X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=1b29b5263f4e7e83835c5bfd9b66b6876c537df8;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=3cd7bc1ef2c7f1c61e3b3d0a989dc4ffce3c4916;hpb=c5677e9860106a821a3e6e0429b20ede7b9a732a;p=jalview.git diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java index 3cd7bc1..1b29b52 100755 --- a/src/jalview/io/ClustalFile.java +++ b/src/jalview/io/ClustalFile.java @@ -1,33 +1,28 @@ /* - * 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 fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; -import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; -import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied; - import jalview.datamodel.*; import jalview.util.*; @@ -38,12 +33,12 @@ public class ClustalFile extends AlignFile { } - public ClustalFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException + public ClustalFile(String inFile, String type) throws IOException { super(inFile, type); } - public ClustalFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException + public ClustalFile(FileParse source) throws IOException { super(source); } @@ -57,9 +52,9 @@ public class ClustalFile extends AlignFile { int i = 0; boolean flag = false; - boolean rna=false; - boolean top=false; - StringBuffer pssecstr=new StringBuffer(),consstr=new StringBuffer(); + boolean rna = false; + boolean top = false; + StringBuffer pssecstr = new StringBuffer(), consstr = new StringBuffer(); Vector headers = new Vector(); Hashtable seqhash = new Hashtable(); StringBuffer tempseq; @@ -70,9 +65,9 @@ public class ClustalFile extends AlignFile { while ((line = nextLine()) != null) { - if (line.length()==0) + if (line.length() == 0) { - top=true; + top = true; } if (line.indexOf(" ") != 0) { @@ -109,7 +104,7 @@ public class ClustalFile extends AlignFile { tempseq.append(str.nextToken()); } - top=false; + top = false; } } } @@ -117,13 +112,17 @@ public class ClustalFile extends AlignFile { flag = true; } - } else { + } + else + { if (line.matches("\\s+(-|\\.|\\(|\\[|\\]|\\))+")) { if (top) { pssecstr.append(line.trim()); - } else { + } + else + { consstr.append(line.trim()); } } @@ -164,26 +163,32 @@ public class ClustalFile extends AlignFile + headers.elementAt(i)); } } - AlignmentAnnotation lastssa=null; - if (pssecstr.length()==maxLength) + AlignmentAnnotation lastssa = null; + if (pssecstr.length() == maxLength) { - Vector ss=new Vector(); - AlignmentAnnotation ssa=lastssa=StockholmFile.parseAnnotationRow(ss, "secondary structure", pssecstr.toString()); - ssa.label="Secondary Structure"; + Vector ss = new Vector(); + AlignmentAnnotation ssa = lastssa = StockholmFile + .parseAnnotationRow(ss, "secondary structure", + pssecstr.toString()); + ssa.label = "Secondary Structure"; annotations.addElement(ssa); } - if (consstr.length()==maxLength) + if (consstr.length() == maxLength) { - Vector ss=new Vector(); - AlignmentAnnotation ssa=StockholmFile.parseAnnotationRow(ss, "secondary structure", consstr.toString()); - ssa.label="Consensus Secondary Structure"; - if (lastssa==null || !lastssa.getRNAStruc().equals(ssa.getRNAStruc().replace('-', '.'))) + Vector ss = new Vector(); + AlignmentAnnotation ssa = StockholmFile.parseAnnotationRow(ss, + "secondary structure", consstr.toString()); + ssa.label = "Consensus Secondary Structure"; + if (lastssa == null + || !lastssa.getRNAStruc().equals( + ssa.getRNAStruc().replace('-', '.'))) { annotations.addElement(ssa); } } } } + public String print() { return print(getSeqsAsArray()); @@ -192,7 +197,7 @@ public class ClustalFile extends AlignFile public String print(SequenceI[] s) { - StringBuffer out = new StringBuffer("CLUSTAL"+newline+newline); + StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline); int max = 0; int maxid = 0;