package jalview.datamodel;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.BitSet;
import java.util.List;
*/
public class SearchResults implements SearchResultsI
{
+ private int count;
- private List<SearchResultMatchI> matches = new ArrayList<SearchResultMatchI>();
+ private ArrayList<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
+ public class Match implements SearchResultMatchI, Comparable<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
}
}
- /* (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()
{
}
/**
- * Returns the string of characters in the matched region, prefixed by the
- * start position, e.g. "12CGT" or "208K"
+ * Returns a representation as "seqid/start-end"
*/
@Override
public String toString()
{
- final int from = Math.max(start - 1, 0);
- String startPosition = String.valueOf(from);
- return startPosition + getCharacters();
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultMatchI#getCharacters()
- */
- @Override
- 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;
+ StringBuilder sb = new StringBuilder();
+ if (sequence != null)
+ {
+ sb.append(sequence.getName()).append("/");
+ }
+ sb.append(start).append("-").append(end);
+ return sb.toString();
}
/**
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);
+ }
+ @Override
+ public boolean adjacent(SequenceI seq, int from, int to)
+ {
+ return (sequence == seq && ((start <= from && end >= to) || (from<=(end+1) && to >=(end+1)) || (from<=(start-1) && to>=(start-1))));
+ }
+
+ @Override
+ public int compareTo(SearchResultMatchI o)
+ {
+ if (start<o.getStart())
+ {
+ return -1;
+ }
+ if (start > o.getStart())
+ {
+ return +1;
+ }
+ if (end < o.getEnd())
+ {
+ return -1;
+ }
+ if (end > o.getEnd())
+ {
+ return +1;
+ }
+ if (sequence!=o.getSequence())
+ {
+ int hashc =sequence.hashCode(),oseq=o.getSequence().hashCode();
+ return (hashc < oseq) ? -1 : 1;
+ }
+ return 0;
}
+
}
- /* (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 appendResult(SequenceI sequence, int start, int end)
+ {
+
+ Match m = new Match(sequence, start, end);
+
+ boolean appending=false;
+
+ // we dynamically maintain an interval to add as we test each range in the list
+
+ int cstart=start,cend=end;
+ List<SearchResultMatchI> toRemove=new ArrayList<>();
+ for (SearchResultMatchI thatm:matches)
+ {
+ if (thatm.getSequence()==sequence)
+ {
+ if (thatm.contains(sequence,cstart,cend))
+ {
+ // found a match containing the current range. nothing else to do except report if we operated on the list
+ return appending;
+ }
+ if (thatm.adjacent(sequence, cstart, cend))
+ {
+ // update the match to add with the adjacent start/end
+ start = Math.min(m.start, thatm.getStart());
+ end = Math.max(m.end, thatm.getEnd());
+ // and check if we keep or remove the old one
+ if (thatm.getStart()!=start || thatm.getEnd()!=end)
+ {
+ toRemove.add(thatm);
+ count--;
+ cstart = start;
+ cend = end;
+ appending=true;
+ } else {
+ return false;
+ }
+ }
+ }
+ }
+ matches.removeAll(toRemove);
+ {
+ matches.add(new Match(sequence,cstart,cend));
+ count++;
+ }
+ return appending;
+ }
@Override
public boolean involvesSequence(SequenceI sequence)
{
+ final int start = sequence.getStart();
+ final int end = sequence.getEnd();
+
SequenceI ds = sequence.getDatasetSequence();
- Match m;
- for (SearchResultMatchI _m : matches)
+ for (SearchResultMatchI m : matches)
{
- m = (Match) _m;
- if (m.sequence != null
- && (m.sequence == sequence || m.sequence == ds))
+ SequenceI matched = m.getSequence();
+ if (matched != null && (matched == sequence || matched == ds)
+ && (m.getEnd() >= start) && (m.getStart() <= end))
{
return true;
}
return false;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResults(jalview.datamodel.SequenceI, int, int)
- */
@Override
public int[] getResults(SequenceI sequence, int start, int end)
{
m = (Match) _m;
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())
+ if (m.sequence == sequence
+ || 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)
else
{
// debug
- // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
+ // jalview.bin.Console.errPrintln("Outwith bounds!" + matchStart+">"+end +" or "
// + matchEnd+"<"+start);
}
}
{
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)
return count;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getSize()
- */
@Override
- public int getSize()
+ public int getCount()
{
- return matches.size();
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResultSequence(int)
- */
- @Override
- public SequenceI getResultSequence(int index)
- {
- return matches.get(index).getSequence();
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResultStart(int)
- */
- @Override
- public int getResultStart(int i)
- {
- return matches.get(i).getStart();
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResultEnd(int)
- */
- @Override
- public int getResultEnd(int i)
- {
- return matches.get(i).getEnd();
+ 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<SearchResultMatchI> getResults()
{
}
/**
- * 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 the results as a list of matches [seq1/from-to, seq2/from-to, ...]
*
* @return
*/
@Override
public String toString()
{
- StringBuilder result = new StringBuilder(256);
- for (SearchResultMatchI m : matches)
- {
- result.append(m.toString());
- }
- return result.toString();
+ return matches == null ? "" : matches.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 (SearchResultMatchI 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
+ * 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()
}
/**
- * 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)
SearchResultsI sr = (SearchResultsI) obj;
return matches.equals(sr.getResults());
}
+
+ @Override
+ public void addSearchResults(SearchResultsI toAdd)
+ {
+ matches.addAll(toAdd.getResults());
+ }
+
+ @Override
+ public List<SequenceI> getMatchingSubSequences()
+ {
+ List<SequenceI> 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;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff