X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FSequenceAccessionTools.java;h=82bcae97c5cd2b0719613e8359f8b0eb1b7e37a5;hb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;hp=3efcb2b47a00dc70d8ad1260ba5f7cf353a2c4e8;hpb=6117c7791be423249668dd14e17cfee32040bb25;p=jalview.git

diff --git a/forester/java/src/org/forester/util/SequenceAccessionTools.java b/forester/java/src/org/forester/util/SequenceAccessionTools.java
index 3efcb2b..82bcae9 100644
--- a/forester/java/src/org/forester/util/SequenceAccessionTools.java
+++ b/forester/java/src/org/forester/util/SequenceAccessionTools.java
@@ -43,28 +43,28 @@ public final class SequenceAccessionTools {
     //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)" );
+            .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)" );
+            .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)" );
+            .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|_)" );
+            .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|_)" );
+            + 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|_)" );
+            + 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|_)" );
+            .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 
+    // 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. 
+    // 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)" );
+            .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" );
 
     private SequenceAccessionTools() {
         // Hiding the constructor.