Title:
- * - *Description:
- * - *Copyright: Copyright (c) 2004
- * - *Company: Dundee University
- * - * @author not attributable - * @version 1.0 - */ +import java.util.*; + +import jalview.datamodel.*; + public class SeqsetUtils { - public static Hashtable uniquify(SequenceI[] sequences) + + /** + * 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.addElement(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 = new SequenceFeature[sfeatures.size()]; + for (int is = 0, isize = sfeatures.size(); is < isize; is++) + { + sfarray[is] = (SequenceFeature) sfeatures.elementAt(is); + } + 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 + // 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 = new String("Sequence" + i); - map.put(safename, sequences[i].getName()); - sequences[i].setName(safename); + 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) { - // recover unsafe sequence names for a sequence set - boolean allfound = true; - for (int i = 0; i < sequences.length; i++) + return deuniquify(map, sequences, true); + } + + /** + * 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[] + * @param quiet + * when false, don't complain about sequences without any data in the + * map. + * @return boolean + */ + public static boolean deuniquify(Hashtable map, SequenceI[] sequences, + boolean quiet) + { + 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++) { - if (map.containsKey(sequences[i].getName())) + unmatched.addElement(sequences[i]); + } + while (keys.hasMoreElements()) + { + Object key = keys.nextElement(); + if (key instanceof String) { - String unsafename = (String) map.get(sequences[i].getName()); - sequences[i].setName(unsafename); + if ((msq = matcher.findIdMatch((String) key)) != null) + { + Hashtable sqinfo = (Hashtable) map.get(key); + unmatched.removeElement(msq); + SeqCharacterUnhash(msq, sqinfo); + } + else + { + if (!quiet) + { + System.err.println("Can't find '" + ((String) key) + + "' in uniquified alignment"); + } + } } - else + } + if (unmatched.size() > 0 && !quiet) + { + System.err.println("Did not find matches for :"); + for (Enumeration i = unmatched.elements(); i.hasMoreElements(); System.out + .println(((SequenceI) i.nextElement()).getName())) { - allfound = false; + ; } + return false; } - return allfound; + + 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; + } }