X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=2eaf8a3d8ffe210147491569cd8b2d724fad5fec;hb=d423f22792e47dbc800ae220a58677f988971d06;hp=fdb74bd8a3acd0616b9c49f39f3d929bccc4325f;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index fdb74bd..2eaf8a3 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,268 +1,468 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-*/
-
-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 int pdbstart=0, pdbend=0, seqstart=0, seqend=0;
-
- //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.err.println("PDBReader: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("PDB Sequence is :\nSequence = " + 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(jalview.gui.AlignViewport av, Sequence seq) {
-jalview.gui.SequenceRenderer sr = new jalview.gui.SequenceRenderer(av);
-
-
- for (int i = 0; i < bonds.size(); i++) {
- Bond tmp = (Bond)bonds.elementAt(i);
- try {
-
- if (tmp.at1.resNumber >= (offset + pdbstart - 1) && tmp.at1.resNumber <= (offset + pdbend - 1)) {
-
- int pos = seqstart + (tmp.at1.resNumber - pdbstart - offset) ;
- int index = seq.findIndex(pos);
-
-
- tmp.startCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);
-
- } else {
- tmp.startCol = Color.gray;
- }
-
- if (tmp.at2.resNumber >= (offset + pdbstart -1) && tmp.at2.resNumber <= (pdbend+offset-1)) {
-
- int pos = seqstart + (tmp.at2.resNumber - pdbstart-offset);
- int index = seq.findIndex(pos);
-
- tmp.endCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, 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 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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 .
+ */
+package MCview;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.structure.StructureMapping;
+
+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;
+ }
+
+ 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 makeExactMapping(AlignSeq as, SequenceI s1)
+ {
+ int pdbpos = as.getSeq2Start() - 2;
+ int alignpos = s1.getStart() + as.getSeq1Start() - 3;
+
+ 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 = (Residue) residues.elementAt(pdbpos);
+ Enumeration en = res.atoms.elements();
+ while (en.hasMoreElements())
+ {
+ Atom atom = (Atom) en.nextElement();
+ 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 k)
+ {
+ min = k;
+ }
+ else if (max < k)
+ {
+ max = k;
+ }
+ }
+ }
+ sq
+ .addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
+ "PDB Residue Numbering for " + this.pdbid + ":"
+ + this.id, an, (float) min, (float) max,
+ AlignmentAnnotation.LINE_GRAPH));
+ }
+ }
+}