X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResults.java;h=909a0fef644be43cff883bbf3eb047bb670285eb;hb=41fe43633ee3cc43a45a356176689731ff73ba67;hp=1bf54757897f3e1b13136e086f28506fcba8eeeb;hpb=1145ab823ba8ffd317754588efeb259d70c1f4a1;p=jalview.git diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java index 1bf5475..909a0fe 100755 --- a/src/jalview/datamodel/SearchResults.java +++ b/src/jalview/datamodel/SearchResults.java @@ -33,8 +33,9 @@ import java.util.List; */ public class SearchResults implements SearchResultsI { + private int count; - private List matches = new ArrayList(); + private List matches = new ArrayList<>(); /** * One match consists of a sequence reference, start and end positions. @@ -42,17 +43,17 @@ public class SearchResults implements SearchResultsI */ public class Match implements SearchResultMatchI { - SequenceI sequence; + final SequenceI sequence; /** * Start position of match in sequence (base 1) */ - int start; + final int start; /** * End position (inclusive) (base 1) */ - int end; + final int end; /** * create a Match on a range of sequence. Match always holds region in @@ -91,27 +92,18 @@ public class SearchResults implements SearchResultsI } } - /* (non-Javadoc) - * @see jalview.datamodel.SearchResultMatchI#getSequence() - */ @Override public SequenceI getSequence() { return sequence; } - /* (non-Javadoc) - * @see jalview.datamodel.SearchResultMatchI#getStart() - */ @Override public int getStart() { return start; } - /* (non-Javadoc) - * @see jalview.datamodel.SearchResultMatchI#getEnd() - */ @Override public int getEnd() { @@ -133,11 +125,6 @@ public class SearchResults implements SearchResultsI return sb.toString(); } - 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 @@ -164,33 +151,59 @@ public class SearchResults implements SearchResultsI return false; } SearchResultMatchI m = (SearchResultMatchI) obj; - return (sequence == m.getSequence() && start == m.getStart() && end == m - .getEnd()); + 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); } } - /* (non-Javadoc) - * @see jalview.datamodel.SearchResultsI#addResult(jalview.datamodel.SequenceI, int, int) - */ @Override public SearchResultMatchI addResult(SequenceI seq, int start, int end) { Match m = new Match(seq, start, end); - matches.add(m); + if (!matches.contains(m)) + { + matches.add(m); + count++; + } return m; } - /* (non-Javadoc) - * @see jalview.datamodel.SearchResultsI#involvesSequence(jalview.datamodel.SequenceI) - */ + @Override + public void addResult(SequenceI seq, int[] positions) + { + /* + * we only increment the match count by 1 - or not at all, + * if the matches are all duplicates of existing + */ + int beforeCount = count; + for (int i = 0; i < positions.length - 1; i += 2) + { + addResult(seq, positions[i], positions[i + 1]); + } + if (count > beforeCount) + { + count = beforeCount + 1; + } + } + @Override public boolean involvesSequence(SequenceI sequence) { + final int start = sequence.getStart(); + final int end = sequence.getEnd(); + SequenceI ds = sequence.getDatasetSequence(); - for (SearchResultMatchI _m : matches) + for (SearchResultMatchI m : matches) { - SequenceI matched = _m.getSequence(); - if (matched != null && (matched == sequence || matched == ds)) + SequenceI matched = m.getSequence(); + if (matched != null && (matched == sequence || matched == ds) + && (m.getEnd() >= start) && (m.getStart() <= end)) { return true; } @@ -198,9 +211,6 @@ public class SearchResults implements SearchResultsI return false; } - /* (non-Javadoc) - * @see jalview.datamodel.SearchResultsI#getResults(jalview.datamodel.SequenceI, int, int) - */ @Override public int[] getResults(SequenceI sequence, int start, int end) { @@ -219,20 +229,15 @@ public class SearchResults implements SearchResultsI m = (Match) _m; mfound = false; - if (m.sequence == sequence) + if (m.sequence == sequence + || m.sequence == sequence.getDatasetSequence()) { 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; + matchEnd = m.start == m.end ? matchStart + : sequence.findIndex(m.end) - 1; } + if (mfound) { if (matchStart <= end && matchEnd >= start) @@ -264,7 +269,7 @@ public class SearchResults implements SearchResultsI else { // debug - // System.err.println("Outwith bounds!" + matchStart+">"+end +" or " + // System.err.println("Outwith bounds!" + matchStart+">"+end +" or " // + matchEnd+"<"+start); } } @@ -277,9 +282,12 @@ public class SearchResults implements SearchResultsI { int count = 0; BitSet mask = new BitSet(); + int startRes = sqcol.getStartRes(); + int endRes = sqcol.getEndRes(); + for (SequenceI s : sqcol.getSequences()) { - int[] cols = getResults(s, sqcol.getStartRes(), sqcol.getEndRes()); + int[] cols = getResults(s, startRes, endRes); if (cols != null) { for (int pair = 0; pair < cols.length; pair += 2) @@ -297,27 +305,18 @@ public class SearchResults implements SearchResultsI return count; } - /* (non-Javadoc) - * @see jalview.datamodel.SearchResultsI#getSize() - */ @Override - public int getSize() + public int getCount() { - return matches.size(); + return count; } - /* (non-Javadoc) - * @see jalview.datamodel.SearchResultsI#isEmpty() - */ @Override public boolean isEmpty() { return matches.isEmpty(); } - /* (non-Javadoc) - * @see jalview.datamodel.SearchResultsI#getResults() - */ @Override public List getResults() { @@ -350,8 +349,10 @@ public class SearchResults implements SearchResultsI } /** - * Two SearchResults are considered equal if they contain the same matches in - * the same order. + * Two SearchResults are considered equal if they contain the same matches + * (Sequence, start position, end position) in the same order + * + * @see Match#equals(Object) */ @Override public boolean equals(Object obj) @@ -363,4 +364,33 @@ public class SearchResults implements SearchResultsI SearchResultsI sr = (SearchResultsI) obj; return matches.equals(sr.getResults()); } + + @Override + public void addSearchResults(SearchResultsI toAdd) + { + matches.addAll(toAdd.getResults()); + } + + @Override + public List getMatchingSubSequences() + { + List seqs = new ArrayList<>(); + + /* + * assemble dataset sequences, and template new sequence features, + * for the amend features dialog + */ + for (SearchResultMatchI match : matches) + { + SequenceI seq = match.getSequence(); + while (seq.getDatasetSequence() != null) + { + seq = seq.getDatasetSequence(); + } + // getSubSequence is index-base0, findIndex returns index-base1 + seqs.add(seq.getSubSequence(seq.findIndex(match.getStart()) - 1, + seq.findIndex(match.getEnd()))); + } + return seqs; + } }