X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=d4b818b4d64c554c8433b687e811fc1168985c00;hb=8359bd8f5bae0bfc1a63ba114b7a4d67fbb62efe;hp=42334e3cc60b169995f1184a5bb5afc46820266a;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java index 42334e3..d4b818b 100755 --- a/src/jalview/io/PIRFile.java +++ b/src/jalview/io/PIRFile.java @@ -1,145 +1,148 @@ /* -* 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) 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.analysis.*; +import java.io.*; +import java.util.*; +import jalview.analysis.*; import jalview.datamodel.*; -import java.io.*; +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 + { + StringBuffer sequence; + String line = null; + + while ( (line = nextLine()) != null) + { + if(line.length()==0) + { + //System.out.println("blank line"); + continue; + } -import java.util.*; + Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1)); + sequence = new StringBuffer(); -public class PIRFile extends AlignFile { - Vector words = new Vector(); //Stores the words in a line after splitting + newSeq.setDescription(nextLine()); // this is the title line - public PIRFile() { - } + boolean starFound = false; - public PIRFile(String inStr) { - super(inStr); - } + while(!starFound) + { + line = nextLine(); + sequence.append(line); - public PIRFile(String inFile, String type) throws IOException { - super(inFile, type); - } + if (line == null) + break; - public void parse() { - try { - String id; - String start; - String 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(); + if (line.indexOf("*") > -1) + { + starFound = true; + } } - } - public String print() { - return print(getSeqsAsArray()); - } + if(sequence.length()>0) + { + sequence.setLength(sequence.length() - 1); - public static String print(SequenceI[] s) { - return print(s, 72, true); + newSeq.setSequence(sequence.toString()); + seqs.addElement(newSeq); + } + } } - - public static String print(SequenceI[] s, int len) { - return print(s, len, true); + catch (Exception ex) + { + ex.printStackTrace(); } - - 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++; + } + + 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; + + while ( (i < s.length) && (s[i] != null)) + { + String seq = s[i].getSequence(); + seq = seq + "*"; + + 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)); + out.append( is_NA ? " bases\n" : " residues\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"); + } + } - return out.toString(); + i++; } - 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); - } + return out.toString(); + } + }