X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=1e1b777d2d1347f71e889e9b5bfc43cc9658c565;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=0691d82d47e10dd93bb8721fb3866f8ce860a917;hpb=c3c305755d392741176209a0274a47897ac4d8a8;p=jalview.git diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index 0691d82..1e1b777 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -1,178 +1,290 @@ -/* -* 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 java.io.*; - -import java.util.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public abstract class AlignFile extends FileParse -{ - int noSeqs = 0; - int maxLength = 0; - Vector seqs; - Vector headers; - 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); - } - - return s; - } - - /** - * Initialise objects to store sequence data in. - */ - protected void initData() - { - seqs = new Vector(); - headers = new Vector(); - } - - /** - * 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) - { - for (int i = 0; i < sequence.length(); i++) - if (jalview.schemes.ResidueProperties.aaIndex[sequence.charAt(i)]==-1) - { - invalidCharacter = sequence.charAt(i); - return false; - } - - return true; - } - - char invalidCharacter; - - /** - * 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) - { - seq = new Sequence(id.substring(0, space),""); - seq.setDescription(id.substring(space+1)); - } - else - { - seq = new Sequence(id, ""); - } - - 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); - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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. + * + * 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 . + */ +package jalview.io; + +import java.io.*; +import java.util.*; + +import jalview.datamodel.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public abstract class AlignFile extends FileParse +{ + int noSeqs = 0; + + int maxLength = 0; + + /** + * Sequences to be added to form a new alignment. + */ + protected Vector seqs; + + /** + * annotation to be added to generated alignment object + */ + protected Vector annotations; + + /** + * Properties to be added to generated alignment object + */ + protected Hashtable properties; + + 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(); + } + + /** + * Attempt to read from the position where some other parsing process left + * off. + * + * @param source + * @throws IOException + */ + public AlignFile(FileParse source) throws IOException + { + super(source); + 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); + } + + return s; + } + + /** + * called by AppletFormatAdapter to generate an annotated alignment, rather + * than bare sequences. + * + * @param al + */ + public void addAnnotations(Alignment al) + { + addProperties(al); + for (int i = 0; i < annotations.size(); i++) + { + al.addAnnotation((AlignmentAnnotation) annotations.elementAt(i)); + } + + } + + /** + * Add any additional information extracted from the file to the alignment + * properties. + * + * @note implicitly called by addAnnotations() + * @param al + */ + public void addProperties(Alignment al) + { + if (properties != null && properties.size() > 0) + { + Enumeration keys = properties.keys(); + Enumeration vals = properties.elements(); + while (keys.hasMoreElements()) + { + al.setProperty(keys.nextElement(), vals.nextElement()); + } + } + } + + /** + * Store a non-null key-value pair in a hashtable used to set alignment + * properties note: null keys will raise an error, null values will result in + * the key/value pair being silently ignored. + * + * @param key + * - non-null key object + * @param value + * - non-null value + */ + protected void setAlignmentProperty(Object key, Object value) + { + if (key == null) + { + throw new Error( + "Implementation error: Cannot have null alignment property key."); + } + if (value == null) + { + return; // null properties are ignored. + } + if (properties == null) + { + properties = new Hashtable(); + } + properties.put(key, value); + } + + protected Object getAlignmentProperty(Object key) + { + if (properties != null && key != null) + { + return properties.get(key); + } + return null; + } + + /** + * 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++) + { + seqs.addElement(s[i]); + } + } + + /** + * 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) + { + seq = new Sequence(id.substring(0, space), ""); + seq.setDescription(id.substring(space + 1)); + } + else + { + seq = new Sequence(id, ""); + } + + 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); + } + + /** + * vector of String[] treeName, newickString pairs + */ + Vector newickStrings = null; + + protected void addNewickTree(String treeName, String newickString) + { + if (newickStrings == null) + { + newickStrings = new Vector(); + } + newickStrings.addElement(new String[] + { treeName, newickString }); + } + + protected int getTreeCount() + { + if (newickStrings == null) + { + return 0; + } + return newickStrings.size(); + } + +}