X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFileIOTester.java;h=2d572fefa8fa28614d8c2061e311dd13c3f07a81;hb=47168f025aefdaa044802bd5f8f510ffe43a4808;hp=2b975a2a083ae2682575af86fd94b312da53da1e;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/test/jalview/io/FileIOTester.java b/test/jalview/io/FileIOTester.java
index 2b975a2..2d572fe 100644
--- a/test/jalview/io/FileIOTester.java
+++ b/test/jalview/io/FileIOTester.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
@@ -49,21 +51,39 @@ public class FileIOTester
   public static void tearDownAfterClass() throws Exception
   {
   }
+  // TODO: make a better/more comprehensive test harness for identify/io
+  
   final static File ALIGN_FILE = new File("test/jalview/io/test_gz_fasta.gz");
   final static File NOTGZALIGN_FILE = new File("test/jalview/io/test_gz_fasta_notgz.gz");
+  final static File STARS_FA_FILE1 = new File("test/jalview/io/test_fasta_stars.fa");
+  final static File STARS_FA_FILE2 = new File("test/jalview/io/test_fasta_stars2.fa");
 
-  private void assertValidFasta(String src, FileParse fp)
+  private void assertValidFormat(String fmt, String src, FileParse fp)
   {
     assertTrue("Couldn't resolve "+src+" as a valid file",fp.isValid());
     String type = new IdentifyFile().Identify(fp);
-    assertTrue("Gzipped data from '"+src+"' identified as '"+type+"'",type.equalsIgnoreCase("FASTA"));
+    assertTrue("Data from '"+src+"' Expected to be '"+fmt+"' identified as '"+type+"'",type.equalsIgnoreCase(fmt));
+  }
+  @Test
+  public void testStarsInFasta1() throws IOException
+  {
+    String uri;
+    FileParse fp = new FileParse(uri=STARS_FA_FILE1.getAbsoluteFile().toString(),AppletFormatAdapter.FILE);
+    assertValidFormat("FASTA", uri, fp);
+  }
+  @Test
+  public void testStarsInFasta2() throws IOException
+  {
+    String uri;
+    FileParse fp = new FileParse(uri=STARS_FA_FILE2.getAbsoluteFile().toString(),AppletFormatAdapter.FILE);
+    assertValidFormat("FASTA", uri, fp);
   }
   @Test
   public void testGzipIo() throws IOException
   {     
     String uri;
     FileParse fp = new FileParse(uri=ALIGN_FILE.getAbsoluteFile().toURI().toString(),AppletFormatAdapter.URL);
-    assertValidFasta(uri, fp);
+    assertValidFormat("FASTA", uri, fp);
   }
 
   @Test
@@ -71,20 +91,20 @@ public class FileIOTester
   {
     String filepath;
     FileParse fp = new FileParse(filepath=ALIGN_FILE.getAbsoluteFile().toString(), AppletFormatAdapter.FILE);
-    assertValidFasta(filepath, fp);
+    assertValidFormat("FASTA",filepath, fp);
   }
   @Test
   public void testNonGzipURLIO() throws IOException
   {
     String uri;
     FileParse fp = new FileParse(uri=NOTGZALIGN_FILE.getAbsoluteFile().toURI().toString(),AppletFormatAdapter.URL);
-    assertValidFasta(uri, fp);
+    assertValidFormat("FASTA",uri, fp);
   }
   @Test
   public void testNonGziplocalFileIO() throws IOException
   {
     String filepath;
     FileParse fp = new FileParse(filepath=NOTGZALIGN_FILE.getAbsoluteFile().toString(), AppletFormatAdapter.FILE);
-    assertValidFasta(filepath, fp);
+    assertValidFormat("FASTA",filepath, fp);
   }
 }