X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=07dc6b544357331d8f0d9558af973e48280e159c;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=410628f4dab5dd7aef266b436919f1a5d7add2db;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java index 410628f..07dc6b5 100755 --- a/src/jalview/io/PIRFile.java +++ b/src/jalview/io/PIRFile.java @@ -1,135 +1,198 @@ -/* -* 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 jalview.io; - -import jalview.datamodel.*; -import jalview.analysis.*; - -import java.io.*; -import java.util.*; - -public class PIRFile extends AlignFile { - - Vector words = new Vector(); //Stores the words in a line after splitting - - public PIRFile() - {} - - public PIRFile(String inStr) { - super(inStr); - } - - public PIRFile(String inFile, String type) throws IOException { - super(inFile,type); - } - - public void parse() { - try{ - String id, start, end; - StringBuffer sequence; - String line = null; - while( (line = nextLine())!=null) - { - try{ - id = line.substring(line.indexOf(";") + 1, line.indexOf("/")); - line = line.substring(line.indexOf("/") + 1); - start = line.substring(0, line.indexOf("-")); - end = line.substring(line.indexOf("-") + 1); - }catch(Exception ex) - { id="No id"; start="0"; end="0"; } - - sequence = new StringBuffer(); - - line = nextLine(); // this is the title line - - boolean starFound = false; - do - { - line = nextLine(); - sequence.append( line ); - if(line.indexOf("*")>-1) - starFound = true; - - }while(!starFound); - - sequence.setLength( sequence.length()-1); - - Sequence newSeq = new Sequence(id, - sequence.toString(), - Integer.parseInt(start), - Integer.parseInt(end)); - seqs.addElement(newSeq); - } - - } - catch(Exception ex){ex.printStackTrace();} - } - - public String print() { - return print(getSeqsAsArray()); - } - public static String print(SequenceI[] s) { - return print(s,72,true); - } - public static String print(SequenceI[] s, int len) { - return print(s,len,true); - } - public static String print(SequenceI[] s, int len,boolean gaps) { - StringBuffer out = new StringBuffer(); - int i = 0; - - while (i < s.length && s[i] != null) { - String seq = ""; - if (gaps) { - seq = s[i].getSequence() + "*"; - } else { - seq = AlignSeq.extractGaps(s[i].getSequence(),"-"); - seq = AlignSeq.extractGaps(seq,"."); - seq = AlignSeq.extractGaps(seq," "); - seq = seq + "*"; - } - - out.append(">P1;" + s[i].getName() + "/" + s[i].getStart()+ "-" + s[i].getEnd() + "\n"); - out.append(" Dummy title\n"); - int nochunks = seq.length() / len + 1; - - for (int j = 0; j < nochunks; j++) { - int start = j*len; - int end = start + len; - - if (end < seq.length()) { - out.append(seq.substring(start,end) + "\n"); - } else if (start < seq.length()) { - out.append(seq.substring(start) + "\n"); - } - } - i++; - } - return out.toString(); - } - - public static void main(String[] args) { - String inStr = ">P1;LCAT_MOUSE_90.35\nMGLPGSPWQRVLLLLGLLLPPATPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNRLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDFNLFLPLGVDCWIDNTRIVYNHSSGRVSNAPGVQIRVPGFGKTESVEYVDDNKLAGY\n\n>LCAT_PAPAN_95.78\nMGPPGSPWQWVPLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGY\nLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYHKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLL\n"; - PIRFile fa = new PIRFile(inStr); - } -} - - - +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 jalview.io; + +import java.io.*; +import java.util.*; + +import jalview.datamodel.*; + +public class PIRFile extends AlignFile +{ + public static boolean useModellerOutput = false; + + Vector words = new Vector(); // Stores the words in a line after splitting + + public PIRFile() + { + } + + public PIRFile(String inFile, String type) throws IOException + { + super(inFile, type); + } + + public PIRFile(FileParse source) throws IOException + { + super(source); + } + + public void parse() throws IOException + { + StringBuffer sequence; + String line = null; + ModellerDescription md; + + while ((line = nextLine()) != null) + { + if (line.length() == 0) + { + // System.out.println("blank line"); + continue; + } + if (line.indexOf("C;") == 0 || line.indexOf("#") == 0) + { + continue; + } + Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1)); + + sequence = new StringBuffer(); + + newSeq.setDescription(nextLine()); // this is the title line + + boolean starFound = false; + + while (!starFound) + { + line = nextLine(); + sequence.append(line); + + if (line == null) + { + break; + } + + if (line.indexOf("*") > -1) + { + starFound = true; + } + } + + if (sequence.length() > 0) + { + sequence.setLength(sequence.length() - 1); + newSeq.setSequence(sequence.toString()); + + seqs.addElement(newSeq); + + md = new ModellerDescription(newSeq.getDescription()); + md.updateSequenceI(newSeq); + } + } + } + + public String print() + { + return print(getSeqsAsArray()); + } + + public String print(SequenceI[] s) + { + boolean is_NA = jalview.util.Comparison.isNucleotide(s); + int len = 72; + StringBuffer out = new StringBuffer(); + int i = 0; + ModellerDescription md; + + while ((i < s.length) && (s[i] != null)) + { + String seq = s[i].getSequenceAsString(); + seq = seq + "*"; + + if (is_NA) + { + // modeller doesn't really do nucleotides, so we don't do anything fancy + // Official tags area as follows, for now we'll use P1 and DL + // Protein (complete) P1 + // Protein (fragment) F1 + // DNA (linear) Dl + // DNA (circular) DC + // RNA (linear) RL + // RNA (circular) RC + // tRNA N3 + // other functional RNA N1 + + out.append(">N1;" + s[i].getName()); + out.append(newline); + if (s[i].getDescription() == null) + { + out.append(s[i].getName() + " " + + (s[i].getEnd() - s[i].getStart() + 1)); + out.append(is_NA ? " bases" : " residues"); + out.append(newline); + } + else + { + out.append(s[i].getDescription()); + out.append(newline); + } + } + else + { + + if (useModellerOutput) + { + out.append(">P1;" + s[i].getName()); + out.append(newline); + md = new ModellerDescription(s[i]); + out.append(md.getDescriptionLine()); + out.append(newline); + } + else + { + out.append(">P1;" + printId(s[i])); + out.append(newline); + if (s[i].getDescription() != null) + { + out.append(s[i].getDescription()); + out.append(newline); + } + else + { + out.append(s[i].getName() + " " + + (s[i].getEnd() - s[i].getStart() + 1) + " residues"); + out.append(newline); + } + } + } + int nochunks = (seq.length() / len) + 1; + + for (int j = 0; j < nochunks; j++) + { + int start = j * len; + int end = start + len; + + if (end < seq.length()) + { + out.append(seq.substring(start, end)); + out.append(newline); + } + else if (start < seq.length()) + { + out.append(seq.substring(start)); + out.append(newline); + } + } + + i++; + } + + return out.toString(); + } + +}