X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=a4fb83064032610e75fb73708b50ec56d98c9118;hb=57c960648b550f10c7db40e39c7bb6a761d732b1;hp=3c7e0b263e4ff805cf5b384c4a4c5da7809e2652;hpb=8630b85f5394dfbc86a6c3c22ec17ffcc6ed1ea1;p=jalview.git diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index 3c7e0b2..a4fb830 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -1,20 +1,19 @@ /* - * 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 + * 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 + * + * 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; @@ -25,29 +24,35 @@ import jalview.datamodel.*; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public abstract class AlignFile - extends FileParse +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; /** @@ -59,11 +64,13 @@ public abstract class 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) + * + * @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 AlignFile(String inFile, String type) throws IOException { super(inFile, type); @@ -73,6 +80,20 @@ public abstract class AlignFile } /** + * 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() @@ -94,10 +115,11 @@ public abstract class AlignFile return s; } + /** - * called by AppletFormatAdapter to generate - * an annotated alignment, rather than bare - * sequences. + * called by AppletFormatAdapter to generate an annotated alignment, rather + * than bare sequences. + * * @param al */ public void addAnnotations(Alignment al) @@ -105,21 +127,31 @@ public abstract class AlignFile addProperties(al); for (int i = 0; i < annotations.size(); i++) { - al.addAnnotation( - (AlignmentAnnotation) annotations.elementAt(i) - ); + // detect if annotations.elementAt(i) rna secondary structure + // if so then do: + /* + * SequenceFeature[] pairArray = + * Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i)); + * Rna.HelixMap(pairArray); + */ + AlignmentAnnotation an = (AlignmentAnnotation) annotations + .elementAt(i); + an.validateRangeAndDisplay(); + al.addAnnotation(an); } } + /** - * Add any additional information extracted - * from the file to the alignment properties. + * 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) + if (properties != null && properties.size() > 0) { Enumeration keys = properties.keys(); Enumeration vals = properties.elements(); @@ -129,26 +161,44 @@ public abstract class AlignFile } } } + + /** + * 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) + if (key == null) + { + throw new Error( + "Implementation error: Cannot have null alignment property key."); + } + if (value == null) { - throw new Error("Implementation error: Cannot have null alignment property key."); + return; // null properties are ignored. } - if (properties==null) + if (properties == null) { properties = new Hashtable(); } properties.put(key, value); } + protected Object getAlignmentProperty(Object key) { - if (properties!=null && key!=null) + if (properties != null && key != null) { return properties.get(key); } return null; } + /** * Initialise objects to store sequence data in. */ @@ -160,8 +210,9 @@ public abstract class AlignFile /** * DOCUMENT ME! - * - * @param s DOCUMENT ME! + * + * @param s + * DOCUMENT ME! */ protected void setSeqs(SequenceI[] s) { @@ -176,8 +227,7 @@ public abstract class AlignFile /** * This method must be implemented to parse the contents of the file. */ - public abstract void parse() - throws IOException; + public abstract void parse() throws IOException; /** * Print out in alignment file format the Sequences in the seqs Vector. @@ -191,7 +241,7 @@ public abstract class AlignFile /** * A general parser for ids. - * + * * @String id Id to be parsed */ Sequence parseId(String id) @@ -213,10 +263,9 @@ public abstract class AlignFile } /** - * Creates the output id. - * Adds prefix Uniprot format source|id - * And suffix Jalview /start-end - * + * 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) @@ -224,4 +273,28 @@ public abstract class AlignFile 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(); + } + }