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.List;
28 * Holds a list of search result matches, where each match is a contiguous
29 * stretch of a single sequence.
34 public class SearchResults
37 private List<Match> matches = new ArrayList<Match>();
40 * One match consists of a sequence reference, start and end positions.
41 * Discontiguous ranges in a sequence require two or more Match objects.
48 * Start position of match in sequence (base 1)
53 * End position (inclusive) (base 1)
63 * start position of matched range (base 1)
65 * end of matched range (inclusive, base 1)
67 public Match(SequenceI seq, int start, int end)
72 * always hold in forwards order, even if given in reverse order
73 * (such as from a mapping to a reverse strand); this avoids
74 * trouble for routines that highlight search results etc
88 public SequenceI getSequence()
104 * Returns the string of characters in the matched region, prefixed by the
105 * start position, e.g. "12CGT" or "208K"
108 public String toString()
110 final int from = Math.max(start - 1, 0);
111 String startPosition = String.valueOf(from);
112 return startPosition + getCharacters();
116 * Returns the string of characters in the matched region.
118 public String getCharacters()
120 char[] chars = sequence.getSequence();
121 // convert start/end to base 0 (with bounds check)
122 final int from = Math.max(start - 1, 0);
123 final int to = Math.min(end, chars.length + 1);
124 return String.valueOf(Arrays.copyOfRange(chars, from, to));
127 public void setSequence(SequenceI seq)
133 * Hashcode is the hashcode of the matched sequence plus a hash of start and
134 * end positions. Match objects that pass the test for equals are guaranteed
135 * to have the same hashcode.
138 public int hashCode()
140 int hash = sequence == null ? 0 : sequence.hashCode();
147 * Two Match objects are equal if they are for the same sequence, start and
151 public boolean equals(Object obj)
153 if (obj == null || !(obj instanceof Match))
157 Match m = (Match) obj;
158 return (this.sequence == m.sequence && this.start == m.start && this.end == m.end);
163 * This method replaces the old search results which merely held an alignment
164 * index of search matches. This broke when sequences were moved around the
174 public void addResult(SequenceI seq, int start, int end)
176 matches.add(new Match(seq, start, end));
180 * Quickly check if the given sequence is referred to in the search results
183 * (specific alignment sequence or a dataset sequence)
184 * @return true if the results involve sequence
186 public boolean involvesSequence(SequenceI sequence)
188 SequenceI ds = sequence.getDatasetSequence();
189 for (Match m : matches)
191 if (m.sequence != null
192 && (m.sequence == sequence || m.sequence == ds))
201 * This Method returns the search matches which lie between the start and end
202 * points of the sequence in question. It is optimised for returning objects
203 * for drawing on SequenceCanvas
205 public int[] getResults(SequenceI sequence, int start, int end)
207 if (matches.isEmpty())
214 int resultLength, matchStart = 0, matchEnd = 0;
216 for (Match m : matches)
219 if (m.sequence == sequence)
222 // locate aligned position
223 matchStart = sequence.findIndex(m.start) - 1;
224 matchEnd = sequence.findIndex(m.end) - 1;
226 else if (m.sequence == sequence.getDatasetSequence())
229 // locate region in local context
230 matchStart = sequence.findIndex(m.start) - 1;
231 matchEnd = sequence.findIndex(m.end) - 1;
235 if (matchStart <= end && matchEnd >= start)
237 if (matchStart < start)
249 result = new int[] { matchStart, matchEnd };
253 resultLength = result.length;
254 tmp = new int[resultLength + 2];
255 System.arraycopy(result, 0, tmp, 0, resultLength);
257 result[resultLength] = matchStart;
258 result[resultLength + 1] = matchEnd;
264 // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
265 // + matchEnd+"<"+start);
274 return matches.size();
277 public SequenceI getResultSequence(int index)
279 return matches.get(index).sequence;
283 * Returns the start position of the i'th match in the search results.
288 public int getResultStart(int i)
290 return matches.get(i).start;
294 * Returns the end position of the i'th match in the search results.
299 public int getResultEnd(int i)
301 return matches.get(i).end;
305 * Returns true if no search result matches are held.
309 public boolean isEmpty()
311 return matches.isEmpty();
315 * Returns the list of matches.
319 public List<Match> getResults()
325 * Return the results as a string of characters (bases) prefixed by start
326 * position(s). Meant for use when the context ensures that all matches are to
327 * regions of the same sequence (otherwise the result is meaningless).
332 public String toString()
334 StringBuilder result = new StringBuilder(256);
335 for (Match m : matches)
337 result.append(m.toString());
339 return result.toString();
343 * Return the results as a string of characters (bases). Meant for use when
344 * the context ensures that all matches are to regions of the same sequence
345 * (otherwise the result is meaningless).
349 public String getCharacters()
351 StringBuilder result = new StringBuilder(256);
352 for (Match m : matches)
354 result.append(m.getCharacters());
356 return result.toString();
360 * Hashcode is has derived from the list of matches. This ensures that when
361 * two SearchResults objects satisfy the test for equals(), then they have the
365 public int hashCode()
367 return matches.hashCode();
371 * Two SearchResults are considered equal if they contain the same matches in
375 public boolean equals(Object obj)
377 if (obj == null || !(obj instanceof SearchResults))
381 SearchResults sr = (SearchResults) obj;
382 return ((ArrayList<Match>) this.matches).equals(sr.matches);