X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxUtil.java;h=627e1523c31579758399dbe04b893f4a52f9d9e1;hb=a9cc2cc5c9cda0ab49f26ccfb7a1aa30531e6ecf;hp=60fea3323298836c473f560f24246f3c02655930;hpb=575173234369a898f321845df1c12b2c83676a4a;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index 60fea33..627e152 100644
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -88,6 +88,12 @@ import org.forester.ws.seqdb.UniProtTaxonomy;
 
 public final class AptxUtil {
 
+    final static String           UNIPROT_KB                     = "http://www.uniprot.org/uniprot/";
+    final static Pattern          UNIPROT_KB_PATTERN_1             = Pattern
+            .compile( "\\bsp|tr.\\S([A-Z0-9]{5,6})\\b" );
+
+    final static Pattern          UNIPROT_KB_PATTERN_2             = Pattern
+                                                                         .compile( "\\b[A-Z0-9]{5,6}_[A-Z9][A-Z]{2}[A-Z0-9]{2}|RAT|PIG|PEA\\b" );
     private final static Pattern  seq_identifier_pattern_1       = Pattern
                                                                          .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})\\s*$" );
     private final static Pattern  seq_identifier_pattern_2       = Pattern