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]; - - 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; - } - - 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) 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.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())); + if (seq.getDescription() != null) + { + sqinfo.put("Description", seq.getDescription()); + } + Vector sfeat = new Vector(); + jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures(); + if (sfarray != null && sfarray.length > 0) + { + for (int i = 0; i < sfarray.length; i++) + { + sfeat.add(sfarray[i]); + } + } + sqinfo.put("SeqFeatures", sfeat); + 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 true if name was not updated from sqinfo Name entry + */ + 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"); + Vector sfeatures = (Vector) sqinfo.get( + "SeqFeatures"); + Vector pdbid = (Vector) sqinfo.get("PdbId"); + String description = (String) sqinfo.get("Description"); + 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)) + { + SequenceFeature[] sfarray = (SequenceFeature[]) sfeatures.toArray(); + sq.setSequenceFeatures(sfarray); + } + if (description != null) + { + sq.setDescription(description); + } + 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 < j; i++) + { + unmatched.add(sequences[i]); + } + while (keys.hasMoreElements()) + { + Object key = keys.nextElement(); + if (key instanceof String) + { + if ( (msq = matcher.findIdMatch( (String) key)) != null) + { + Hashtable sqinfo = (Hashtable) map.get(key); + unmatched.remove(msq); + SeqCharacterUnhash(msq, sqinfo); + } + else + { + System.err.println("Can't find '" + ( (String) key) + + "' in uniquified alignment"); + } + } + } + if (unmatched.size() > 0) + { + System.err.println("Did not find matches for :"); + for (Enumeration i = unmatched.elements(); i.hasMoreElements(); + System.out.println( ( (SequenceI) i.nextElement()).getName())) + { + ; + } + return false; + } + + return true; + } + + /** + * returns a subset of the sequenceI seuqences, + * including only those that contain at least one residue. + * @param sequences SequenceI[] + * @return SequenceI[] + */ + public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences) + { + // Identify first row of alignment with residues for prediction + boolean ungapped[] = new boolean[sequences.length]; + int msflen = 0; + for (int i = 0, j = sequences.length; i < j; i++) + { + String tempseq = jalview.analysis.AlignSeq.extractGaps( + jalview.util.Comparison.GapChars, + sequences[i].getSequenceAsString()); + + if (tempseq.length() == 0) + { + ungapped[i] = false; + } + else + { + ungapped[i] = true; + msflen++; + } + } + if (msflen == 0) + { + return null; // no minimal set + } + // compose minimal set + SequenceI[] mset = new SequenceI[msflen]; + for (int i = 0, j = sequences.length, k = 0; i < j; i++) + { + if (ungapped[i]) + { + mset[k++] = sequences[i]; + } + } + ungapped = null; + return mset; + } +}