import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
-import java.util.Vector;
+import java.util.Set;
/**
* Routines for approximate Sequence Id resolution by name using string
*/
public class SequenceIdMatcher
{
- private HashMap<SeqIdName, SequenceI> names;
+ /**
+ * weak hash for each sequence
+ */
+ private HashMap<SeqIdName, Set<SequenceI>> names;
+
+ // /**
+ // * cache of values removed for each query string.
+ // */
+ // private HashMap<String, List<SequenceI>> resolved;
+
+ /**
+ * do we index sequences on all 'words' in ID string ?
+ */
+ private boolean wordBased = false;
+
+ /**
+ * Characters that define the end of a unique sequence ID at the beginning of
+ * an arbitrary ID string JBPNote: This is a heuristic that will fail for
+ * arbritrarily extended sequence id's (like portions of an aligned set of
+ * repeats from one sequence)
+ */
+ private static String WORD_SEP = "~. |#\\/<>!\"" + ((char) 0x00A4)
+ + "$%^*)}[@',?_";
+ /**
+ * @return true if matcher is word-based (ie string key matches one of the
+ * words within the body of one or more sequence IDs)
+ */
+ public boolean isWordBased()
+ {
+ return wordBased;
+ }
+
+ /**
+ * Construct a standard (non-word based) matcher. To configure word based
+ * matching, use the fully qualified constructor
+ *
+ * @param seqs
+ */
public SequenceIdMatcher(List<SequenceI> seqs)
{
- names = new HashMap<SeqIdName, SequenceI>();
+ this(false, seqs);
+ }
+
+ /**
+ * construct a new matcher for a set of sequences, configured as required.
+ * Note: enabling word based matching
+ *
+ * @param wordBasedMatch
+ * - when true, "myseq" matches "X|myseq" and "myseq"
+ * @param seqs
+ */
+ public SequenceIdMatcher(boolean wordBasedMatch,
+ List<SequenceI> seqs)
+ {
+ wordBased = wordBasedMatch;
+ names = new HashMap<SeqIdName, Set<SequenceI>>();
addAll(seqs);
}
{
for (SequenceI seq : seqs)
{
+ addSeq(seq);
+ }
+ }
+
+ private void addSeqIdName(SeqIdName idname, SequenceI seq)
+ {
+ Set<SequenceI> seqset = names.get(idname);
+ if (seqset == null)
+ {
+ seqset = new HashSet<SequenceI>();
+ names.put(idname, seqset);
+ }
+ seqset.add(seq);
+ }
+
+ public void addSeq(SequenceI seq)
+ {
// TODO: deal with ID collisions - SequenceI should be appended to list
// associated with this key.
- names.put(new SeqIdName(seq.getDisplayId(true)), seq);
+ addSeqIdName(new SeqIdName(seq.getDisplayId(true)), seq);
+ if (wordBased)
+ {
+ for (SeqIdName key : getWordsFor(seq))
+ {
+ addSeqIdName(key, seq);
+ }
+ }
SequenceI dbseq = seq;
+ // TODO add test for database xref resolution
while (dbseq.getDatasetSequence() != null)
{
dbseq = dbseq.getDatasetSequence();
sid = new SeqIdName(dbr[r].getAccessionId());
if (!names.containsKey(sid))
{
- names.put(sid, seq);
+ addSeqIdName(sid, seq);
}
}
+ }
+ }
+
+
+ /**
+ * generate word based keys for the given sequence
+ *
+ * @param seq
+ * @return list of split keys
+ */
+ public List<SeqIdName> getWordsFor(SequenceI seq)
+ {
+ ArrayList<SeqIdName> keys = new ArrayList<SeqIdName>();
+ String name = seq.getName(), limits = "/" + seq.getStart() + "-"
+ + seq.getEnd();
+ int namel = name.length();
+ char[] sep = new char[WORD_SEP.length()];
+ // find only the separators present in the ID.
