X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2FMCview%2FPDBChain.java;h=e4e619c577052c6a7a0803760c994c33af058f92;hb=77ac7f545e96bd4bde47991f77291a71eb5b90e6;hp=15de7c3048bac932772d34960d8818bf499597f4;hpb=485ceb23bbae52bb2b0fd1def01e1f6822ececcf;p=jalview.git
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 15de7c3..e4e619c 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,260 +1,616 @@
-/* Copyright (C) 1998 Michele Clamp
- *
- * 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-package MCview;
-
-import jalview.datamodel.*;
-import jalview.schemes.ResidueProperties;
-
-import java.awt.*;
-import java.util.*;
-
-
-public class PDBChain {
-
- 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 = false;
-
- //public DrawableSequence ds;
-
- public PDBChain(String id) {
- this.id = id;
- }
-
-
- 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";
- }
- return tmp;
- }
- public void makeCaBondList() {
- for (int i = 0; i < (residues.size() - 1) ; i++) {
- Residue tmpres = (Residue)residues.elementAt(i);
- Residue tmpres2 = (Residue)residues.elementAt(i+1);
- myAtom at1 = tmpres.findAtom("CA");
- myAtom at2 = tmpres2.findAtom("CA");
- if ((at1 != null) && (at2 != null)) {
- if (at1.chain.equals(at2.chain)) {
- makeBond(at1,at2);
- }
- }
- }
- }
-
- public void makeBond(myAtom at1, myAtom 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));
- }
-
- public void makeResidueList() {
- int count = 0;
- String seq = "";
- for (int i = 0; i < atoms.size(); i++) {
-
- myAtom tmp = (myAtom)atoms.elementAt(i);
- String resName = tmp.resName;
- int resNumber = tmp.resNumber;
- int res = resNumber;
-
- if (i ==0) {
- offset = resNumber;
- }
- Vector resAtoms = new Vector();
-
- resAtoms.addElement((myAtom)atoms.elementAt(i));
- i++;
- resNumber = ((myAtom)atoms.elementAt(i)).resNumber;
-
- //Add atoms to a vector while the residue number
- //remains the same
- while ((resNumber == res) && (i < atoms.size())) {
-
- resAtoms.addElement((myAtom)atoms.elementAt(i));
- i++;
- if (i < atoms.size()) {
- resNumber = ((myAtom)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));
- count++;
- Residue tmpres = (Residue)residues.lastElement();
- myAtom tmpat = (myAtom)tmpres.atoms.elementAt(0);
-
- // Keep totting up the sequence
- if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {
- System.out.println("Null aa3Hash for " + tmpat.resName);
- } else {
- String tmpres2 =
- ResidueProperties.aa[((Integer)ResidueProperties.getAA3Hash().get(tmpat.resName)).intValue()];
- seq = seq + tmpres2;
- }
- // System.out.println(tmpat.resName + " " + tmpres2);
- }
- sequence = new Sequence("PDB_seq",seq,1,seq.length());
- System.out.println("Sequence = " + seq);
- System.out.println("No of residues = " +residues.size());
- }
-
- public void setChargeColours() {
- for (int i = 0; i < bonds.size(); i++) {
- try {
- Bond b = (Bond)bonds.elementAt(i);
-
- if (b.at1.resName.toUpperCase().equals("ASP") || b.at1.resName.toUpperCase().equals("GLU")) {
- b.startCol = Color.red;
- } else if (b.at1.resName.toUpperCase().equals("LYS") || b.at1.resName.toUpperCase().equals("ARG")) {
- b.startCol = Color.blue;
- } else if (b.at1.resName.toUpperCase().equals("CYS")) {
- b.startCol = Color.yellow;
- } else {
- int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();
- b.startCol = Color.lightGray;
- }
- if (b.at2.resName.toUpperCase().equals("ASP") || b.at2.resName.toUpperCase().equals("GLU")) {
- b.endCol = Color.red;
- } else if (b.at2.resName.toUpperCase().equals("LYS") || b.at2.resName.toUpperCase().equals("ARG")) {
- b.endCol = Color.blue;
- } else if (b.at2.resName.toUpperCase().equals("CYS")) {
- b.endCol = Color.yellow;
- } else {
- int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();
- b.endCol = Color.lightGray;
- }
- } catch (Exception e) {
- Bond b = (Bond)bonds.elementAt(i);
- b.startCol = Color.gray;
- b.endCol = Color.gray;
- }
- }
- }
-
- public void setHydrophobicityColours() {
- float hydmin = (float)ResidueProperties.getHydmin();
- float hydmax = (float)ResidueProperties.getHydmax();
- double[] hyd = ResidueProperties.getHyd();
-
- Hashtable AA3Hash = ResidueProperties.getAA3Hash();
-
- for (int i = 0; i < bonds.size(); i++) {
- try {
- Bond b = (Bond)bonds.elementAt(i);
-
- int atno = ((Integer)AA3Hash.get(b.at1.resName.toUpperCase())).intValue();
