/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
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
{
- Match[] matches;
+ 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
*/
public void addResult(SequenceI seq, int start, int end)
{
- if (matches == null)
- {
- matches = new Match[]
- { new Match(seq, start, end) };
- return;
- }
-
- int mSize = matches.length;
-
- Match[] tmp = new Match[mSize + 1];
- int m;
- for (m = 0; m < mSize; m++)
- {
- tmp[m] = matches[m];
- }
-
- tmp[m] = new Match(seq, start, end);
-
- matches = tmp;
+ matches.add(new Match(seq, start, end));
}
/**
*/
public boolean involvesSequence(SequenceI sequence)
{
- if (matches == null || matches.length == 0)
- {
- return false;
- }
SequenceI ds = sequence.getDatasetSequence();
- for (int m = 0; m < matches.length; m++)
+ for (Match m : matches)
{
- if (matches[m].sequence != null
- && (matches[m].sequence == sequence || matches[m].sequence == ds))
+ if (m.sequence != null
+ && (m.sequence == sequence || m.sequence == ds))
{
return true;
}
*/
public int[] getResults(SequenceI sequence, int start, int end)
{
- if (matches == null)
+ if (matches.isEmpty())
{
return null;
}
int[] tmp = null;
int resultLength, matchStart = 0, matchEnd = 0;
boolean mfound;
- for (int m = 0; m < matches.length; m++)
+ for (Match m : matches)
{
mfound = false;
- if (matches[m].sequence == sequence)
+ if (m.sequence == sequence)
{
mfound = true;
// locate aligned position
- matchStart = sequence.findIndex(matches[m].start) - 1;
- matchEnd = sequence.findIndex(matches[m].end) - 1;
+ matchStart = sequence.findIndex(m.start) - 1;
+ matchEnd = sequence.findIndex(m.end) - 1;
}
- else if (matches[m].sequence == sequence.getDatasetSequence())
+ else if (m.sequence == sequence.getDatasetSequence())
{
mfound = true;
// locate region in local context
- matchStart = sequence.findIndex(matches[m].start) - 1;
- matchEnd = sequence.findIndex(matches[m].end) - 1;
+ matchStart = sequence.findIndex(m.start) - 1;
+ matchEnd = sequence.findIndex(m.end) - 1;
}
if (mfound)
{
if (result == null)
{
- result = new int[]
- { matchStart, matchEnd };
+ result = new int[] { matchStart, matchEnd };
}
else
{
public int getSize()
{
- return matches == null ? 0 : matches.length;
+ return matches.size();
}
public SequenceI getResultSequence(int index)
{
- return matches[index].sequence;
+ return matches.get(index).sequence;
}
- public int getResultStart(int index)
+ /**
+ * Returns the start position of the i'th match in the search results.
+ *
+ * @param i
+ * @return
+ */
+ public int getResultStart(int i)
{
- return matches[index].start;
+ return matches.get(i).start;
}
- public int getResultEnd(int index)
+ /**
+ * Returns the end position of the i'th match in the search results.
+ *
+ * @param i
+ * @return
+ */
+ public int getResultEnd(int i)
{
- return matches[index].end;
+ return matches.get(i).end;
}
- class Match
+ /**
+ * Returns true if no search result matches are held.
+ *
+ * @return
+ */
+ public boolean isEmpty()
{
- SequenceI sequence;
+ return matches.isEmpty();
+ }
- int start;
+ /**
+ * Returns the list of matches.
+ *
+ * @return
+ */
+ public List<Match> getResults()
+ {
+ return matches;
+ }
- int end;
+ /**
+ * 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();
+ }
- public Match(SequenceI seq, int start, int end)
+ /**
+ * 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)
{
- sequence = seq;
- this.start = start;
- this.end = end;
+ 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