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 + * Keys are Name, Start, End, SeqFeatures, PdbId + * + * @param seq + * SequenceI * @return Hashtable */ public static Hashtable SeqCharacterHash(SequenceI seq) @@ -59,23 +49,26 @@ public class SeqsetUtils { for (int i = 0; i < sfarray.length; i++) { - sfeat.add(sfarray[i]); + sfeat.addElement(sfarray[i]); } } sqinfo.put("SeqFeatures", sfeat); - sqinfo.put("PdbId", - (seq.getPDBId() != null) ? seq.getPDBId() : new Vector()); + sqinfo.put("PdbId", (seq.getPDBId() != null) ? seq.getPDBId() + : new Vector()); sqinfo.put("datasetSequence", - (seq.getDatasetSequence() != null) ? seq.getDatasetSequence() : - new Sequence("THISISAPLACEHOLDER", "")); + (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 + * 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) @@ -88,8 +81,7 @@ public class SeqsetUtils 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 sfeatures = (Vector) sqinfo.get("SeqFeatures"); Vector pdbid = (Vector) sqinfo.get("PdbId"); String description = (String) sqinfo.get("Description"); Sequence seqds = (Sequence) sqinfo.get("datasetSequence"); @@ -106,24 +98,28 @@ public class SeqsetUtils sq.setPDBId(pdbid); } - if ( (start != null) && (end != null)) + if ((start != null) && (end != null)) { sq.setStart(start.intValue()); sq.setEnd(end.intValue()); } - if ( (sfeatures != null) && (sfeatures.size() > 0)) + if ((sfeatures != null) && (sfeatures.size() > 0)) { - SequenceFeature[] sfarray = (SequenceFeature[]) sfeatures.toArray(); + 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)) + if ((seqds != null) + && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds + .getLength() == 0)) { sq.setDatasetSequence(seqds); } @@ -132,8 +128,11 @@ public class SeqsetUtils } /** - * Form of the unique name used in uniquify for the i'th sequence in an ordered vector of sequences. - * @param i int + * 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) @@ -142,18 +141,26 @@ public class SeqsetUtils } /** - * 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 + * 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) + 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]; + // String[] un_names = new String[sequences.length]; for (int i = 0; i < sequences.length; i++) { @@ -170,61 +177,73 @@ public class SeqsetUtils } /** - * 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[] + * 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) { 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. + * 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); + 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++) { - unmatched.add(sequences[i]); + unmatched.addElement(sequences[i]); } while (keys.hasMoreElements()) { Object key = keys.nextElement(); if (key instanceof String) { - if ( (msq = matcher.findIdMatch( (String) key)) != null) + if ((msq = matcher.findIdMatch((String) key)) != null) { Hashtable sqinfo = (Hashtable) map.get(key); - unmatched.remove(msq); + unmatched.removeElement(msq); SeqCharacterUnhash(msq, sqinfo); } else { if (!quiet) - { - System.err.println("Can't find '" + ( (String) key) + - "' in uniquified alignment"); - } + { + System.err.println("Can't find '" + ((String) key) + + "' in uniquified alignment"); + } } } } 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())) + for (Enumeration i = unmatched.elements(); i.hasMoreElements(); System.out + .println(((SequenceI) i.nextElement()).getName())) { ; } @@ -235,9 +254,11 @@ public class SeqsetUtils } /** - * returns a subset of the sequenceI seuqences, - * including only those that contain at least one residue. - * @param sequences SequenceI[] + * 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) @@ -248,8 +269,8 @@ public class SeqsetUtils for (int i = 0, j = sequences.length; i < j; i++) { String tempseq = jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, - sequences[i].getSequenceAsString()); + jalview.util.Comparison.GapChars, + sequences[i].getSequenceAsString()); if (tempseq.length() == 0) {