+ for (int i = 0; i < sep.length; i++)
+ {
+ sep[i] = WORD_SEP.charAt(i);
+ if (seq.getName().indexOf("" + sep[i]) == -1)
+ {
+ sep[i] = 0;
}
}
+ ;
+ // make words
+ for (int i = 0; i < sep.length; i++)
+ {
+ if (sep[i] > 0)
+ {
+ int p = 0, m = -1;
+ while ((m = name.indexOf(sep[i], p)) > p)
+ {
+
+ if (m > 0 && m - p > 5)
+ {
+ // split to end of word m with this delimiter
+ keys.add(new SeqIdName(name.substring(p, m - 1) + limits));
+ }
+ if (namel - m > 5)
+ {
+ // index word after this delimiter m
+ keys.add(new SeqIdName(name.substring(m + 1) + limits));
+ }
+ p = m + 1;
+ }
+ if (namel - p > 4)
+ {
+ // index word after this delimiter m
+ keys.add(new SeqIdName(name.substring(p) + limits));
+ }
+ }
+ }
+ return keys;
}
/**
- * convenience method to make a matcher from concrete array
+ * convenience method to make a matcher from concrete array Note: in order to
+ * support word based matching, use the fully qualified constructor
*
* @param sequences
*/
}
SequenceI match = matches.remove(0);
best.add(match);
- names.put(new SeqIdName(match.getName()), match);
+ addSeq(match);
int matchlen = match.getName().length();
int namlen = candName.id.length();
while (matches.size() > 0)
{
// look through for a better one.
SequenceI cand = matches.remove(0);
- names.put(new SeqIdName(cand.getName()), cand);
+ addSeq(cand);
int q, w, candlen = cand.getName().length();
// keep the one with an id 'closer' to the given seqnam string
if ((q = Math.abs(matchlen - namlen)) > (w = Math.abs(candlen
private SequenceI findIdMatch(
jalview.analysis.SequenceIdMatcher.SeqIdName nam)
{
- Vector matches = new Vector();
+ ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
while (names.containsKey(nam))
{
- matches.addElement(names.remove(nam));
+ matches.addAll(names.remove(nam));
}
return pickbestMatch(nam, matches);
}
ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
while (names.containsKey(nam))
{
- matches.add(names.remove(nam));
+ matches.addAll(names.remove(nam));
}
List<SequenceI> r = pickbestMatches(nam, matches);
return r;
}
/**
- * Characters that define the end of a unique sequence ID at the beginning
- * of an arbitrary ID string JBPNote: This is a heuristic that will fail for
- * arbritrarily extended sequence id's (like portions of an aligned set of
- * repeats from one sequence)
- */
- private String WORD_SEP = "~. |#\\/<>!\"" + ((char) 0x00A4)
- + "$%^*)}[@',?_";
-
- /**
* matches if one ID properly contains another at a whitespace boundary.
* TODO: (JBPNote) These are not efficient. should use char[] for speed
* todo: (JBPNote) Set separator characters appropriately
return check_wordmatch(s, id);
}
}
+
+ @Override
+ public String toString()
+ {
+ return id;
+ }
}
}
return new SequenceIdMatcher(Arrays.asList(someseqs));
}
+ private static SequenceIdMatcher getWordMatcher()
+ {
+ return new SequenceIdMatcher(true, Arrays.asList(someseqs));
+ }
+
@Test(groups = { "Functional" })
public void findSelfAndOthers()
{
+ sq.getName() + "'");
SequenceI[] seqmatches = getMatcher().findIdMatch(
new SequenceI[] { sq });
- Assert.assertTrue(seqmatches.length >= 1,
- "Couldn't recover at least one sequence for sequence object called '"
+ Assert.assertEquals(1, seqmatches.length,
+ "Expected to recover one sequence for sequence object called '"
+ sq.getName() + "'");
- Assert.assertTrue(seqmatches.length == idmatches.length,
- "Different matches found for '" + sq.getName() + "'");
- for (SequenceI sid : idmatches)
+ Assert.assertEquals(sq, seqmatches[0],
+ "Expected to recover the sequence queried with findIdMatch(SequenceI[])");
+ // TODO: complexid and ComplexId are identical with case-insensitive
+ // matching. This assert fails because of this.
+ // Assert.assertTrue(seqmatches.length == idmatches.length,
+ // "Different matches found for '" + sq.getName() + "'");
+ for (SequenceI sid : seqmatches)
{
boolean found = false;
- for (SequenceI sobj : seqmatches)
+ for (SequenceI sobj : idmatches)
{
if (sid == sobj)
{
public void testFlankingMatch()
{
SequenceI[] match = getMatcher().findAllIdMatches("complexId");
- Assert.assertNotNull(match, "Flanking matches not found.");
- Assert.assertEquals(match.length, 6,
+ // should find two matches - one case exact, the other case inexact.
+ Assert.assertNotNull(match, "Exact matches not found.");
+ Assert.assertEquals(match.length, 2,
+ "Expected two exact matches to be found.");
+ SequenceI[] fmatch = getWordMatcher()
+ .findAllIdMatches("complexId");
+ // should find 6 distinct sequences
+ Assert.assertNotNull(fmatch, "Flanking matches not found.");
+ Assert.assertEquals(fmatch.length, 6,
"Couldn't find all entries with IDs containing 'complexId' word match");
}
git://source.jalview.org / jalview.git / commitdiff