-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.BitSet;
+import java.util.List;
+
+/**
+ * Holds a list of search result matches, where each match is a contiguous
+ * stretch of a single sequence.
+ *
+ * @author gmcarstairs amwaterhouse
+ *
+ */
+public class SearchResults implements SearchResultsI
+{
+
+ private List<SearchResultMatchI> matches = new ArrayList<>();
+
+ /**
+ * 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 implements SearchResultMatchI
+ {
+ final SequenceI sequence;
+
+ /**
+ * Start position of match in sequence (base 1)
+ */
+ final int start;
+
+ /**
+ * End position (inclusive) (base 1)
+ */
+ final int end;
+
+ /**
+ * create a Match on a range of sequence. Match always holds region in
+ * forwards order, even if given in reverse order (such as from a mapping to
+ * a reverse strand); this avoids trouble for routines that highlight search
+ * results etc
+ *
+ * @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;
+
+ /*
+ * always hold in forwards order, even if given in reverse order
+ * (such as from a mapping to a reverse strand); this avoids
+ * trouble for routines that highlight search results etc
+ */
+ if (start <= end)
+ {
+ this.start = start;
+ this.end = end;
+ }
+ else
+ {
+ // TODO: JBP could mark match as being specified in reverse direction
+ // for use
+ // by caller ? e.g. visualizing reverse strand highlight
+ this.start = end;
+ this.end = start;
+ }
+ }
+
+ @Override
+ public SequenceI getSequence()
+ {
+ return sequence;
+ }
+
+ @Override
+ public int getStart()
+ {
+ return start;
+ }
+
+ @Override
+ public int getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Returns a representation as "seqid/start-end"
+ */
+ @Override
+ public String toString()
+ {
+ StringBuilder sb = new StringBuilder();
+ if (sequence != null)
+ {
+ sb.append(sequence.getName()).append("/");
+ }
+ sb.append(start).append("-").append(end);
+ return sb.toString();
+ }
+
+ /**
+ * 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 SearchResultMatchI))
+ {
+ return false;
+ }
+ SearchResultMatchI m = (SearchResultMatchI) obj;
+ return (sequence == m.getSequence() && start == m.getStart()
+ && end == m.getEnd());
+ }
+
+ @Override
+ public boolean contains(SequenceI seq, int from, int to)
+ {
+ return (sequence == seq && start <= from && end >= to);
+ }
+ }
+
+ @Override
+ public SearchResultMatchI addResult(SequenceI seq, int start, int end)
+ {
+ Match m = new Match(seq, start, end);
+ if (!matches.contains(m))
+ {
+ matches.add(m);
+ }
+ return m;
+ }
+
+ @Override
+ public boolean involvesSequence(SequenceI sequence)
+ {
+ SequenceI ds = sequence.getDatasetSequence();
+ for (SearchResultMatchI _m : matches)
+ {
+ SequenceI matched = _m.getSequence();
+ if (matched != null && (matched == sequence || matched == ds))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ @Override
+ 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;
+ Match m;
+ for (SearchResultMatchI _m : matches)
+ {
+ m = (Match) _m;
+
+ mfound = false;
+ if (m.sequence == sequence
+ || m.sequence == sequence.getDatasetSequence())
+ {
+ mfound = true;
+ matchStart = sequence.findIndex(m.start) - 1;
+ matchEnd = m.start == m.end ? matchStart : 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;
+ }
+
+ @Override
+ public int markColumns(SequenceCollectionI sqcol, BitSet bs)
+ {
+ int count = 0;
+ BitSet mask = new BitSet();
+ int startRes = sqcol.getStartRes();
+ int endRes = sqcol.getEndRes();
+
+ for (SequenceI s : sqcol.getSequences())
+ {
+ int[] cols = getResults(s, startRes, endRes);
+ if (cols != null)
+ {
+ for (int pair = 0; pair < cols.length; pair += 2)
+ {
+ mask.set(cols[pair], cols[pair + 1] + 1);
+ }
+ }
+ }
+ // compute columns that were newly selected
+ BitSet original = (BitSet) bs.clone();
+ original.and(mask);
+ count = mask.cardinality() - original.cardinality();
+ // and mark ranges not already marked
+ bs.or(mask);
+ return count;
+ }
+
+ @Override
+ public int getSize()
+ {
+ return matches.size();
+ }
+
+ @Override
+ public boolean isEmpty()
+ {
+ return matches.isEmpty();
+ }
+
+ @Override
+ public List<SearchResultMatchI> getResults()
+ {
+ return matches;
+ }
+
+ /**
+ * Return the results as a list of matches [seq1/from-to, seq2/from-to, ...]
+ *
+ * @return
+ */
+ @Override
+ public String toString()
+ {
+ return matches == null ? "" : matches.toString();
+ }
+
+ /**
+ * Hashcode is derived from the list of matches. This ensures that when two
+ * SearchResults objects satisfy the test for equals(), then they have the
+ * same hashcode.
+ *
+ * @see Match#hashCode()
+ * @see java.util.AbstractList#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 SearchResultsI))
+ {
+ return false;
+ }
+ SearchResultsI sr = (SearchResultsI) obj;
+ return matches.equals(sr.getResults());
+ }
+
+ @Override
+ public void addSearchResults(SearchResultsI toAdd)
+ {
+ matches.addAll(toAdd.getResults());
+ }
+}
git://source.jalview.org / jalview.git / blobdiff