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<Match> matches = new ArrayList<Match>();
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 Match))
171 Match m = (Match) obj;
172 return (this.sequence == m.sequence && this.start == m.start && this.end == m.end);
177 * @see jalview.datamodel.SearchResultsI#addResult(jalview.datamodel.SequenceI, int, int)
180 public void addResult(SequenceI seq, int start, int end)
182 matches.add(new Match(seq, start, end));
186 * @see jalview.datamodel.SearchResultsI#involvesSequence(jalview.datamodel.SequenceI)
189 public boolean involvesSequence(SequenceI sequence)
191 SequenceI ds = sequence.getDatasetSequence();
192 for (Match m : matches)
194 if (m.sequence != null
195 && (m.sequence == sequence || m.sequence == ds))
204 * @see jalview.datamodel.SearchResultsI#getResults(jalview.datamodel.SequenceI, int, int)
207 public int[] getResults(SequenceI sequence, int start, int end)
209 if (matches.isEmpty())
216 int resultLength, matchStart = 0, matchEnd = 0;
218 for (Match m : matches)
221 if (m.sequence == sequence)
224 // locate aligned position
225 matchStart = sequence.findIndex(m.start) - 1;
226 matchEnd = sequence.findIndex(m.end) - 1;
228 else if (m.sequence == sequence.getDatasetSequence())
231 // locate region in local context
232 matchStart = sequence.findIndex(m.start) - 1;
233 matchEnd = sequence.findIndex(m.end) - 1;
237 if (matchStart <= end && matchEnd >= start)
239 if (matchStart < start)
251 result = new int[] { matchStart, matchEnd };
255 resultLength = result.length;
256 tmp = new int[resultLength + 2];
257 System.arraycopy(result, 0, tmp, 0, resultLength);
259 result[resultLength] = matchStart;
260 result[resultLength + 1] = matchEnd;
266 // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
267 // + matchEnd+"<"+start);
275 public int markColumns(SequenceCollectionI sqcol, BitSet bs)
278 for (SequenceI s : sqcol.getSequences())
280 BitSet mask = new BitSet();
281 int[] cols = getResults(s, sqcol.getStartRes(), sqcol.getEndRes());
284 for (int pair = 0; pair < cols.length; pair += 2)
286 mask.set(cols[pair], cols[pair + 1] + 1);
289 // find columns that were already selected
290 BitSet compl = (BitSet) mask.clone();
292 count += compl.cardinality();
293 // and mark ranges not already marked
300 * @see jalview.datamodel.SearchResultsI#getSize()
305 return matches.size();
309 * @see jalview.datamodel.SearchResultsI#getResultSequence(int)
312 public SequenceI getResultSequence(int index)
314 return matches.get(index).sequence;
318 * @see jalview.datamodel.SearchResultsI#getResultStart(int)
321 public int getResultStart(int i)
323 return matches.get(i).start;
327 * @see jalview.datamodel.SearchResultsI#getResultEnd(int)
330 public int getResultEnd(int i)
332 return matches.get(i).end;
336 * @see jalview.datamodel.SearchResultsI#isEmpty()
339 public boolean isEmpty()
341 return matches.isEmpty();
345 * @see jalview.datamodel.SearchResultsI#getResults()
348 public List<Match> getResults()
354 * Return the results as a string of characters (bases) prefixed by start
355 * position(s). Meant for use when the context ensures that all matches are to
356 * regions of the same sequence (otherwise the result is meaningless).
361 public String toString()
363 StringBuilder result = new StringBuilder(256);
364 for (SearchResultMatchI m : matches)
366 result.append(m.toString());
368 return result.toString();
372 * Return the results as a string of characters (bases). Meant for use when
373 * the context ensures that all matches are to regions of the same sequence
374 * (otherwise the result is meaningless).
378 public String getCharacters()
380 StringBuilder result = new StringBuilder(256);
381 for (SearchResultMatchI m : matches)
383 result.append(m.getCharacters());
385 return result.toString();
389 * Hashcode is has derived from the list of matches. This ensures that when
390 * two SearchResults objects satisfy the test for equals(), then they have the
394 public int hashCode()
396 return matches.hashCode();
400 * Two SearchResults are considered equal if they contain the same matches in
404 public boolean equals(Object obj)
406 if (obj == null || !(obj instanceof SearchResults))
410 SearchResults sr = (SearchResults) obj;
411 return ((ArrayList<Match>) this.matches).equals(sr.matches);