- float red = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);
-
- if (red > (float)1.0) {
- red = (float)1.0;
- }
- if (red < (float)0.0) {
- red = (float)0.0;
- }
-
- b.startCol = new Color(red,(float)0.0,(float)1.0-red);
- atno = ((Integer)AA3Hash.get(b.at2.resName.toUpperCase())).intValue();
-
- red = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);
-
- if (red > (float)1.0) {
- red = (float)1.0;
- }
- if (red < (float)0.0) {
- red = (float)0.0;
- }
-
- b.endCol = new Color(red,(float)0.2,(float)1.0-red);
- } catch (Exception e) {
- Bond b = (Bond)bonds.elementAt(i);
- b.startCol = Color.gray;
- b.endCol = Color.gray;
- }
- }
- }
-
-
- public void colourBySequence(Sequence seq) {
-
-// for (int i = 0; i < bonds.size(); i++) {
-// Bond tmp = (Bond)bonds.elementAt(i);
-// try {
-//
-// if (tmp.at1.resNumber >= (offset + seq.pdbstart - 1) && tmp.at1.resNumber <= (offset + seq.pdbend - 1)) {
-//
-// int pos = seq.seqtart() + (tmp.at1.resNumber - seq.pdbstart - offset) ;
-// int index = seq.findIndex(pos);
-//
-// tmp.startCol = (Color)seq.getResidueBoxColour(index);
-//
-// } else {
-// tmp.startCol = Color.gray;
-// }
-//
-// if (tmp.at2.resNumber >= (offset + seq.pdbstart -1) && tmp.at2.resNumber <= (seq.pdbend+offset-1)) {
-//
-// int pos = seq.seqstart + (tmp.at2.resNumber - seq.pdbstart-offset);
-// int index = seq.findIndex(pos);
-//
-// tmp.endCol = (Color)seq.getResidueBoxColour(index);
-//
-// } else {
-// tmp.endCol = Color.gray;
-// }
-// } catch (Exception e) {
-// tmp.startCol = Color.lightGray;
-// tmp.endCol = Color.lightGray;
-// }
-// }
- }
-
- public void setChainColours() {
- for (int i = 0; i < bonds.size(); i++) {
- Bond tmp = (Bond)bonds.elementAt(i);
- try {
- tmp.startCol = (Color) ResidueProperties.getChainColours().get(id);
- tmp.endCol = (Color) ResidueProperties.getChainColours().get(id);
- } catch (Exception e) {
- tmp.startCol = Color.lightGray;
- tmp.endCol = Color.lightGray;
- }
- }
- }
-}
-
-
+/*
+ * 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.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
+{
+ /**
+ * 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;
+
+ /**
+ * 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()
+ {
+ StringBuilder tmp = new StringBuilder(256);
+
+ for (Bond b : bonds)
+ {
+ tmp.append(b.at1.resName).append(" ").append(b.at1.resNumber)
+ .append(" ").append(offset).append(newline);
+ }
+
+ 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) != '-')
+ {
+ alignpos++;
+ }
+
+ if (as.astr2.charAt(i) != '-')
+ {
+ pdbpos++;
+ }
+
+ if (as.astr1.charAt(i) == as.astr2.charAt(i))
+ {
+ 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;
+ }
+ }
+ /**
+ * 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)
+ {
+ 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())
+ {
+ resNumber = atoms.elementAt(i).resNumber;
+ insCode = atoms.elementAt(i).insCode;
+ }
+ else
+ {
+ resNumber++;
+ }
+ }
+
+ // We need this to keep in step with the outer for i = loop
+ i--;
+
+ // Add inserted residues as features to the base residue
+ Atom currAtom = resAtoms.get(0);
+ if (currAtom.insCode != ' '
+ && residues.lastElement().atoms.get(0).resNumber == currAtom.resNumber)
+ {
+ 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
+ {
+
+ // 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("RES NUM", 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 ((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)
+ {
+ 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
+ {
+ 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 = " ";
+ }
+ 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(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] = 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);
+ }
+ }
+
+ /**
+ * Colour start/end of bonds by charge
+ *
+ * - 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));
+
+ index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
+ b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+
+ } catch (Exception e)
+ {
+ b.startCol = Color.gray;
+ b.endCol = Color.gray;
+ }
+ }
+ }
+
+ public void setChainColours(Color col)
+ {
+ for (Bond b : bonds)
+ {
+ 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())
+ {
+ 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 = 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));
+ }
+ }
+ }
+}