X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fanalysis%2FSequenceIdMatcher.java;h=0744937743bcba699e34bc0421f06133144b08ca;hb=a57e62adb20b8c9be0172f2d5d1e767c3aa528ca;hp=9d33996333997931356a5f3ca6b7530e7cb0ce77;hpb=15af442616b10419a3ec3eb080f8378879688fd1;p=jalview.git diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java index 9d33996..0744937 100755 --- a/src/jalview/analysis/SequenceIdMatcher.java +++ b/src/jalview/analysis/SequenceIdMatcher.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 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 @@ -27,7 +27,9 @@ import jalview.datamodel.*; * SequenceIdMatcher *
Description:
* Routine which does approximate Sequence Id resolution by name using - * string containment (on word boundaries) rather than equivalence + * 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
@@ -48,28 +50,57 @@ public class SequenceIdMatcher } } - SequenceI findIdMatch(SequenceI seq) + /** + * 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) { - SeqIdName nam = new SeqIdName(seq.getName()); - - if (names.containsKey(nam)) + SequenceI match = null; + if (candName == null || matches == null || matches.size() == 0) { - return (SequenceI) names.get(nam); + 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; + } - return null; + /** + * 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); - - if (names.containsKey(nam)) - { - return (SequenceI) names.get(nam); - } - - return null; + return findIdMatch(nam); } /** @@ -96,7 +127,7 @@ public class SequenceIdMatcher if (names.containsKey(nam)) { - namedseqs[i] = (SequenceI) names.get(nam); + namedseqs[i] = findIdMatch(nam); } else { @@ -109,21 +140,41 @@ public class SequenceIdMatcher 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) + if (s != null) + { id = new String(s); + } else + { id = ""; + } } public int hashCode() { - return ((id.length()>=4) ? id.substring(0, 4).hashCode() : id.hashCode()); + return ( (id.length() >= 4) ? id.substring(0, 4).hashCode() : id.hashCode()); } public boolean equals(Object s) @@ -149,39 +200,47 @@ public class SequenceIdMatcher * 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="~. |#\\/<>!\"£$%^*)}[@',?"; - - /** - * matches if one ID properly contains another at a whitespace boundary. - * TODO: (JBPNote) These are not efficient. should use char[] for speed - * todo: (JBPNote) Set separator characters appropriately - * @param s SeqIdName - * @return boolean - */ + private String WORD_SEP = "~. |#\\/<>!\"£$%^*)}[@',?_"; + + /** + * 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()) { + if (id.length() > s.id.length()) + { return id.startsWith(s.id) ? - (WORD_SEP.indexOf(id.charAt(s.id.length()))>-1) + (WORD_SEP.indexOf(id.charAt(s.id.length())) > -1) : false; - } else + } + else + { return s.id.startsWith(id) ? (s.id.equals(id) ? true : - (WORD_SEP.indexOf(s.id.charAt(id.length()))>-1)) + (WORD_SEP.indexOf(s.id.charAt(id.length())) > -1)) : false; + } } public boolean equals(String s) { - if (id.length()>s.length()) { + if (id.length() > s.length()) + { return id.startsWith(s) ? - (WORD_SEP.indexOf(id.charAt(s.length()))>-1) + (WORD_SEP.indexOf(id.charAt(s.length())) > -1) : false; - } else + } + else + { return s.startsWith(id) ? (s.equals(id) ? true : - (WORD_SEP.indexOf(s.charAt(id.length()))>-1)) + (WORD_SEP.indexOf(s.charAt(id.length())) > -1)) : false; + } } } }