Title:
- * - *Description:
- * - *Copyright: Copyright (c) 2004
- * - *Company: Dundee University
- * - * @author not attributable - * @version 1.0 - */ -public class SeqsetUtils -{ - /** - * Store essential properties of a sequence in a hashtable for later recovery - * Keys are Name, Start, End, SeqFeatures, PdbId - * @param seq SequenceI - * @return Hashtable - */ - public static Hashtable SeqCharacterHash(SequenceI seq) { - Hashtable sqinfo = new Hashtable(); - sqinfo.put("Name", seq.getName()); - sqinfo.put("Start", new Integer(seq.getStart())); - sqinfo.put("End", new Integer(seq.getEnd())); - sqinfo.put("SeqFeatures", seq.getSequenceFeatures()); - sqinfo.put("PdbId", (seq.getPDBId()!=null) ? seq.getPDBId() : new String("") ); - return sqinfo; - } - /** - * Recover essential properties of a sequence from a hashtable - * TODO: replace these methods with something more elegant. - * @param sq SequenceI - * @param sqinfo Hashtable - * @return boolean - */ - public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo) { - boolean namePresent = true; - String oldname = (String) sqinfo.get("Name"); - Integer start = (Integer) sqinfo.get("Start"); - Integer end = (Integer) sqinfo.get("End"); - java.util.Vector sfeatures = (java.util.Vector) sqinfo.get("SeqFeatures"); - String pdbid = (String) sqinfo.get("PdbId"); - if (oldname==null) - namePresent = false; - else - sq.setName(oldname); - if (!pdbid.equals("")) - sq.setPDBId(pdbid); - - if ((start!=null) && (end!=null)) { - sq.setStart(start.intValue()); - sq.setEnd(end.intValue()); - } - if (sfeatures!=null) - sq.setSequenceFeatures(sfeatures); - return namePresent; - } - - /** - * Form of the unique name used in uniquify for the i'th sequence in an ordered vector of sequences. - * @param i int - * @return String - */ - public static String unique_name(int i) { - return new String("Sequence"+i); - } - - public static Hashtable uniquify(SequenceI[] sequences, boolean write_names) - { - // Generate a safely named sequence set and a hash to recover the sequence names - Hashtable map = new Hashtable(); - String[] un_names = new String[sequences.length]; - if (!write_names) - - for (int i = 0; i < sequences.length; i++) - { - String safename = new String("Sequence" + i); - map.put(safename, SeqCharacterHash(sequences[i])); - if (write_names) - sequences[i].setName(safename); - } - return map; - } - - public static boolean deuniquify(Hashtable map, SequenceI[] sequences) - { - // recover unsafe sequence names for a sequence set - boolean allfound = true; - for (int i = 0; i < sequences.length; i++) - { - if (map.containsKey(sequences[i].getName())) - { - Hashtable sqinfo = (Hashtable) map.get(sequences[i].getName()); - SeqCharacterUnhash(sequences[i], sqinfo); - } - else - { - allfound = false; - } - } - return allfound; - } - -} +/* + * 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 + */ +package jalview.analysis; + +import java.util.*; + +import jalview.datamodel.*; + +/** + *Title:
+ * + *Description:
+ * + *Copyright: Copyright (c) 2004
+ * + *Company: Dundee University
+ * + * @author not attributable + * @version 1.0 + */ +public class SeqsetUtils +{ + + /** + * Store essential properties of a sequence in a hashtable for later recovery + * Keys are Name, Start, End, SeqFeatures, PdbId + * @param seq SequenceI + * @return Hashtable + */ + public static Hashtable SeqCharacterHash(SequenceI seq) + { + Hashtable sqinfo = new Hashtable(); + sqinfo.put("Name", seq.getName()); + sqinfo.put("Start", new Integer(seq.getStart())); + sqinfo.put("End", new Integer(seq.getEnd())); + sqinfo.put("SeqFeatures", (seq.getSequenceFeatures() !=null) ? seq.getSequenceFeatures() : new Vector()); + sqinfo.put("PdbId", + (seq.getPDBId() != null) ? seq.getPDBId() : new Vector()); + sqinfo.put("datasetSequence", (seq.getDatasetSequence() !=null) ? seq.getDatasetSequence() : new Sequence("THISISAPLACEHOLDER","")); + return sqinfo; + } + + /** + * Recover essential properties of a sequence from a hashtable + * TODO: replace these methods with something more elegant. + * @param sq SequenceI + * @param sqinfo Hashtable + * @return boolean + */ + public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo) + { + boolean namePresent = true; + if (sqinfo==null) + return false; + String oldname = (String) sqinfo.get("Name"); + Integer start = (Integer) sqinfo.get("Start"); + Integer end = (Integer) sqinfo.get("End"); + java.util.Vector sfeatures = (java.util.Vector) sqinfo.get( + "SeqFeatures"); + Vector pdbid = (Vector) sqinfo.get("PdbId"); + Sequence seqds = (Sequence) sqinfo.get("datasetSequence"); + if (oldname == null) + { + namePresent = false; + } + else + { + sq.setName(oldname); + } + if (pdbid!=null && pdbid.size()>0) + { + sq.setPDBId(pdbid); + } + + if ( (start != null) && (end != null)) + { + sq.setStart(start.intValue()); + sq.setEnd(end.intValue()); + } + + if ((sfeatures != null) && (sfeatures.size()>0)) + { + sq.setSequenceFeatures(sfeatures); + } + if ((seqds!=null) && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds.getLength()==0)) { + sq.setDatasetSequence(seqds); + } + + return namePresent; + } + + /** + * Form of the unique name used in uniquify for the i'th sequence in an ordered vector of sequences. + * @param i int + * @return String + */ + public static String unique_name(int i) + { + return new String("Sequence" + i); + } + + /** + * Generates a hash of SeqCharacterHash properties for each sequence + * in a sequence set, and optionally renames the sequences to an + * unambiguous 'safe' name. + * @param sequences SequenceI[] + * @param write_names boolean set this to rename each of the sequences to its unique_name(index) name + * @return Hashtable to be passed to @see deuniquify to recover original names (and properties) for renamed sequences + */ + public static Hashtable uniquify(SequenceI[] sequences, boolean write_names) + { + // Generate a safely named sequence set and a hash to recover the sequence names + Hashtable map = new Hashtable(); + //String[] un_names = new String[sequences.length]; + + for (int i = 0; i < sequences.length; i++) + { + String safename = unique_name(i); + map.put(safename, SeqCharacterHash(sequences[i])); + + if (write_names) + { + sequences[i].setName(safename); + } + } + + + return map; + } + /** + * recover unsafe sequence names and original properties for a sequence + * set using a map generated by @see uniquify(sequences,true) + * @param map Hashtable + * @param sequences SequenceI[] + * @return boolean + */ + public static boolean deuniquify(Hashtable map, SequenceI[] sequences) + { + jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(sequences); + SequenceI msq = null; + Enumeration keys = map.keys(); + Vector unmatched = new Vector(); + for (int i=0, j=sequences.length; i