-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.datamodel;\r
-\r
-public class SearchResults\r
-{\r
-\r
- Match [] matches;\r
-\r
- /**\r
- * This method replaces the old search results which merely\r
- * held an alignment index of search matches. This broke\r
- * when sequences were moved around the alignment\r
- * @param seq Sequence\r
- * @param start int\r
- * @param end int\r
- */\r
- public void addResult(SequenceI seq, int start, int end)\r
- {\r
- if(matches == null)\r
- {\r
- matches = new Match[]{new Match(seq, start, end)};\r
- return;\r
- }\r
-\r
- int mSize = matches.length;\r
-\r
- Match [] tmp = new Match[mSize+1];\r
- int m;\r
- for(m=0; m<mSize; m++)\r
- {\r
- tmp[m] = matches[m];\r
- }\r
-\r
- tmp[m] = new Match(seq, start, end);\r
-\r
- matches = tmp;\r
- }\r
-\r
- /**\r
- * This Method returns the search matches which lie between the\r
- * start and end points of the sequence in question. It is\r
- * optimised for returning objects for drawing on SequenceCanvas\r
- */\r
- public int [] getResults(SequenceI sequence, int start, int end)\r
- {\r
- if(matches==null)\r
- return null;\r
-\r
- int [] result = null;\r
- int [] tmp = null;\r
- int resultLength;\r
-\r
- for(int m=0; m<matches.length; m++)\r
- {\r
- if( matches[m].sequence == sequence )\r
- {\r
- int matchStart = matches[m].sequence.findIndex( matches[m].start ) - 1;\r
- int matchEnd = matches[m].sequence.findIndex( matches[m].end ) - 1;\r
-\r
- if(matchStart<=end && matchEnd>=start)\r
- {\r
- if(matchStart<start)\r
- matchStart = start;\r
-\r
- if(matchEnd>end)\r
- matchEnd = end;\r
-\r
-\r
- if(result==null)\r
- result = new int[]{matchStart, matchEnd};\r
- else\r
- {\r
- resultLength = result.length;\r
- tmp = new int[resultLength+2];\r
- System.arraycopy(result,0,tmp,0,resultLength);\r
- result = tmp;\r
- result[resultLength] = matchStart;\r
- result[resultLength+1] = matchEnd;\r
- }\r
- }\r
- }\r
- }\r
- return result;\r
- }\r
-\r
- public int getSize()\r
- {\r
- return matches==null ? 0 : matches.length;\r
- }\r
-\r
- public SequenceI getResultSequence(int index)\r
- { return matches[index].sequence; }\r
-\r
- public int getResultStart(int index)\r
- { return matches[index].start; }\r
-\r
- public int getResultEnd(int index)\r
- { return matches[index].end; }\r
-\r
- class Match\r
- {\r
- SequenceI sequence;\r
- int start;\r
- int end;\r
-\r
- public Match(SequenceI seq, int start, int end)\r
- {\r
- sequence = seq;\r
- this.start = start;\r
- this.end = end;\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * Holds a list of search result matches, where each match is a contiguous
+ * stretch of a single sequence.
+ *
+ * @author gmcarstairs
+ *
+ */
+public class SearchResults
+{
+
+ private List<Match> matches = new ArrayList<Match>();
+
+ /**
+ * One match consists of a sequence reference, start and end positions.
+ * Discontiguous ranges in a sequence require two or more Match objects.
+ */
+ public class Match
+ {
+ SequenceI sequence;
+
+ /**
+ * Start position of match in sequence (base 1)
+ */
+ int start;
+
+ /**
+ * End position (inclusive) (base 1)
+ */
+ int end;
+
+ /**
+ * Constructor
+ *
+ * @param seq
+ * a sequence
+ * @param start
+ * start position of matched range (base 1)
+ * @param end
+ * end of matched range (inclusive, base 1)
+ */
+ public Match(SequenceI seq, int start, int end)
+ {
+ sequence = seq;
+ this.start = start;
+ this.end = end;
+ }
+
+ public SequenceI getSequence()
+ {
+ return sequence;
+ }
+
+ public int getStart()
+ {
+ return start;
+ }
+
+ public int getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Returns the string of characters in the matched region, prefixed by the
+ * start position, e.g. "12CGT" or "208K"
+ */
+ @Override
+ public String toString()
+ {
+ final int from = Math.max(start - 1, 0);
+ String startPosition = String.valueOf(from);
+ return startPosition + getCharacters();
+ }
+
+ /**
+ * Returns the string of characters in the matched region.
+ */
+ public String getCharacters()
+ {
+ char[] chars = sequence.getSequence();
+ // convert start/end to base 0 (with bounds check)
+ final int from = Math.max(start - 1, 0);
+ final int to = Math.min(end, chars.length + 1);
+ return String.valueOf(Arrays.copyOfRange(chars, from, to));
+ }
+
+ public void setSequence(SequenceI seq)
+ {
+ this.sequence = seq;
+ }
+
+ /**
+ * Hashcode is the hashcode of the matched sequence plus a hash of start and
+ * end positions. Match objects that pass the test for equals are guaranteed
+ * to have the same hashcode.
