phylotastic hackathon at NESCENT 120607

[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 2f50f63..d75a6dd 100644 (file)
--- a/forester/java/src/org/forester/util/SequenceIdParser.java
+++ b/forester/java/src/org/forester/util/SequenceIdParser.java
@@ -32,7 +32,6 @@ import java.util.regex.Matcher;
 import java.util.regex.Pattern;\r
 \r
 import org.forester.phylogeny.data.Identifier;\r
-import org.forester.ws.uniprot.DatabaseTools;\r
 \r
 public final class SequenceIdParser {\r
 \r
@@ -65,9 +64,7 @@ public final class SequenceIdParser {
     private final static Pattern REFSEQ_PATTERN      = Pattern\r
     .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" );\r
 \r
-    \r
-    private final static boolean DEBUG                           = true;\r
-\r
+   \r
     \r
     /**\r
      * Returns null if no match.\r
@@ -76,11 +73,12 @@ public final class SequenceIdParser {
     public final static Identifier parse( final String s ) {\r
         String v = parseGenbankAccessor( s );\r
         if ( !ForesterUtil.isEmpty( v ) ) {\r
-            return new Identifier( v, "ncbi" );\r
+\r
+            return new Identifier( v, Identifier.NCBI );\r
         }\r
         v = parseRefSeqAccessor( s );\r
         if ( !ForesterUtil.isEmpty( v ) ) {\r
-            return new Identifier( v, "ncbi" );\r
+            return new Identifier( v, Identifier.REFSEQ );\r
         }\r
         return null;\r
     }\r
@@ -89,7 +87,7 @@ public final class SequenceIdParser {
      * Returns null if no match.\r
      * \r
      */\r
-    static public String parseGenbankAccessor( final String query ) {\r
+    public static 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
@@ -115,7 +113,7 @@ public final class SequenceIdParser {
      * Returns null if no match.\r
      * \r
      */\r
-    public final static String parseRefSeqAccessor( final String query ) {\r
+    private final static String parseRefSeqAccessor( final String query ) {\r
         Matcher m = REFSEQ_PATTERN.matcher( query );\r
         if ( m.lookingAt() ) {\r
             return m.group( 1 );\r