From: Ben Soares <bsoares@dundee.ac.uk>
Date: Fri, 6 Mar 2020 10:33:42 +0000 (+0000)
Subject: JAL-3529 improved regex in Stockholm UNIPROT accession id test
X-Git-Tag: Develop-2_11_2_0-d20201215~35^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6a33e605b75ae727af5420d9b90d86768ca3dc63;p=jalview.git

JAL-3529 improved regex in Stockholm UNIPROT accession id test
---

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 85ccdcb..74825cf 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -107,9 +107,9 @@ public class StockholmFileTest
     // sequences retrieved in a Pfam domain alignment also have a PFAM database
     // reference
     SequenceI sq = new Sequence("FER2_SPIOL", "AASSDDDFFF");
+    sq.addDBRef(new DBRefEntry("PFAM", "1", "PF00111"));
     sq.addDBRef(new DBRefEntry("UNIPROT", "1", "P00224"));
     sq.addDBRef(new DBRefEntry("PFAM", "1", "P00224.1"));
-    sq.addDBRef(new DBRefEntry("PFAM", "1", "PF00111"));
     AppletFormatAdapter af = new AppletFormatAdapter();
     String toStockholm = af.formatSequences(FileFormat.Stockholm,
             new Alignment(new SequenceI[]
@@ -117,9 +117,10 @@ public class StockholmFileTest
     System.out.println(toStockholm);
     // bleh - java.util.Regex sucks
     assertTrue(
-            Pattern.compile(".*\\s+AC\\s+P00224.*",
-                    java.util.regex.Pattern.DOTALL).matcher(toStockholm)
-                    .matches(),
+            Pattern.compile(
+                    "^#=GS\\s+FER2_SPIOL(/\\d+-\\d+)?\\s+AC\\s+P00224$",
+                    Pattern.MULTILINE).matcher(toStockholm)
+                    .find(),
             "Couldn't locate UNIPROT Accession in generated Stockholm file.");
     AlignmentI fromStockholm = af.readFile(toStockholm,
             DataSourceType.PASTE, FileFormat.Stockholm);