X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=56b760a59da440099c38598ea4856019db640400;hb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;hp=b620205856a418ee7090704173c17fab55ce0cb1;hpb=8d3443821b7a965141364ab8efb3b4681143804a;p=jalview.git
diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index b620205..56b760a 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,137 +1,272 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
package jalview.analysis;
-import java.util.Vector;
-import java.util.Hashtable;
-import jalview.datamodel.SequenceI;
+import java.util.*;
+
+import jalview.datamodel.*;
/**
- *
Title:
+ *
+ * Title:
+ *
* SequenceIdMatcher
- * Description:
- * Routine which does approximate Sequence Id resolution by name using string containment rather than equivalence
- * Copyright: Copyright (c) 2004
- *
- * Company: Dundee University
- *
+ *
+ * Description:
+ *
+ * Routine which does 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.
+ *
+ * Copyright: Copyright (c) 2004
+ *
+ *
+ *
+ * Company: Dundee University
+ *
+ *
* @author not attributable
* @version 1.0
*/
public class SequenceIdMatcher
{
+ private Hashtable names;
- private class SeqIdName
+ public SequenceIdMatcher(SequenceI[] seqs)
{
- String id;
-
- SeqIdName(String s)
- {
- id = new String(s);
- }
-
- public int hashCode()
- {
- return (id.substring(0, 4).hashCode());
- }
-
- public boolean equals(Object s)
+ names = new Hashtable();
+ for (int i = 0; i < seqs.length; i++)
{
- if (s instanceof SeqIdName)
- {
- return this.equals( (SeqIdName) s);
- }
- else
+ names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
+ // add in any interesting identifiers
+ if (seqs[i].getDBRef()!=null)
{
- if (s instanceof String)
+ DBRefEntry dbr[] = seqs[i].getDBRef();
+ SeqIdName sid=null;
+ for (int r=0;r 0)
{
- if (id.startsWith(s) || s.startsWith(id))
+ // look through for a better one.
+ SequenceI cand = (SequenceI) matches.elementAt(0);
+ names.put(new SeqIdName(cand.getName()), cand);
+ int 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)
+ && candlen > matchlen)
{
- return true;
+ match = cand;
+ matchlen = candlen;
}
- return false;
- }
- }
-
- private Hashtable names;
-
- public SequenceIdMatcher(SequenceI[] seqs)
- {
- names = new Hashtable();
- for (int i = 0; i < seqs.length; i++)
- {
- names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
}
+ return match;
}
+ /**
+ * get SequenceI with closest SequenceI.getName() to seq.getName()
+ *
+ * @param seq
+ * SequenceI
+ * @return SequenceI
+ */
SequenceI findIdMatch(SequenceI seq)
{
SeqIdName nam = new SeqIdName(seq.getName());
- if (names.containsKey(nam))
- {
- return (SequenceI) names.get(nam);
- }
- return null;
+ return findIdMatch(nam);
}
SequenceI findIdMatch(String seqnam)
{
SeqIdName nam = new SeqIdName(seqnam);
- if (names.containsKey(nam))
- {
- return (SequenceI) names.get(nam);
- }
- return null;
+ return findIdMatch(nam);
}
/**
* findIdMatch
- *
- * Return pointers to sequences (or sequence object containers)
- * which have same Id as a given set of different sequence objects
- *
- * @param seqs SequenceI[]
+ *
+ * Return pointers to sequences (or sequence object containers) which have
+ * same Id as a given set of different sequence objects
+ *
+ * @param seqs
+ * SequenceI[]
* @return SequenceI[]
*/
-
SequenceI[] findIdMatch(SequenceI[] seqs)
{
- SequenceI[] namedseqs = new SequenceI[seqs.length];
-
+ SequenceI[] namedseqs = null;
int i = 0;
SeqIdName nam;
+
if (seqs.length > 0)
{
+ namedseqs = new SequenceI[seqs.length];
do
{
nam = new SeqIdName(seqs[i].getName());
+
if (names.containsKey(nam))
{
- namedseqs[i] = (SequenceI) names.get(nam);
+ namedseqs[i] = findIdMatch(nam);
}
else
{
namedseqs[i] = null;
}
- }
- while (i++ < seqs.length);
+ } while (++i < seqs.length);
}
+
return namedseqs;
}
+ /**
+ * core findIdMatch search method
+ *
+ * @param nam
+ * SeqIdName
+ * @return SequenceI
+ */
+ private SequenceI findIdMatch(
+ jalview.analysis.SequenceIdMatcher.SeqIdName nam)
+ {
+ Vector matches = new Vector();
+ while (names.containsKey(nam))
+ {
+ matches.addElement(names.remove(nam));
+ }
+ return pickbestMatch(nam, matches);
+ }
+
+ private class SeqIdName
+ {
+ String id;
+
+ SeqIdName(String s)
+ {
+ if (s != null)
+ {
+ id = new String(s);
+ }
+ else
+ {
+ id = "";
+ }
+ }
+
+ public int hashCode()
+ {
+ return ((id.length() >= 4) ? id.substring(0, 4).hashCode() : id
+ .hashCode());
+ }
+
+ public boolean equals(Object s)
+ {
+ if (s instanceof SeqIdName)
+ {
+ return this.equals((SeqIdName) s);
+ }
+ else
+ {
+ if (s instanceof String)
+ {
+ return this.equals((String) s);
+ }
+ }
+
+ return 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 String WORD_SEP = "~. |#\\/<>!\"£$%^*)}[@',?_";
+
+ /**
+ * 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
+ *
+ * @param s
+ * SeqIdName
+ * @return boolean
+ */
+ public boolean equals(SeqIdName s)
+ {
+ if (id.length() > s.id.length())
+ {
+ return id.startsWith(s.id) ? (WORD_SEP.indexOf(id.charAt(s.id
+ .length())) > -1) : false;
+ }
+ else
+ {
+ return s.id.startsWith(id) ? (s.id.equals(id) ? true : (WORD_SEP
+ .indexOf(s.id.charAt(id.length())) > -1)) : false;
+ }
+ }
+
+ public boolean equals(String s)
+ {
+ if (id.length() > s.length())
+ {
+ return id.startsWith(s) ? (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
+ : false;
+ }
+ else
+ {
+ return s.startsWith(id) ? (s.equals(id) ? true : (WORD_SEP
+ .indexOf(s.charAt(id.length())) > -1)) : false;
+ }
+ }
+ }
}