X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FSequenceIdParser.java;h=d828a6a01bd8158b1d2350d2385823feded1470d;hb=663daba455e534e015bd56bae070e9248e3a4533;hp=d75a6dd8e6e2237a02a551cd56698f5d8b24f9c4;hpb=32b66090883b7ca47347fef19152d84bd02c0b9d;p=jalview.git

diff --git a/forester/java/src/org/forester/util/SequenceIdParser.java b/forester/java/src/org/forester/util/SequenceIdParser.java
index d75a6dd..d828a6a 100644
--- a/forester/java/src/org/forester/util/SequenceIdParser.java
+++ b/forester/java/src/org/forester/util/SequenceIdParser.java
@@ -24,7 +24,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.util;
 
@@ -35,8 +35,6 @@ import org.forester.phylogeny.data.Identifier;
 
 public final class SequenceIdParser {
 
-    
-   
     // gb_ADF31344_1_segmented_worms_
     // gb_AAA96518_1
     // gb_EHB07727_1_rodents_
@@ -46,26 +44,27 @@ public final class SequenceIdParser {
     // 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)" );
+                                                                         .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^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)" );
+                                                                         .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^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)" );
-   
+                                                                         .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^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)" );
+    private final static Pattern REFSEQ_PATTERN                  = Pattern
+                                                                         .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" );
+    // See: http://web.expasy.org/docs/userman.html#ID_line
+    private final static Pattern TREMBL_PATTERN                  = Pattern
+                                                                         .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z][0-9][A-Z0-9]{3}[0-9])(?:[^a-zA-Z0-9]|\\Z)" );
+    private final static Pattern GI_PATTERN                      = Pattern
+                                                                         .compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" );
 
-   
-    
     /**
      * Returns null if no match.
      * 
@@ -73,16 +72,31 @@ public final class SequenceIdParser {
     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 );
         }
+        v = parseTrEMBLAccessor( s );
+        if ( !ForesterUtil.isEmpty( v ) ) {
+            return new Identifier( v, Identifier.SP );
+        }
         return null;
     }
-    
+
+    public final static boolean isProtein( final String query ) {
+        final String r1 = parseRefSeqAccessor( query );
+        if ( !ForesterUtil.isEmpty( r1 ) && ( r1.charAt( 1 ) == 'P' ) ) {
+            return true;
+        }
+        final String r2 = parseTrEMBLAccessor( query );
+        if ( !ForesterUtil.isEmpty( r2 ) ) {
+            return true;
+        }
+        return GENBANK_PROTEIN_AC_PATTERN.matcher( query ).lookingAt();
+    }
+
     /**
      * Returns null if no match.
      * 
@@ -108,25 +122,40 @@ public final class SequenceIdParser {
             }
         }
     }
-    
+
     /**
      * Returns null if no match.
      * 
      */
-    private final static String parseRefSeqAccessor( final String query ) {
-        Matcher m = REFSEQ_PATTERN.matcher( query );
+    public final static String parseRefSeqAccessor( final String query ) {
+        final Matcher m = REFSEQ_PATTERN.matcher( query );
         if ( m.lookingAt() ) {
             return m.group( 1 );
         }
         return null;
     }
-    
-    
-    
+
+    /**
+     * Returns null if no match.
+     * 
+     */
+    private final static String parseTrEMBLAccessor( final String query ) {
+        final Matcher m = TREMBL_PATTERN.matcher( query );
+        if ( m.lookingAt() ) {
+            return m.group( 1 );
+        }
+        return null;
+    }
+
     private SequenceIdParser() {
         // Hiding the constructor.
     }
-    
-    
-    
+
+    public static String parseGInumber( final String query ) {
+        final Matcher m = GI_PATTERN.matcher( query );
+        if ( m.find() ) {
+            return m.group( 1 );
+        }
+        return null;
+    }
 }