phylotastic hackathon at NESCENT 120606

[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 7486d8a..8def260 100644 (file)
--- a/forester/java/src/org/forester/util/SequenceIdParser.java
+++ b/forester/java/src/org/forester/util/SequenceIdParser.java
@@ -58,20 +58,75 @@ public final class SequenceIdParser {
                                                                          .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6})(?:[^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
-    private final static boolean DEBUG                           = false;\r
+    private final static boolean DEBUG                           = true;\r
 \r
     \r
-    \r
+    /**\r
+     * Returns null if no match.\r
+     * \r
+     */\r
     public final static Identifier parse( final String s ) {\r
-        String v = DatabaseTools.parseGenbankAccessor( s );\r
+        String v = parseGenbankAccessor( s );\r
+        if ( !ForesterUtil.isEmpty( v ) ) {\r
+            return new Identifier( v, "ncbi" );\r
+        }\r
+        v = parseRefSeqAccessor( s );\r
         if ( !ForesterUtil.isEmpty( v ) ) {\r
-            return new Identifier( v, "genbank" );\r
+            return new Identifier( v, "ncbi" );\r
         }\r
-        \r
         return null;\r
     }\r
     \r
+    /**\r
+     * Returns null if no match.\r
+     * \r
+     * @param query\r
+     * @param db \r
+     * @return\r
+     */\r
+    static public String parseGenbankAccessor( final String query ) {\r
+        Matcher m = GENBANK_NUCLEOTIDE_AC_PATTERN_1.matcher( query );\r
+        if ( m.lookingAt() ) {\r
+            return m.group( 1 );\r
+        }\r
+        else {\r
+            m = GENBANK_NUCLEOTIDE_AC_PATTERN_2.matcher( query );\r
+            if ( m.lookingAt() ) {\r
+                return m.group( 1 );\r
+            }\r
+            else {\r
+                m = GENBANK_PROTEIN_AC_PATTERN.matcher( query );\r
+                if ( m.lookingAt() ) {\r
+                    return m.group( 1 );\r
+                }\r
+                else {\r
+                    return null;\r
+                }\r
+            }\r
+        }\r
+    }\r
     \r
+    public final static String parseRefSeqAccessor( final String query ) {\r
+        Matcher m = GENBANK_NUCLEOTIDE_AC_PATTERN_1.matcher( query );\r
+        if ( m.lookingAt() ) {\r
+            return m.group( 1 );\r
+        }\r
+        else {\r
+            m = GENBANK_NUCLEOTIDE_AC_PATTERN_2.matcher( query );\r
+            if ( m.lookingAt() ) {\r
+                return m.group( 1 );\r
+            }\r
+            else {\r
+                m = GENBANK_PROTEIN_AC_PATTERN.matcher( query );\r
+                if ( m.lookingAt() ) {\r
+                    return m.group( 1 );\r
+                }\r
+                else {\r
+                    return null;\r
+                }\r
+            }\r
+        }\r
+    }\r
     \r
     \r
     \r