X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=fa9a28bf6b99eb04ffaefa5982493f9f9450569f;hb=3e3378e2ccfea39a2b161600c5a2029716acd1b7;hp=410628f4dab5dd7aef266b436919f1a5d7add2db;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java index 410628f..fa9a28b 100755 --- a/src/jalview/io/PIRFile.java +++ b/src/jalview/io/PIRFile.java @@ -1,135 +1,189 @@ /* -* 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 -*/ - + * 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 jalview.io; -import jalview.datamodel.*; -import jalview.analysis.*; - import java.io.*; import java.util.*; -public class PIRFile extends AlignFile { +import jalview.datamodel.*; - Vector words = new Vector(); //Stores the words in a line after splitting +public class PIRFile + extends AlignFile +{ + public static boolean useModellerOutput = false; - public PIRFile() - {} + Vector words = new Vector(); //Stores the words in a line after splitting - public PIRFile(String inStr) { - super(inStr); + public PIRFile() + { } - public PIRFile(String inFile, String type) throws IOException { - super(inFile,type); + public PIRFile(String inFile, String type) + throws IOException + { + super(inFile, type); } - public void parse() { - try{ - String id, start, end; + public void parse() throws IOException + { StringBuffer sequence; String line = null; - while( (line = nextLine())!=null) + ModellerDescription md; + + 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"; } + 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(); - line = nextLine(); // this is the title line + newSeq.setDescription(nextLine()); // this is the title line boolean starFound = false; - do + + while(!starFound) { line = nextLine(); - sequence.append( line ); - if(line.indexOf("*")>-1) - starFound = true; + sequence.append(line); - }while(!starFound); + if (line == null) + break; - sequence.setLength( sequence.length()-1); + if (line.indexOf("*") > -1) + { + starFound = true; + } + } - Sequence newSeq = new Sequence(id, - sequence.toString(), - Integer.parseInt(start), - Integer.parseInt(end)); - seqs.addElement(newSeq); + if (sequence.length() > 0) + { + sequence.setLength(sequence.length() - 1); + newSeq.setSequence(sequence.toString()); + if (!isValidProteinSequence(newSeq.getSequence())) + { + throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS + +" : "+ newSeq.getName() + +" : "+invalidCharacter); + } + + seqs.addElement(newSeq); + + md = new ModellerDescription(newSeq. + getDescription()); + md.updateSequenceI(newSeq); + } } - - } - catch(Exception ex){ex.printStackTrace();} } - public String print() { + 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) { + + 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].getSequence(); + seq = seq + "*"; + - 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 + "*"; + 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() + "\n"); + if (s[i].getDescription() == null) + { + out.append(s[i].getName() + " " + + (s[i].getEnd() - s[i].getStart() + 1)); + out.append(is_NA ? " bases\n" : " residues\n"); + } + else + { + out.append(s[i].getDescription()+"\n"); + } } + else + { - out.append(">P1;" + s[i].getName() + "/" + s[i].getStart()+ "-" + s[i].getEnd() + "\n"); - out.append(" Dummy title\n"); - int nochunks = seq.length() / len + 1; + if(useModellerOutput) + { + out.append(">P1;" + s[i].getName() + "\n"); + md = new ModellerDescription(s[i]); + out.append(md.getDescriptionLine() + "\n"); + } + else + { + out.append(">P1;" + printId(s[i]) + "\n"); + if (s[i].getDescription() != null) + out.append(s[i].getDescription() + "\n"); + else + out.append(s[i].getName() + " " + + (s[i].getEnd() - s[i].getStart() + 1) + + " residues\n"); + } + } + int nochunks = (seq.length() / len) + 1; - for (int j = 0; j < nochunks; j++) { - int start = j*len; + 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()) { + 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); - } } - - -