/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
* <p>Title: </p>\r
* SequenceIdMatcher\r
* <p>Description: </p>\r
- * Routine which does approximate Sequence Id resolution by name using string containment rather than equivalence\r
+ * Routine which does approximate Sequence Id resolution by name using\r
+ * string containment (on word boundaries) rather than equivalence. It also\r
+ * attempts to resolve ties where no exact match is available by picking the\r
+ * the id closest to the query.\r
* <p>Copyright: Copyright (c) 2004</p>\r
*\r
* <p>Company: Dundee University</p>\r
public SequenceIdMatcher(SequenceI[] seqs)\r
{\r
names = new Hashtable();\r
-\r
for (int i = 0; i < seqs.length; i++)\r
{\r
names.put(new SeqIdName(seqs[i].getName()), seqs[i]);\r
}\r
}\r
+ /**\r
+ * returns the closest SequenceI in matches to SeqIdName and returns all the matches\r
+ * to the names hash.\r
+ * @param candName SeqIdName\r
+ * @param matches Vector of SequenceI objects\r
+ * @return SequenceI closest SequenceI to SeqIdName\r
+ */\r
+ private SequenceI pickbestMatch(SeqIdName candName, Vector matches) {\r
+ SequenceI match=null;\r
+ if (candName==null || matches==null || matches.size()==0)\r
+ return null;\r
+ match=(SequenceI) matches.elementAt(0);\r
+ matches.removeElementAt(0);\r
+ names.put(new SeqIdName(match.getName()), match);\r
+ int matchlen=match.getName().length();\r
+ int namlen=candName.id.length();\r
+ while (matches.size()>0) {\r
+ // look through for a better one.\r
+ SequenceI cand=(SequenceI) matches.elementAt(0);\r
+ names.put(new SeqIdName(cand.getName()), cand);\r
+ int candlen = cand.getName().length();\r
+ // keep the one with an id 'closer' to the given seqnam string\r
+ if (Math.abs(matchlen-namlen)>Math.abs(candlen-namlen) && candlen>matchlen) {\r
+ match = cand;\r
+ matchlen = candlen;\r
+ }\r
+ }\r
+ return match;\r
+ }\r
\r
+ /**\r
+ * get SequenceI with closest SequenceI.getName() to seq.getName()\r
+ * @param seq SequenceI\r
+ * @return SequenceI\r
+ */\r
SequenceI findIdMatch(SequenceI seq)\r
{\r
SeqIdName nam = new SeqIdName(seq.getName());\r
-\r
- if (names.containsKey(nam))\r
- {\r
- return (SequenceI) names.get(nam);\r
- }\r
-\r
- return null;\r
+ return findIdMatch(nam);\r
}\r
\r
SequenceI findIdMatch(String seqnam)\r
- {\r
- SeqIdName nam = new SeqIdName(seqnam);\r
-\r
- if (names.containsKey(nam))\r
{\r
- return (SequenceI) names.get(nam);\r
- }\r
-\r
- return null;\r
+ SeqIdName nam = new SeqIdName(seqnam);\r
+ return findIdMatch(nam);\r
}\r
-\r
/**\r
* findIdMatch\r
*\r
*/\r
SequenceI[] findIdMatch(SequenceI[] seqs)\r
{\r
- SequenceI[] namedseqs = new SequenceI[seqs.length];\r
-\r
+ SequenceI[] namedseqs = null;\r
int i = 0;\r
SeqIdName nam;\r
\r
if (seqs.length > 0)\r
{\r
+ namedseqs = new SequenceI[seqs.length];\r
do\r
{\r
nam = new SeqIdName(seqs[i].getName());\r
\r
if (names.containsKey(nam))\r
{\r
- namedseqs[i] = (SequenceI) names.get(nam);\r
+ namedseqs[i] = findIdMatch(nam);\r
}\r
else\r
{\r
namedseqs[i] = null;\r
}\r
}\r
- while (i++ < seqs.length);\r
+ while (++i < seqs.length);\r
}\r
\r
return namedseqs;\r
}\r
\r
+ /**\r
+ * core findIdMatch search method\r
+ * @param nam SeqIdName\r
+ * @return SequenceI\r
+ */\r
+ private SequenceI findIdMatch(jalview.analysis.SequenceIdMatcher.SeqIdName\r
+ nam)\r
+ {\r
+ Vector matches=new Vector();\r
+ while (names.containsKey(nam))\r
+ {\r
+ matches.addElement(names.remove(nam));\r
+ }\r
+ return pickbestMatch(nam, matches);\r
+ }\r
+\r
private class SeqIdName\r
{\r
String id;\r
\r
SeqIdName(String s)\r
{\r
- id = new String(s);\r
+ if (s!=null)\r
+ id = new String(s);\r
+ else\r
+ id = "";\r
}\r
\r
public int hashCode()\r
{\r
- return (id.substring(0, 4).hashCode());\r
+ return ((id.length()>=4) ? id.substring(0, 4).hashCode() : id.hashCode());\r
}\r
\r
public boolean equals(Object s)\r
return false;\r
}\r
\r
+ /**\r
+ * Characters that define the end of a unique sequence ID at\r
+ * the beginning of an arbitrary ID string\r
+ * JBPNote: This is a heuristic that will fail for arbritrarily extended sequence id's\r
+ * (like portions of an aligned set of repeats from one sequence)\r
+ */\r
+ private String WORD_SEP="~. |#\\/<>!\"£$%^*)}[@',?_";\r
+\r
+ /**\r
+ * matches if one ID properly contains another at a whitespace boundary.\r
+ * TODO: (JBPNote) These are not efficient. should use char[] for speed\r
+ * todo: (JBPNote) Set separator characters appropriately\r
+ * @param s SeqIdName\r
+ * @return boolean\r
+ */\r
public boolean equals(SeqIdName s)\r
{\r
- if (id.startsWith(s.id) || s.id.startsWith(id))\r
- {\r
- return true;\r
- }\r
-\r
- return false;\r
+ if (id.length()>s.id.length()) {\r
+ return id.startsWith(s.id) ?\r
+ (WORD_SEP.indexOf(id.charAt(s.id.length()))>-1)\r
+ : false;\r
+ } else\r
+ return s.id.startsWith(id) ?\r
+ (s.id.equals(id) ? true :\r
+ (WORD_SEP.indexOf(s.id.charAt(id.length()))>-1))\r
+ : false;\r
}\r
\r
public boolean equals(String s)\r
{\r
- if (id.startsWith(s) || s.startsWith(id))\r
- {\r
- return true;\r
- }\r
-\r
- return false;\r
+ if (id.length()>s.length()) {\r
+ return id.startsWith(s) ?\r
+ (WORD_SEP.indexOf(id.charAt(s.length()))>-1)\r
+ : false;\r
+ } else\r
+ return s.startsWith(id) ?\r
+ (s.equals(id) ? true :\r
+ (WORD_SEP.indexOf(s.charAt(id.length()))>-1))\r
+ : false;\r
}\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff