X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=e6a48531f322ac5e80ffe03e1d18789544700216;hb=6f9e452300ac8853e5c10ec29828f420f3909341;hp=56b760a59da440099c38598ea4856019db640400;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 56b760a..e6a4853 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,49 +1,37 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.util.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Vector;
/**
- *
- * Title:
- *
- * SequenceIdMatcher
- *
- * Description:
- *
- * 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.
- *
- * Copyright: Copyright (c) 2004
- *
- *
- *
- * Company: Dundee University
- *
- *
- * @author not attributable
- * @version 1.0
*/
public class SequenceIdMatcher
{
@@ -54,13 +42,20 @@ 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]);
+ SequenceI dbseq = seqs[i];
+ while (dbseq.getDatasetSequence()!=null)
+ {
+ dbseq = dbseq.getDatasetSequence();
+ }
// add in any interesting identifiers
- if (seqs[i].getDBRef()!=null)
+ if (dbseq.getDBRef() != null)
{
- DBRefEntry dbr[] = seqs[i].getDBRef();
- SeqIdName sid=null;
- for (int r=0;r 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]);
}
/**
* get SequenceI with closest SequenceI.getName() to seq.getName()
*
* @param seq
- * SequenceI
+ * 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
* same Id as a given set of different sequence objects
*
* @param seqs
- * SequenceI[]
+ * SequenceI[]
* @return SequenceI[]
*/
- SequenceI[] findIdMatch(SequenceI[] seqs)
+ public SequenceI[] findIdMatch(SequenceI[] seqs)
{
SequenceI[] namedseqs = null;
int i = 0;
@@ -171,7 +212,7 @@ public class SequenceIdMatcher
* core findIdMatch search method
*
* @param nam
- * SeqIdName
+ * SeqIdName
* @return SequenceI
*/
private SequenceI findIdMatch(
@@ -185,6 +226,25 @@ public class SequenceIdMatcher
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
{
String id;
@@ -201,14 +261,20 @@ public class SequenceIdMatcher
}
}
+ @Override
public int hashCode()
{
return ((id.length() >= 4) ? id.substring(0, 4).hashCode() : id
.hashCode());
}
+ @Override
public boolean equals(Object s)
{
+ if (s == null)
+ {
+ return false;
+ }
if (s instanceof SeqIdName)
{
return this.equals((SeqIdName) s);
@@ -230,7 +296,8 @@ public class SequenceIdMatcher
* 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.
@@ -238,11 +305,13 @@ public class SequenceIdMatcher
* todo: (JBPNote) Set separator characters appropriately
*
* @param s
- * SeqIdName
+ * SeqIdName
* @return boolean
*/
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