inprogress

[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 b8bebe1..d828a6a 100644 (file)
--- a/forester/java/src/org/forester/util/SequenceIdParser.java
+++ b/forester/java/src/org/forester/util/SequenceIdParser.java
@@ -24,35 +24,138 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
 //\r
 // Contact: phylosoft @ gmail . com\r
-// WWW: www.phylosoft.org/forester\r
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester\r
 \r
 package org.forester.util;\r
 \r
+import java.util.regex.Matcher;\r
+import java.util.regex.Pattern;\r
+\r
 import org.forester.phylogeny.data.Identifier;\r
 \r
 public final class SequenceIdParser {\r
 \r
-    \r
-    // ref_XP_002434188_1_mites___ticks_\r
-    // ref_NP_001121530_1_frogs___toads_\r
     // gb_ADF31344_1_segmented_worms_\r
     // gb_AAA96518_1\r
     // gb_EHB07727_1_rodents_\r
     // dbj_BAF37827_1_turtles_\r
     // emb_CAA73223_1_primates_\r
     // lcl_91970_unknown_\r
-    \r
-    \r
+    // mites|ref_XP_002434188_1\r
+    // ref_XP_002434188_1_mites___ticks_\r
+    // ref_NP_001121530_1_frogs___toads_\r
+    //The format for GenBank Accession numbers are:\r
+    //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals\r
+    //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}(?:\\.\\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}(?:\\.\\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}(?:\\.\\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
+    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
+    // 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
+     * \r
+     */\r
     public final static Identifier parse( final String s ) {\r
-        \r
+        String v = parseGenbankAccessor( s );\r
+        if ( !ForesterUtil.isEmpty( v ) ) {\r
+            return new Identifier( v, Identifier.NCBI );\r
+        }\r
+        v = parseRefSeqAccessor( s );\r
+        if ( !ForesterUtil.isEmpty( v ) ) {\r
+            return new Identifier( v, Identifier.REFSEQ );\r
+        }\r
+        v = parseTrEMBLAccessor( s );\r
+        if ( !ForesterUtil.isEmpty( v ) ) {\r
+            return new Identifier( v, Identifier.SP );\r
+        }\r
+        return null;\r
+    }\r
+\r
+    public final static boolean isProtein( final String query ) {\r
+        final String r1 = parseRefSeqAccessor( query );\r
+        if ( !ForesterUtil.isEmpty( r1 ) && ( r1.charAt( 1 ) == 'P' ) ) {\r
+            return true;\r
+        }\r
+        final String r2 = parseTrEMBLAccessor( query );\r
+        if ( !ForesterUtil.isEmpty( r2 ) ) {\r
+            return true;\r
+        }\r
+        return GENBANK_PROTEIN_AC_PATTERN.matcher( query ).lookingAt();\r
+    }\r
+\r
+    /**\r
+     * Returns null if no match.\r
+     * \r
+     */\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
+        }\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
+     * Returns null if no match.\r
+     * \r
+     */\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
+        }\r
+        return null;\r
+    }\r
+\r
+    /**\r
+     * Returns null if no match.\r
+     * \r
+     */\r
+    private final static String parseTrEMBLAccessor( final String query ) {\r
+        final Matcher m = TREMBL_PATTERN.matcher( query );\r
+        if ( m.lookingAt() ) {\r
+            return m.group( 1 );\r
+        }\r
         return null;\r
     }\r
-    \r
-    \r
+\r
     private SequenceIdParser() {\r
         // Hiding the constructor.\r
     }\r
-    \r
-    \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