/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import jalview.datamodel.*;
/**
- * <p>
- * Title:
- * </p>
- * SequenceIdMatcher
- * <p>
- * Description:
- * </p>
- * Routine which does approximate Sequence Id resolution by name using string
+ * Routines for approximate Sequence Id resolution by name using string
* containment (on word boundaries) rather than equivalence. It also attempts to
* resolve ties where no exact match is available by picking the the id closest
* to the query.
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- *
- * <p>
- * Company: Dundee University
- * </p>
- *
- * @author not attributable
- * @version 1.0
*/
public class SequenceIdMatcher
{
names = new Hashtable();
for (int i = 0; i < seqs.length; i++)
{
- names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
+ // TODO: deal with ID collisions - SequenceI should be appended to list associated with this key.
+ names.put(new SeqIdName(seqs[i].getDisplayId(true)), seqs[i]);
// add in any interesting identifiers
if (seqs[i].getDBRef() != null)
{
*/
private SequenceI pickbestMatch(SeqIdName candName, Vector matches)
{
+ SequenceI[] st= pickbestMatches(candName, matches);
+ return st==null || st.length==0 ? null : st[0];
+ }
+ /**
+ * returns the closest SequenceI in matches to SeqIdName and returns all the
+ * matches to the names hash.
+ *
+ * @param candName
+ * SeqIdName
+ * @param matches
+ * Vector of SequenceI objects
+ * @return Object[] { SequenceI closest SequenceI to SeqIdName, SequenceI[] ties }
+ */
+ private SequenceI[] pickbestMatches(SeqIdName candName, Vector matches)
+ {
+ ArrayList best=new ArrayList();
SequenceI match = null;
if (candName == null || matches == null || matches.size() == 0)
{
}
match = (SequenceI) matches.elementAt(0);
matches.removeElementAt(0);
+ best.add(match);
names.put(new SeqIdName(match.getName()), match);
int matchlen = match.getName().length();
int namlen = candName.id.length();
{
// look through for a better one.
SequenceI cand = (SequenceI) matches.elementAt(0);
+ matches.remove(0);
names.put(new SeqIdName(cand.getName()), cand);
- int candlen = cand.getName().length();
+ int q,w,candlen = cand.getName().length();
// keep the one with an id 'closer' to the given seqnam string
- if (Math.abs(matchlen - namlen) > Math.abs(candlen - namlen)
+ if ((q=Math.abs(matchlen - namlen)) > (w=Math.abs(candlen - namlen))
&& candlen > matchlen)
{
+ best.clear();
match = cand;
matchlen = candlen;
+ best.add(match);
+ }
+ if (q==w && candlen==matchlen)
+ {
+ // record any ties
+ best.add(cand);
}
}
- return match;
+ if (best.size()==0) { return null; };
+ return (SequenceI[]) best.toArray(new SequenceI[0]);
}
/**
* SequenceI
* @return SequenceI
*/
- SequenceI findIdMatch(SequenceI seq)
+ public SequenceI findIdMatch(SequenceI seq)
{
SeqIdName nam = new SeqIdName(seq.getName());
return findIdMatch(nam);
}
- SequenceI findIdMatch(String seqnam)
+ public SequenceI findIdMatch(String seqnam)
{
SeqIdName nam = new SeqIdName(seqnam);
return findIdMatch(nam);
}
/**
+ * Find all matches for a given sequence name.
+ * @param seqnam string to query Matcher with.
+ */
+ public SequenceI[] findAllIdMatches(String seqnam)
+ {
+
+ SeqIdName nam = new SeqIdName(seqnam);
+ return findAllIdMatches(nam);
+ }
+
+ /**
* findIdMatch
*
* Return pointers to sequences (or sequence object containers) which have
* SequenceI[]
* @return SequenceI[]
*/
- SequenceI[] findIdMatch(SequenceI[] seqs)
+ public SequenceI[] findIdMatch(SequenceI[] seqs)
{
SequenceI[] namedseqs = null;
int i = 0;
}
return pickbestMatch(nam, matches);
}
+ /**
+ * core findIdMatch search method for finding all equivalent matches
+ *
+ * @param nam
+ * SeqIdName
+ * @return SequenceI[]
+ */
+ private SequenceI[] findAllIdMatches(
+ jalview.analysis.SequenceIdMatcher.SeqIdName nam)
+ {
+ Vector matches = new Vector();
+ while (names.containsKey(nam))
+ {
+ matches.addElement(names.remove(nam));
+ }
+ SequenceI[] r=pickbestMatches(nam, matches);
+ return r;
+ }
+
private class SeqIdName
{
* arbritrarily extended sequence id's (like portions of an aligned set of
* repeats from one sequence)
*/
- private String WORD_SEP = "~. |#\\/<>!\"£$%^*)}[@',?_";
+ private String WORD_SEP = "~. |#\\/<>!\""+((char)0x00A4)+"$%^*)}[@',?_";
/**
* matches if one ID properly contains another at a whitespace boundary.
*/
public boolean equals(SeqIdName s)
{
+ // TODO: JAL-732 patch for cases when name includes a list of IDs, and the match contains one ID flanked
if (id.length() > s.id.length())
{
return id.startsWith(s.id) ? (WORD_SEP.indexOf(id.charAt(s.id