X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=3f0fea0034f6b38c241a38ac4e8519b295d4a4ce;hb=4b2392caa53f1de3400e7916d1d9c7b815d446f4;hp=5bc7bd5928b6c29a17ab9b13f7c19c466fb5ab36;hpb=a7f8fa9c06d82efbbdbc6a0bf1054bb21610b353;p=jalview.git diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java index 5bc7bd5..3f0fea0 100755 --- a/src/jalview/io/PIRFile.java +++ b/src/jalview/io/PIRFile.java @@ -1,55 +1,52 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * 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. - * + * 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 . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; -import java.io.*; -import java.util.*; - -import javax.xml.parsers.ParserConfigurationException; - -import org.xml.sax.SAXException; +import jalview.bin.Cache; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.util.Comparison; -import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; -import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; -import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied; - -import jalview.datamodel.*; +import java.io.IOException; public class PIRFile extends AlignFile { - public static boolean useModellerOutput = false; - - Vector words = new Vector(); // Stores the words in a line after splitting + // Vector words = new Vector(); // Stores the words in a line after splitting public PIRFile() { } - public PIRFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed + public PIRFile(String inFile, DataSourceType sourceType) + throws IOException { - super(inFile, type); + super(inFile, sourceType); } - public PIRFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed + public PIRFile(FileParse source) throws IOException { super(source); } + @Override public void parse() throws IOException { StringBuffer sequence; @@ -104,19 +101,15 @@ public class PIRFile extends AlignFile } } - public String print() + @Override + public String print(SequenceI[] s, boolean jvsuffix) { - return print(getSeqsAsArray()); - } - - public String print(SequenceI[] s) - { - boolean is_NA = jalview.util.Comparison.isNucleotide(s); + boolean is_NA = Comparison.isNucleotide(s); int len = 72; StringBuffer out = new StringBuffer(); int i = 0; ModellerDescription md; - + boolean useModellerOutput = Cache.getDefault("PIR_MODELLER", false); while ((i < s.length) && (s[i] != null)) { String seq = s[i].getSequenceAsString(); @@ -152,7 +145,6 @@ public class PIRFile extends AlignFile } else { - if (useModellerOutput) { out.append(">P1;" + s[i].getName()); @@ -163,7 +155,7 @@ public class PIRFile extends AlignFile } else { - out.append(">P1;" + printId(s[i])); + out.append(">P1;" + printId(s[i], jvsuffix)); out.append(newline); if (s[i].getDescription() != null) { @@ -178,7 +170,8 @@ public class PIRFile extends AlignFile } } } - int nochunks = (seq.length() / len) + 1; + int nochunks = (seq.length() / len) + + (seq.length() % len > 0 ? 1 : 0); for (int j = 0; j < nochunks; j++) {