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.datamodel;
23 import java.util.ArrayList;
24 import java.util.Arrays;
25 import java.util.BitSet;
26 import java.util.List;
29 * Holds a list of search result matches, where each match is a contiguous
30 * stretch of a single sequence.
32 * @author gmcarstairs amwaterhouse
35 public class SearchResults implements SearchResultsI
38 private List<SearchResultMatchI> matches = new ArrayList<SearchResultMatchI>();
41 * One match consists of a sequence reference, start and end positions.
42 * Discontiguous ranges in a sequence require two or more Match objects.
44 public class Match implements SearchResultMatchI
49 * Start position of match in sequence (base 1)
54 * End position (inclusive) (base 1)
64 * start position of matched range (base 1)
66 * end of matched range (inclusive, base 1)
68 public Match(SequenceI seq, int start, int end)
73 * always hold in forwards order, even if given in reverse order
74 * (such as from a mapping to a reverse strand); this avoids
75 * trouble for routines that highlight search results etc
90 * @see jalview.datamodel.SearchResultMatchI#getSequence()
93 public SequenceI getSequence()
99 * @see jalview.datamodel.SearchResultMatchI#getStart()
102 public int getStart()
108 * @see jalview.datamodel.SearchResultMatchI#getEnd()
117 * Returns the string of characters in the matched region, prefixed by the
118 * start position, e.g. "12CGT" or "208K"
121 public String toString()
123 final int from = Math.max(start - 1, 0);
124 String startPosition = String.valueOf(from);
125 return startPosition + getCharacters();
129 * @see jalview.datamodel.SearchResultMatchI#getCharacters()
132 public String getCharacters()
134 char[] chars = sequence.getSequence();
135 // convert start/end to base 0 (with bounds check)
136 final int from = Math.max(start - 1, 0);
137 final int to = Math.min(end, chars.length + 1);
138 return String.valueOf(Arrays.copyOfRange(chars, from, to));
141 public void setSequence(SequenceI seq)
147 * Hashcode is the hashcode of the matched sequence plus a hash of start and
148 * end positions. Match objects that pass the test for equals are guaranteed
149 * to have the same hashcode.
152 public int hashCode()
154 int hash = sequence == null ? 0 : sequence.hashCode();
161 * Two Match objects are equal if they are for the same sequence, start and
165 public boolean equals(Object obj)
167 if (obj == null || !(obj instanceof SearchResultMatchI))
171 SearchResultMatchI m = (SearchResultMatchI) obj;
172 return (sequence == m.getSequence() && start == m.getStart() && end == m
178 * @see jalview.datamodel.SearchResultsI#addResult(jalview.datamodel.SequenceI, int, int)
181 public void addResult(SequenceI seq, int start, int end)
183 matches.add(new Match(seq, start, end));
187 * @see jalview.datamodel.SearchResultsI#involvesSequence(jalview.datamodel.SequenceI)
190 public boolean involvesSequence(SequenceI sequence)
192 SequenceI ds = sequence.getDatasetSequence();
194 for (SearchResultMatchI _m : matches)
197 if (m.sequence != null
198 && (m.sequence == sequence || m.sequence == ds))
207 * @see jalview.datamodel.SearchResultsI#getResults(jalview.datamodel.SequenceI, int, int)
210 public int[] getResults(SequenceI sequence, int start, int end)
212 if (matches.isEmpty())
219 int resultLength, matchStart = 0, matchEnd = 0;
222 for (SearchResultMatchI _m : matches)
227 if (m.sequence == sequence)
230 // locate aligned position
231 matchStart = sequence.findIndex(m.start) - 1;
232 matchEnd = sequence.findIndex(m.end) - 1;
234 else if (m.sequence == sequence.getDatasetSequence())
237 // locate region in local context
238 matchStart = sequence.findIndex(m.start) - 1;
239 matchEnd = sequence.findIndex(m.end) - 1;
243 if (matchStart <= end && matchEnd >= start)
245 if (matchStart < start)
257 result = new int[] { matchStart, matchEnd };
261 resultLength = result.length;
262 tmp = new int[resultLength + 2];
263 System.arraycopy(result, 0, tmp, 0, resultLength);
265 result[resultLength] = matchStart;
266 result[resultLength + 1] = matchEnd;
272 // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
273 // + matchEnd+"<"+start);
281 public int markColumns(SequenceCollectionI sqcol, BitSet bs)
284 BitSet mask = new BitSet();
285 for (SequenceI s : sqcol.getSequences())
287 int[] cols = getResults(s, sqcol.getStartRes(), sqcol.getEndRes());
290 for (int pair = 0; pair < cols.length; pair += 2)
292 mask.set(cols[pair], cols[pair + 1] + 1);
296 // compute columns that were newly selected
297 BitSet original = (BitSet) bs.clone();
299 count = mask.cardinality() - original.cardinality();
300 // and mark ranges not already marked
306 * @see jalview.datamodel.SearchResultsI#getSize()
311 return matches.size();
315 * @see jalview.datamodel.SearchResultsI#getResultSequence(int)
318 public SequenceI getResultSequence(int index)
320 return matches.get(index).getSequence();
324 * @see jalview.datamodel.SearchResultsI#getResultStart(int)
327 public int getResultStart(int i)
329 return matches.get(i).getStart();
333 * @see jalview.datamodel.SearchResultsI#getResultEnd(int)
336 public int getResultEnd(int i)
338 return matches.get(i).getEnd();
342 * @see jalview.datamodel.SearchResultsI#isEmpty()
345 public boolean isEmpty()
347 return matches.isEmpty();
351 * @see jalview.datamodel.SearchResultsI#getResults()
354 public List<SearchResultMatchI> getResults()
360 * Return the results as a string of characters (bases) prefixed by start
361 * position(s). Meant for use when the context ensures that all matches are to
362 * regions of the same sequence (otherwise the result is meaningless).
367 public String toString()
369 StringBuilder result = new StringBuilder(256);
370 for (SearchResultMatchI m : matches)
372 result.append(m.toString());
374 return result.toString();
378 * Return the results as a string of characters (bases). Meant for use when
379 * the context ensures that all matches are to regions of the same sequence
380 * (otherwise the result is meaningless).
384 public String getCharacters()
386 StringBuilder result = new StringBuilder(256);
387 for (SearchResultMatchI m : matches)
389 result.append(m.getCharacters());
391 return result.toString();
395 * Hashcode is has derived from the list of matches. This ensures that when
396 * two SearchResults objects satisfy the test for equals(), then they have the
400 public int hashCode()
402 return matches.hashCode();
406 * Two SearchResults are considered equal if they contain the same matches in
410 public boolean equals(Object obj)
412 if (obj == null || !(obj instanceof SearchResultsI))
416 SearchResultsI sr = (SearchResultsI) obj;
417 return matches.equals(sr.getResults());