+ */
+ @Override
+ public int hashCode()
+ {
+ int hash = sequence == null ? 0 : sequence.hashCode();
+ hash += 31 * start;
+ hash += 67 * end;
+ return hash;
+ }
+
+ /**
+ * Two Match objects are equal if they are for the same sequence, start and
+ * end positions
+ */
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == null || !(obj instanceof Match))
+ {
+ return false;
+ }
+ Match m = (Match) obj;
+ return (this.sequence == m.sequence && this.start == m.start && this.end == m.end);
+ }
+ }
+
+ /**
+ * This method replaces the old search results which merely held an alignment
+ * index of search matches. This broke when sequences were moved around the
+ * alignment
+ *
+ * @param seq
+ * Sequence
+ * @param start
+ * int
+ * @param end
+ * int
+ */
+ public void addResult(SequenceI seq, int start, int end)
+ {
+ matches.add(new Match(seq, start, end));
+ }
+
+ /**
+ * Quickly check if the given sequence is referred to in the search results
+ *
+ * @param sequence
+ * (specific alignment sequence or a dataset sequence)
+ * @return true if the results involve sequence
+ */
+ public boolean involvesSequence(SequenceI sequence)
+ {
+ SequenceI ds = sequence.getDatasetSequence();
+ for (Match m : matches)
+ {
+ if (m.sequence != null
+ && (m.sequence == sequence || m.sequence == ds))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * This Method returns the search matches which lie between the start and end
+ * points of the sequence in question. It is optimised for returning objects
+ * for drawing on SequenceCanvas
+ */
+ public int[] getResults(SequenceI sequence, int start, int end)
+ {
+ if (matches.isEmpty())
+ {
+ return null;
+ }
+
+ int[] result = null;
+ int[] tmp = null;
+ int resultLength, matchStart = 0, matchEnd = 0;
+ boolean mfound;
+ for (Match m : matches)
+ {
+ mfound = false;
+ if (m.sequence == sequence)
+ {
+ mfound = true;
+ // locate aligned position
+ matchStart = sequence.findIndex(m.start) - 1;
+ matchEnd = sequence.findIndex(m.end) - 1;
+ }
+ else if (m.sequence == sequence.getDatasetSequence())
+ {
+ mfound = true;
+ // locate region in local context
+ matchStart = sequence.findIndex(m.start) - 1;
+ matchEnd = sequence.findIndex(m.end) - 1;
+ }
+ if (mfound)
+ {
+ if (matchStart <= end && matchEnd >= start)
+ {
+ if (matchStart < start)
+ {
+ matchStart = start;
+ }
+
+ if (matchEnd > end)
+ {
+ matchEnd = end;
+ }
+
+ if (result == null)
+ {
+ result = new int[] { matchStart, matchEnd };
+ }
+ else
+ {
+ resultLength = result.length;
+ tmp = new int[resultLength + 2];
+ System.arraycopy(result, 0, tmp, 0, resultLength);
+ result = tmp;
+ result[resultLength] = matchStart;
+ result[resultLength + 1] = matchEnd;
+ }
+ }
+ else
+ {
+ // debug
+ // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
+ // + matchEnd+"<"+start);
+ }
+ }
+ }
+ return result;
+ }
+
+ public int getSize()
+ {
+ return matches.size();
+ }
+
+ public SequenceI getResultSequence(int index)
+ {
+ return matches.get(index).sequence;
+ }
+
+ /**
+ * Returns the start position of the i'th match in the search results.
+ *
+ * @param i
+ * @return
+ */
+ public int getResultStart(int i)
+ {
+ return matches.get(i).start;
+ }
+
+ /**
+ * Returns the end position of the i'th match in the search results.
+ *
+ * @param i
+ * @return
+ */
+ public int getResultEnd(int i)
+ {
+ return matches.get(i).end;
+ }
+
+ /**
+ * Returns true if no search result matches are held.
+ *
+ * @return
+ */
+ public boolean isEmpty()
+ {
+ return matches.isEmpty();
+ }
+
+ /**
+ * Returns the list of matches.
+ *
+ * @return
+ */
+ public List<Match> getResults()
+ {
+ return matches;
+ }
+
+ /**
+ * Return the results as a string of characters (bases) prefixed by start
+ * position(s). Meant for use when the context ensures that all matches are to
+ * regions of the same sequence (otherwise the result is meaningless).
+ *
+ * @return
+ */
+ @Override
+ public String toString()
+ {
+ StringBuilder result = new StringBuilder(256);
+ for (Match m : matches)
+ {
+ result.append(m.toString());
+ }
+ return result.toString();
+ }
+
+ /**
+ * Return the results as a string of characters (bases). Meant for use when
+ * the context ensures that all matches are to regions of the same sequence
+ * (otherwise the result is meaningless).
+ *
+ * @return
+ */
+ public String getCharacters()
+ {
+ StringBuilder result = new StringBuilder(256);
+ for (Match m : matches)
+ {
+ result.append(m.getCharacters());
+ }
+ return result.toString();
+ }
+
+ /**
+ * Hashcode is has derived from the list of matches. This ensures that when
+ * two SearchResults objects satisfy the test for equals(), then they have the
+ * same hashcode.
+ */
+ @Override
+ public int hashCode()
+ {
+ return matches.hashCode();
+ }
+
+ /**
+ * Two SearchResults are considered equal if they contain the same matches in
+ * the same order.
+ */
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == null || !(obj instanceof SearchResults))
+ {
+ return false;
+ }
+ SearchResults sr = (SearchResults) obj;
+ return ((ArrayList<Match>) this.matches).equals(sr.matches);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff