X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FSequenceAccessionTools.java;h=aaa42aa182dc9bd8b5deb4137a19d04f66508386;hb=3b40e07c1b3964dee89b5d24209946ac54a5e21f;hp=5ab000e3ae7cdcd4df43f838c5cfa7cf798ccaa1;hpb=6726c4b54521e8f4f1ca3e293124776a507cbdfa;p=jalview.git

diff --git a/forester/java/src/org/forester/util/SequenceAccessionTools.java b/forester/java/src/org/forester/util/SequenceAccessionTools.java
index 5ab000e..aaa42aa 100644
--- a/forester/java/src/org/forester/util/SequenceAccessionTools.java
+++ b/forester/java/src/org/forester/util/SequenceAccessionTools.java
@@ -38,38 +38,33 @@ import org.forester.phylogeny.data.Sequence;
 
 public final class SequenceAccessionTools {
 
-    // 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
-    public final static Pattern  GENBANK_NUC_PATTERN_1 = Pattern
-                                                               .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );
-    public final static Pattern  GENBANK_NUC_PATTERN_2 = Pattern
-                                                               .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );
-    public final static Pattern  GENBANK_PROT_PATTERN  = Pattern
-                                                               .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );
-    public final static Pattern  GI_PATTERN            = Pattern.compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" );
-    public final static Pattern  UNIPROT_KB_PATTERN_0  = Pattern
-                                                               .compile( "(?:\\b|_)([A-Z][0-9][A-Z0-9]{3}[0-9])(?:\\b|_)" );
-    public final static Pattern  UNIPROT_KB_PATTERN_1  = Pattern
-                                                               .compile( "(?:\\b|_)(?:sp|tr)[\\.|\\-_=/\\\\]([A-Z][0-9][A-Z0-9]{3}[0-9])(?:\\b|_)" );
-    public final static Pattern  UNIPROT_KB_PATTERN_2  = Pattern
-                                                               .compile( "(?:\\b|_)(?:[A-Z0-9]{2,5}|(?:[A-Z][0-9][A-Z0-9]{3}[0-9]))_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA)(?:\\b|_)" );
-    public final static Pattern  ENSEMBL_PATTERN       = Pattern.compile( "(?:\\b|_)(ENS[A-Z]*[0-9]+)(?:\\b|_)" );
-    // RefSeq accession numbers can be distinguished from GenBank accessions 
+    public final static Pattern  GENBANK_NUC_PATTERN_1       = Pattern
+                                                                     .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );
+    public final static Pattern  GENBANK_NUC_PATTERN_2       = Pattern
+                                                                     .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );
+    public final static Pattern  GENBANK_PROT_PATTERN        = Pattern
+                                                                     .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );
+    public final static Pattern  GI_PATTERN                  = Pattern
+                                                                     .compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" );
+    public final static String   UNIPROT_KB_BASE_PATTERN_STR = "((?:[OPQ][0-9][A-Z0-9]{3}[0-9])|(?:[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}))";
+    public final static Pattern  UNIPROT_KB_PATTERN_0        = Pattern.compile( "(?:\\b|_)"
+                                                                     + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" );
+    public final static Pattern  UNIPROT_KB_PATTERN_1        = Pattern.compile( "(?:\\b|_)(?:sp|tr)[\\.|\\-_=/\\\\]"
+                                                                     + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" );
+    public final static Pattern  UNIPROT_KB_PATTERN_2        = Pattern
+                                                                     .compile( "(?:\\b|_)(?:[A-Z0-9]{2,5}|"
+                                                                             + UNIPROT_KB_BASE_PATTERN_STR
+                                                                             + ")_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA)(?:\\b|_)" );
+    public final static Pattern  ENSEMBL_PATTERN             = Pattern.compile( "(?:\\b|_)(ENS[A-Z]*[0-9]+)(?:\\b|_)" );
+    // 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)" );
+    // 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 SequenceAccessionTools() {
         // Hiding the constructor.