X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=4b1900cd618f9696051ef58e6eadb0b503936a9b;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=7c974e26873a4dc72bb95abd3f71100be68f9e6d;hpb=7ae574fd34bd7ffd1ea23be7602d6b3dc57aa49f;p=jalview.git
diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 7c974e2..4b1900c 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,226 +1,312 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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.*;
-
-import jalview.datamodel.*;
-
-/**
- * Title:
- * SequenceIdMatcher
- * 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;
-
- public SequenceIdMatcher(SequenceI[] seqs)
- {
- names = new Hashtable();
- for (int i = 0; i < seqs.length; i++)
- {
- names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
- }
- }
- /**
- * 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 SequenceI closest SequenceI to SeqIdName
- */
- private SequenceI pickbestMatch(SeqIdName candName, Vector matches) {
- SequenceI match=null;
- if (candName==null || matches==null || matches.size()==0)
- return null;
- match=(SequenceI) matches.elementAt(0);
- matches.removeElementAt(0);
- names.put(new SeqIdName(match.getName()), match);
- int matchlen=match.getName().length();
- int namlen=candName.id.length();
- while (matches.size()>0) {
- // 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) {
- match = cand;
- matchlen = candlen;
- }
- }
- 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());
- return findIdMatch(nam);
- }
-
- SequenceI findIdMatch(String seqnam)
- {
- SeqIdName nam = new SeqIdName(seqnam);
- 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 SequenceI[]
- */
- SequenceI[] findIdMatch(SequenceI[] seqs)
- {
- 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] = findIdMatch(nam);
- }
- else
- {
- namedseqs[i] = null;
- }
- }
- 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;
- }
- }
-}
+/*
+ * 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.
+ *
+ * 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 .
+ */
+package jalview.analysis;
+
+import java.util.*;
+
+import jalview.datamodel.*;
+
+/**
+ * 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.
+ */
+public class SequenceIdMatcher
+{
+ private Hashtable names;
+
+ public SequenceIdMatcher(SequenceI[] seqs)
+ {
+ 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.
+ names.put(new SeqIdName(seqs[i].getDisplayId(true)), seqs[i]);
+ // add in any interesting identifiers
+ if (seqs[i].getDBRef() != null)
+ {
+ DBRefEntry dbr[] = seqs[i].getDBRef();
+ SeqIdName sid = null;
+ for (int r = 0; r < dbr.length; r++)
+ {
+ sid = new SeqIdName(dbr[r].getAccessionId());
+ if (!names.contains(sid))
+ {
+ names.put(sid, seqs[i]);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * 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 SequenceI closest SequenceI to SeqIdName
+ */
+ 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)
+ {
+ return null;
+ }
+ 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();
+ while (matches.size() > 0)
+ {
+ // look through for a better one.
+ SequenceI cand = (SequenceI) matches.elementAt(0);
+ matches.remove(0);
+ names.put(new SeqIdName(cand.getName()), 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 - namlen))
+ && candlen > matchlen)
+ {
+ best.clear();
+ match = cand;
+ matchlen = candlen;
+ best.add(match);
+ }
+ if (q==w && candlen==matchlen)
+ {
+ // record any ties
+ best.add(cand);
+ }
+ }
+ 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
+ * @return SequenceI
+ */
+ public SequenceI findIdMatch(SequenceI seq)
+ {
+ SeqIdName nam = new SeqIdName(seq.getName());
+ return findIdMatch(nam);
+ }
+
+ 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[]
+ * @return SequenceI[]
+ */
+ public SequenceI[] findIdMatch(SequenceI[] seqs)
+ {
+ 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] = findIdMatch(nam);
+ }
+ else
+ {
+ namedseqs[i] = null;
+ }
+ } 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);
+ }
+ /**
+ * 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;
+
+ 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 = "~. |#\\/<>!\""+((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
+ *
+ * @param s
+ * 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
+ .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;
+ }
+ }
+ }
+}