2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.analysis;
23 import jalview.datamodel.PDBEntry;
24 import jalview.datamodel.Sequence;
25 import jalview.datamodel.SequenceFeature;
26 import jalview.datamodel.SequenceI;
28 import java.util.Enumeration;
29 import java.util.Hashtable;
30 import java.util.Vector;
32 public class SeqsetUtils
36 * Store essential properties of a sequence in a hashtable for later recovery
37 * Keys are Name, Start, End, SeqFeatures, PdbId
43 public static Hashtable SeqCharacterHash(SequenceI seq)
45 Hashtable sqinfo = new Hashtable();
46 sqinfo.put("Name", seq.getName());
47 sqinfo.put("Start", new Integer(seq.getStart()));
48 sqinfo.put("End", new Integer(seq.getEnd()));
49 if (seq.getDescription() != null)
51 sqinfo.put("Description", seq.getDescription());
53 Vector sfeat = new Vector();
54 jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
55 if (sfarray != null && sfarray.length > 0)
57 for (int i = 0; i < sfarray.length; i++)
59 sfeat.addElement(sfarray[i]);
62 if (seq.getDatasetSequence() == null)
64 sqinfo.put("SeqFeatures", sfeat);
66 (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
67 : new Vector<PDBEntry>());
71 sqinfo.put("datasetSequence",
72 (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
73 : new Sequence("THISISAPLACEHOLDER", ""));
79 * Recover essential properties of a sequence from a hashtable TODO: replace
80 * these methods with something more elegant.
86 * @return boolean true if name was not updated from sqinfo Name entry
88 public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
90 boolean namePresent = true;
95 String oldname = (String) sqinfo.get("Name");
96 Integer start = (Integer) sqinfo.get("Start");
97 Integer end = (Integer) sqinfo.get("End");
98 Vector sfeatures = (Vector) sqinfo.get("SeqFeatures");
99 Vector<PDBEntry> pdbid = (Vector<PDBEntry>) sqinfo.get("PdbId");
100 String description = (String) sqinfo.get("Description");
101 Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
110 if (pdbid != null && pdbid.size() > 0)
115 if ((start != null) && (end != null))
117 sq.setStart(start.intValue());
118 sq.setEnd(end.intValue());
121 if ((sfeatures != null) && (sfeatures.size() > 0))
123 SequenceFeature[] sfarray = new SequenceFeature[sfeatures.size()];
124 for (int is = 0, isize = sfeatures.size(); is < isize; is++)
126 sfarray[is] = (SequenceFeature) sfeatures.elementAt(is);
128 sq.setSequenceFeatures(sfarray);
130 if (description != null)
132 sq.setDescription(description);
135 && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds
138 if (sfeatures != null)
141 .println("Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");
143 sq.setDatasetSequence(seqds);
150 * Form of the unique name used in uniquify for the i'th sequence in an
151 * ordered vector of sequences.
157 public static String unique_name(int i)
159 return new String("Sequence" + i);
163 * Generates a hash of SeqCharacterHash properties for each sequence in a
164 * sequence set, and optionally renames the sequences to an unambiguous 'safe'
170 * boolean set this to rename each of the sequences to its
171 * unique_name(index) name
172 * @return Hashtable to be passed to
173 * @see deuniquify to recover original names (and properties) for renamed
176 public static Hashtable uniquify(SequenceI[] sequences,
179 // Generate a safely named sequence set and a hash to recover the sequence
181 Hashtable map = new Hashtable();
182 // String[] un_names = new String[sequences.length];
184 for (int i = 0; i < sequences.length; i++)
186 String safename = unique_name(i);
187 map.put(safename, SeqCharacterHash(sequences[i]));
191 sequences[i].setName(safename);
199 * recover unsafe sequence names and original properties for a sequence set
200 * using a map generated by
202 * @see uniquify(sequences,true)
209 public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
211 return deuniquify(map, sequences, true);
215 * recover unsafe sequence names and original properties for a sequence set
216 * using a map generated by
218 * @see uniquify(sequences,true)
224 * when false, don't complain about sequences without any data in the
228 public static boolean deuniquify(Hashtable map, SequenceI[] sequences,
231 jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
233 SequenceI msq = null;
234 Enumeration keys = map.keys();
235 Vector unmatched = new Vector();
236 for (int i = 0, j = sequences.length; i < j; i++)
238 unmatched.addElement(sequences[i]);
240 while (keys.hasMoreElements())
242 Object key = keys.nextElement();
243 if (key instanceof String)
245 if ((msq = matcher.findIdMatch((String) key)) != null)
247 Hashtable sqinfo = (Hashtable) map.get(key);
248 unmatched.removeElement(msq);
249 SeqCharacterUnhash(msq, sqinfo);
255 System.err.println("Can't find '" + ((String) key)
256 + "' in uniquified alignment");
261 if (unmatched.size() > 0 && !quiet)
263 System.err.println("Did not find matches for :");
264 for (Enumeration i = unmatched.elements(); i.hasMoreElements(); System.out
265 .println(((SequenceI) i.nextElement()).getName()))
276 * returns a subset of the sequenceI seuqences, including only those that
277 * contain at least one residue.
281 * @return SequenceI[]
283 public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences)
285 // Identify first row of alignment with residues for prediction
286 boolean ungapped[] = new boolean[sequences.length];
288 for (int i = 0, j = sequences.length; i < j; i++)
290 String tempseq = jalview.analysis.AlignSeq.extractGaps(
291 jalview.util.Comparison.GapChars,
292 sequences[i].getSequenceAsString());
294 if (tempseq.length() == 0)
306 return null; // no minimal set
308 // compose minimal set
309 SequenceI[] mset = new SequenceI[msflen];
310 for (int i = 0, j = sequences.length, k = 0; i < j; i++)
314 mset[k++] = sequences[i];