(no commit message)

[jalview.git] / forester / java / src / org / forester / util / SequenceAccessionTools.java

diff --git a/forester/java/src/org/forester/util/SequenceAccessionTools.java b/forester/java/src/org/forester/util/SequenceAccessionTools.java
index 3efcb2b..82bcae9 100644 (file)
--- 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\r
     //http://www.ncbi.nlm.nih.gov/Sequin/acc.html\r
     public final static Pattern  GENBANK_NUC_PATTERN_1       = Pattern\r
-                                                                     .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
+            .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
     public final static Pattern  GENBANK_NUC_PATTERN_2       = Pattern\r
-                                                                     .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
+            .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
     public final static Pattern  GENBANK_PROT_PATTERN        = Pattern\r
-                                                                     .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
+            .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" );\r
     public final static Pattern  GI_PATTERN                  = Pattern\r
-                                                                     .compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" );\r
+            .compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" );\r
     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}))";\r
     public final static Pattern  UNIPROT_KB_PATTERN_0        = Pattern.compile( "(?:\\b|_)"\r
-                                                                     + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" );\r
+            + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" );\r
     public final static Pattern  UNIPROT_KB_PATTERN_1        = Pattern.compile( "(?:\\b|_)(?:sp|tr)[\\.|\\-_=/\\\\]"\r
-                                                                     + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" );\r
+            + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" );\r
     public final static Pattern  UNIPROT_KB_PATTERN_2        = Pattern\r
-                                                                     .compile( "(?:\\b|_)(?:[A-Z0-9]{2,5}|"\r
-                                                                             + UNIPROT_KB_BASE_PATTERN_STR\r
-                                                                             + ")_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA)(?:\\b|_)" );\r
+            .compile( "(?:\\b|_)(?:[A-Z0-9]{2,5}|"\r
+                    + UNIPROT_KB_BASE_PATTERN_STR\r
+                    + ")_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA)(?:\\b|_)" );\r
     public final static Pattern  ENSEMBL_PATTERN             = Pattern.compile( "(?:\\b|_)(ENS[A-Z]*[0-9]+)(?:\\b|_)" );\r
-    // RefSeq accession numbers can be distinguished from GenBank accessions \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
+    // 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
+            .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" );\r
 \r
     private SequenceAccessionTools() {\r
         // Hiding the constructor.\r