X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=3ca2563b1e80d83ce47c28a1e0fb1510090c406c;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=2ad32f0787e97f9ea99e2ca342503440a2061880;hpb=60f2d6c034560415fd0139c8bc7df0c19cae1186;p=jalview.git diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index 2ad32f0..3ca2563 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -1,17 +1,17 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) + * Copyright (C) 2008 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 @@ -25,29 +25,35 @@ 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 +65,13 @@ 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); @@ -71,8 +79,11 @@ public abstract class AlignFile parse(); } + /** - * Attempt to read from the position where some other parsing process left off. + * Attempt to read from the position where some other parsing process left + * off. + * * @param source * @throws IOException */ @@ -82,6 +93,7 @@ public abstract class AlignFile initData(); parse(); } + /** * Return the seqs Vector */ @@ -104,10 +116,11 @@ 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) @@ -115,21 +128,21 @@ public abstract class AlignFile addProperties(al); for (int i = 0; i < annotations.size(); i++) { - al.addAnnotation( - (AlignmentAnnotation) annotations.elementAt(i) - ); + al.addAnnotation((AlignmentAnnotation) annotations.elementAt(i)); } } + /** - * 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(); @@ -139,36 +152,44 @@ 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 + * 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."); + throw new Error( + "Implementation error: Cannot have null alignment property key."); } - if (value==null) + if (value == null) { 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. */ @@ -180,8 +201,9 @@ public abstract class AlignFile /** * DOCUMENT ME! - * - * @param s DOCUMENT ME! + * + * @param s + * DOCUMENT ME! */ protected void setSeqs(SequenceI[] s) { @@ -196,8 +218,7 @@ 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. @@ -211,7 +232,7 @@ public abstract class AlignFile /** * A general parser for ids. - * + * * @String id Id to be parsed */ Sequence parseId(String id) @@ -233,20 +254,20 @@ 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) { return seq.getDisplayId(jvSuffix); } + /** * vector of String[] treeName, newickString pairs */ - Vector newickStrings=null; + Vector newickStrings = null; protected void addNewickTree(String treeName, String newickString) { @@ -254,12 +275,13 @@ public abstract class AlignFile { newickStrings = new Vector(); } - newickStrings.addElement(new String[] { treeName, newickString}); + newickStrings.addElement(new String[] + { treeName, newickString }); } protected int getTreeCount() { - if (newickStrings==null) + if (newickStrings == null) { return 0; }