/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
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++)
{
- // TODO: deal with ID collisions - SequenceI should be appended to list associated with this key.
+ // 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];
+ 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.
* SeqIdName
* @param matches
* Vector of SequenceI objects
- * @return Object[] { SequenceI closest SequenceI to SeqIdName, SequenceI[] ties }
+ * @return Object[] { SequenceI closest SequenceI to SeqIdName, SequenceI[]
+ * ties }
*/
private SequenceI[] pickbestMatches(SeqIdName candName, Vector matches)
{
- ArrayList best=new ArrayList();
+ ArrayList best = new ArrayList();
SequenceI match = null;
if (candName == null || matches == null || matches.size() == 0)
{
SequenceI cand = (SequenceI) matches.elementAt(0);
matches.remove(0);
names.put(new SeqIdName(cand.getName()), cand);
- int q,w,candlen = cand.getName().length();
+ 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 - namlen))
+ if ((q = Math.abs(matchlen - namlen)) > (w = Math.abs(candlen
+ - namlen))
&& candlen > matchlen)
{
best.clear();
matchlen = candlen;
best.add(match);
}
- if (q==w && candlen==matchlen)
+ if (q == w && candlen == matchlen)
{
// record any ties
best.add(cand);
}
}
- if (best.size()==0) { return null; };
+ if (best.size() == 0)
+ {
+ return null;
+ }
+ ;
return (SequenceI[]) best.toArray(new SequenceI[0]);
}
}
/**
- * Find all matches for a given sequence name.
- * @param seqnam string to query Matcher with.
+ * Find all matches for a given sequence name.
+ *
+ * @param seqnam
+ * string to query Matcher with.
*/
public SequenceI[] findAllIdMatches(String seqnam)
{
}
return pickbestMatch(nam, matches);
}
+
/**
* core findIdMatch search method for finding all equivalent matches
*
{
matches.addElement(names.remove(nam));
}
- SequenceI[] r=pickbestMatches(nam, matches);
+ SequenceI[] r = pickbestMatches(nam, matches);
return r;
}
-
private class SeqIdName
{
String id;
* arbritrarily extended sequence id's (like portions of an aligned set of
* repeats from one sequence)
*/
- private String WORD_SEP = "~. |#\\/<>!\""+((char)0x00A4)+"$%^*)}[@',?_";
+ private String WORD_SEP = "~. |#\\/<>!\"" + ((char) 0x00A4)
+ + "$%^*)}[@',?_";
/**
* 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
+ // 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
git://source.jalview.org / jalview.git / blobdiff