X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAlignFile.java;h=f1153616ae196df362581540fd2dfd5ef3695bc9;hb=cbd8cafe5f1d302cf490d34a96f8231659afd402;hp=d22dc12affec96ce09f97bd011adf368f81bb256;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index d22dc12..f115361 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -1,29 +1,27 @@ /* -* 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) 2007 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 java.io.*; - import java.util.*; +import jalview.datamodel.*; /** * DOCUMENT ME! @@ -31,122 +29,146 @@ import java.util.*; * @author $author$ * @version $Revision$ */ -public abstract class AlignFile extends FileParse +public abstract class AlignFile + extends FileParse { - int noSeqs = 0; - int maxLength = 0; - Vector seqs; - Vector headers; - long start; - long end; - - /** - * Creates a new AlignFile object. - */ - public AlignFile() + int noSeqs = 0; + int maxLength = 0; + Vector seqs; + Vector annotations; + long start; + long end; + boolean jvSuffix = true; + + /** + * Creates a new AlignFile object. + */ + public AlignFile() + { + } + + /** + * Constructor which parses the data from a file of some specified type. + * @param inFile Filename to read from. + * @param type What type of file to read from (File, URL) + */ + public AlignFile(String inFile, String type) + throws IOException + { + super(inFile, type); + + initData(); + + parse(); + } + + /** + * Return the seqs Vector + */ + public Vector getSeqs() + { + return seqs; + } + + /** + * Return the Sequences in the seqs Vector as an array of Sequences + */ + public SequenceI[] getSeqsAsArray() + { + SequenceI[] s = new SequenceI[seqs.size()]; + + for (int i = 0; i < seqs.size(); i++) { + s[i] = (SequenceI) seqs.elementAt(i); } - /** - * Creates a new AlignFile object. - * - * @param inStr DOCUMENT ME! - */ - public AlignFile(String inStr) - { - initData(); - System.out.println("is this ever called??"); - - try - { - parse(); - } - catch (Exception ex) - { - } - } + return s; + } - /** - * Constructor which parses the data from a file of some specified type. - * @param inFile Filename to read from. - * @param type What type of file to read from (File, URL) - */ - public AlignFile(String inFile, String type) throws IOException + public void addAnnotations(Alignment al) + { + for (int i = 0; i < annotations.size(); i++) { - super(inFile, type); - - initData(); - - parse(); + al.addAnnotation( + (AlignmentAnnotation) annotations.elementAt(i) + ); } - /** - * Return the seqs Vector - */ - public Vector getSeqs() + } + + /** + * Initialise objects to store sequence data in. + */ + protected void initData() + { + seqs = new Vector(); + annotations = new Vector(); + } + + /** + * DOCUMENT ME! + * + * @param s DOCUMENT ME! + */ + protected void setSeqs(SequenceI[] s) + { + seqs = new Vector(); + + for (int i = 0; i < s.length; i++) { - return seqs; + seqs.addElement(s[i]); } - - /** - * Return the Sequences in the seqs Vector as an array of Sequences - */ - public SequenceI[] getSeqsAsArray() - { - SequenceI[] s = new SequenceI[seqs.size()]; - - for (int i = 0; i < seqs.size(); i++) - { - s[i] = (SequenceI) seqs.elementAt(i); - } - - return s; - } - - /** - * Initialise objects to store sequence data in. - */ - protected void initData() + } + + /** + * This method must be implemented to parse the contents of the file. + */ + public abstract void parse() + throws IOException; + + /** + * Print out in alignment file format the Sequences in the seqs Vector. + */ + public abstract String print(); + + public void addJVSuffix(boolean b) + { + jvSuffix = b; + } + + /** + * A general parser for ids. + * + * @String id Id to be parsed + */ + Sequence parseId(String id) + { + Sequence seq = null; + id = id.trim(); + int space = id.indexOf(" "); + if (space > -1) { - seqs = new Vector(); - headers = new Vector(); + seq = new Sequence(id.substring(0, space), ""); + seq.setDescription(id.substring(space + 1)); } - - /** - * DOCUMENT ME! - * - * @param s DOCUMENT ME! - */ - protected void setSeqs(SequenceI[] s) - { - seqs = new Vector(); - - for (int i = 0; i < s.length; i++) - { - seqs.addElement(s[i]); - } - } - - // Checks whether sequence is valid aa characters - protected boolean isValidProteinSequence(String sequence) + else { - for (int i = 0; i < sequence.length(); i++) - if (!jalview.schemes.ResidueProperties.aaHash.containsKey( - String.valueOf(sequence.charAt(i)))) - { - return false; - } - - return true; + seq = new Sequence(id, ""); } - /** - * This method must be implemented to parse the contents of the file. - */ - public abstract void parse() throws IOException; + return seq; + } + + /** + * Creates the output id. + * Adds prefix Uniprot format source|id + * And suffix Jalview /start-end + * + * @String id Id to be parsed + */ + String printId(SequenceI seq) + { + return seq.getDisplayId(jvSuffix); + } - /** - * Print out in alignment file format the Sequences in the seqs Vector. - */ - public abstract String print(); }