X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FSequenceIdParser.java;h=d75a6dd8e6e2237a02a551cd56698f5d8b24f9c4;hb=32b66090883b7ca47347fef19152d84bd02c0b9d;hp=09e208a15aec4f705375e54178a99b492284f262;hpb=978fa1fa2b3cad823dd117d8281bf50aab8f205f;p=jalview.git

diff --git a/forester/java/src/org/forester/util/SequenceIdParser.java b/forester/java/src/org/forester/util/SequenceIdParser.java
index 09e208a..d75a6dd 100644
--- a/forester/java/src/org/forester/util/SequenceIdParser.java
+++ b/forester/java/src/org/forester/util/SequenceIdParser.java
@@ -28,21 +28,105 @@
 
 package org.forester.util;
 
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.forester.phylogeny.data.Identifier;
+
 public final class SequenceIdParser {
 
     
-    // ref_XP_002434188_1_mites___ticks_
-    // ref_NP_001121530_1_frogs___toads_
+   
     // gb_ADF31344_1_segmented_worms_
     // gb_AAA96518_1
     // gb_EHB07727_1_rodents_
     // dbj_BAF37827_1_turtles_
     // emb_CAA73223_1_primates_
     // lcl_91970_unknown_
+    // mites|ref_XP_002434188_1
+    // ref_XP_002434188_1_mites___ticks_
+    // ref_NP_001121530_1_frogs___toads_
+    
+    //The format for GenBank Accession numbers are:
+    //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
+    //Protein:    3 letters + 5 numerals
+    //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
+    private final static Pattern GENBANK_NUCLEOTIDE_AC_PATTERN_1 = Pattern
+                                                                         .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5})(?:[^a-zA-Z0-9]|\\Z)" );
+    private final static Pattern GENBANK_NUCLEOTIDE_AC_PATTERN_2 = Pattern
+                                                                         .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6})(?:[^a-zA-Z0-9]|\\Z)" );
+    private final static Pattern GENBANK_PROTEIN_AC_PATTERN      = Pattern
+                                                                         .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5})(?:[^a-zA-Z0-9]|\\Z)" );
+   
+    // RefSeq accession numbers can be distinguished from GenBank accessions 
+    // by their distinct prefix format of 2 characters followed by an
+    // underscore character ('_'). For example, a RefSeq protein accession is NP_015325. 
+    private final static Pattern REFSEQ_PATTERN      = Pattern
+    .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" );
+
+   
+    
+    /**
+     * Returns null if no match.
+     * 
+     */
+    public final static Identifier parse( final String s ) {
+        String v = parseGenbankAccessor( s );
+        if ( !ForesterUtil.isEmpty( v ) ) {
+
+            return new Identifier( v, Identifier.NCBI );
+        }
+        v = parseRefSeqAccessor( s );
+        if ( !ForesterUtil.isEmpty( v ) ) {
+            return new Identifier( v, Identifier.REFSEQ );
+        }
+        return null;
+    }
+    
+    /**
+     * Returns null if no match.
+     * 
+     */
+    public static String parseGenbankAccessor( final String query ) {
+        Matcher m = GENBANK_NUCLEOTIDE_AC_PATTERN_1.matcher( query );
+        if ( m.lookingAt() ) {
+            return m.group( 1 );
+        }
+        else {
+            m = GENBANK_NUCLEOTIDE_AC_PATTERN_2.matcher( query );
+            if ( m.lookingAt() ) {
+                return m.group( 1 );
+            }
+            else {
+                m = GENBANK_PROTEIN_AC_PATTERN.matcher( query );
+                if ( m.lookingAt() ) {
+                    return m.group( 1 );
+                }
+                else {
+                    return null;
+                }
+            }
+        }
+    }
+    
+    /**
+     * Returns null if no match.
+     * 
+     */
+    private final static String parseRefSeqAccessor( final String query ) {
+        Matcher m = REFSEQ_PATTERN.matcher( query );
+        if ( m.lookingAt() ) {
+            return m.group( 1 );
+        }
+        return null;
+    }
     
     
     
     private SequenceIdParser() {
         // Hiding the constructor.
     }
+    
+    
+    
 }