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[jalview.git] / forester / java / src / org / forester / util / SequenceIdParser.java

diff --git a/forester/java/src/org/forester/util/SequenceIdParser.java b/forester/java/src/org/forester/util/SequenceIdParser.java
index c96d0f4..d828a6a 100644 (file)
--- a/forester/java/src/org/forester/util/SequenceIdParser.java
+++ b/forester/java/src/org/forester/util/SequenceIdParser.java
@@ -49,11 +49,11 @@ public final class SequenceIdParser {
     //Protein:    3 letters + 5 numerals\r
     //http://www.ncbi.nlm.nih.gov/Sequin/acc.html\r
     private final static Pattern GENBANK_NUCLEOTIDE_AC_PATTERN_1 = Pattern\r
-                                                                         .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5})(?:[^a-zA-Z0-9]|\\Z)" );\r
+                                                                         .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
     private final static Pattern GENBANK_NUCLEOTIDE_AC_PATTERN_2 = Pattern\r
-                                                                         .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6})(?:[^a-zA-Z0-9]|\\Z)" );\r
+                                                                         .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
     private final static Pattern GENBANK_PROTEIN_AC_PATTERN      = Pattern\r
-                                                                         .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5})(?:[^a-zA-Z0-9]|\\Z)" );\r
+                                                                         .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
     // RefSeq accession numbers can be distinguished from GenBank accessions \r
     // by their distinct prefix format of 2 characters followed by an\r
     // underscore character ('_'). For example, a RefSeq protein accession is NP_015325. \r
@@ -62,6 +62,8 @@ public final class SequenceIdParser {
     // See: http://web.expasy.org/docs/userman.html#ID_line\r
     private final static Pattern TREMBL_PATTERN                  = Pattern\r
                                                                          .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z][0-9][A-Z0-9]{3}[0-9])(?:[^a-zA-Z0-9]|\\Z)" );\r
+    private final static Pattern GI_PATTERN                      = Pattern\r
+                                                                         .compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" );\r
 \r
     /**\r
      * Returns null if no match.\r
@@ -125,7 +127,7 @@ public final class SequenceIdParser {
      * Returns null if no match.\r
      * \r
      */\r
-    private final static String parseRefSeqAccessor( final String query ) {\r
+    public final static String parseRefSeqAccessor( final String query ) {\r
         final Matcher m = REFSEQ_PATTERN.matcher( query );\r
         if ( m.lookingAt() ) {\r
             return m.group( 1 );\r
@@ -148,4 +150,12 @@ public final class SequenceIdParser {
     private SequenceIdParser() {\r
         // Hiding the constructor.\r
     }\r
+\r
+    public static String parseGInumber( final String query ) {\r
+        final Matcher m = GI_PATTERN.matcher( query );\r
+        if ( m.find() ) {\r
+            return m.group( 1 );\r
+        }\r
+        return null;\r
+    }\r
 }\r