+ * - LYS and ARG blue
+ * - CYS yellow
+ * - others light gray
+ *
+ */
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;
}
@@ -387,67 +528,108 @@ public class PDBChain
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 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 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;
+ }
}
- 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));
}
}
}