X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=2c7bd9dbd49205afa07ec946bed02cedea67cd94;hb=013c39d4eaab0ed509d21e83676fa4da284d7fde;hp=99a0a2b6b05400dd460674f53b30fbf9e138540e;hpb=fbf0a6e1eb4869dc676334a30c9e40b60a7659ac;p=jalview.git diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 99a0a2b..2c7bd9d 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -1,171 +1,211 @@ -/* -* 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 -*/ -package MCview; - -import jalview.datamodel.*; - -import java.io.*; - -import java.util.*; -import java.awt.Color; - - -public class PDBfile extends jalview.io.AlignFile { - public Vector chains; - public String id; - - public PDBfile(String inFile, String inType) throws IOException - { - super(inFile, inType); - } - - public String print() - { - return null; - } - - public void parse() throws IOException - { - chains = new Vector(); - - PDBChain tmpchain; - String line; - boolean modelFlag = false; - boolean terFlag = false; - - - int index = 0; - while((line = nextLine())!=null) - { - if (line.indexOf("HEADER") == 0) - { - id = line.substring(62, 67).trim(); - continue; - } - - if(line.indexOf("MODEL")==0) - modelFlag = true; - - if(line.indexOf("TER")==0) - terFlag = true; - - if(modelFlag && line.indexOf("ENDMDL")==0) - break; - - if ( line.indexOf("ATOM")==0 - || (line.indexOf("HETATM")==0 && !terFlag) - ) - { - terFlag = false; - - - //Jalview is only interested in CA bonds???? - if (!line.substring(12, 15).trim().equals("CA")) - { - continue; - } - - Atom tmpatom = new Atom(line); - tmpchain = findChain(tmpatom.chain); - if (tmpchain != null) - { - tmpchain.atoms.addElement(tmpatom); - } - else - { - tmpchain = new PDBChain(tmpatom.chain); - chains.addElement(tmpchain); - tmpchain.atoms.addElement(tmpatom); - } - } - index ++; - } - - makeResidueList(); - makeCaBondList(); - - if(id==null) - { - id = inFile.getName(); - } - for (int i = 0; i < chains.size(); i++) - { - SequenceI seq = ( (PDBChain) chains.elementAt(i)). - sequence; - seq.setName(id + "|" + seq.getName()); - Sequence dataset = new Sequence(seq. - getName(), - seq.getSequence().toString(), seq.getStart(), seq.getEnd()); - - PDBEntry entry = new PDBEntry(); - entry.setId(id); - if(inFile!=null) - entry.setFile(inFile.getAbsolutePath()); - - seq.setDatasetSequence(dataset); - dataset.addPDBId(entry); - - getSeqs().addElement(seq); - } - } - - public void makeResidueList() { - for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).makeResidueList(); - } - } - - public void makeCaBondList() { - for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).makeCaBondList(); - } - } - - public PDBChain findChain(String id) { - for (int i = 0; i < chains.size(); i++) { - if (((PDBChain) chains.elementAt(i)).id.equals(id)) { - return (PDBChain) chains.elementAt(i); - } - } - - return null; - } - - public void setChargeColours() { - for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).setChargeColours(); - } - } - - public void setColours(jalview.schemes.ColourSchemeI cs) { - for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).setChainColours(cs); - } - } - - public void setChainColours() - { - for (int i = 0; i < chains.size(); i++) - { - ((PDBChain) chains.elementAt(i)).setChainColours( - Color.getHSBColor(1.0f / (float)i, .4f, 1.0f) - ); - } - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 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 java.io.*; +import java.util.*; + +import java.awt.*; + +import jalview.datamodel.*; + +public class PDBfile + extends jalview.io.AlignFile +{ + public Vector chains; + public String id; + + /** + * set to true to add chain alignment annotation as visible annotation. + */ + boolean VisibleChainAnnotation=false; + public PDBfile(String inFile, String inType) + throws IOException + { + super(inFile, inType); + } + + public String print() + { + return null; + } + + public void parse() + throws IOException + { + // TODO set the filename sensibly + id = (inFile==null) ? "PDBFILE" : inFile.getName(); + try + { + chains = new Vector(); + + PDBChain tmpchain; + String line; + boolean modelFlag = false; + boolean terFlag = false; + + int index = 0; + while ( (line = nextLine()) != null) + { + if (line.indexOf("HEADER") == 0) + { + id = line.substring(62, 67).trim(); + continue; + } + // Were we to do anything with SEQRES - we start it here + if (line.indexOf("SEQRES") == 0) + { + } + + if (line.indexOf("MODEL") == 0) + { + modelFlag = true; + } + + if (line.indexOf("TER") == 0) + { + terFlag = true; + } + + if (modelFlag && line.indexOf("ENDMDL") == 0) + { + break; + } + if (line.indexOf("ATOM") == 0 + || (line.indexOf("HETATM") == 0 && !terFlag) + ) + { + terFlag = false; + + //Jalview is only interested in CA bonds???? + if (!line.substring(12, 15).trim().equals("CA")) + { + continue; + } + + Atom tmpatom = new Atom(line); + tmpchain = findChain(tmpatom.chain); + if (tmpchain != null) + { + tmpchain.atoms.addElement(tmpatom); + } + else + { + tmpchain = new PDBChain(id, tmpatom.chain); + chains.addElement(tmpchain); + tmpchain.atoms.addElement(tmpatom); + } + } + index++; + } + + makeResidueList(); + makeCaBondList(); + + if (id == null) + { + id = inFile.getName(); + } + for (int i = 0; i < chains.size(); i++) + { + SequenceI dataset = ( (PDBChain) chains.elementAt(i)). + sequence; + dataset.setName(id + "|" + dataset.getName()); + PDBEntry entry = new PDBEntry(); + entry.setId(id); + if (inFile != null) + { + entry.setFile(inFile.getAbsolutePath()); + } + dataset.addPDBId(entry); + SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects maintain reference to dataset + seqs.addElement(chainseq); + AlignmentAnnotation[] chainannot = chainseq.getAnnotation(); + if (chainannot!=null) + { + for (int ai=0; ai