More work to disorder prediction client & services.

[jabaws.git] / testsrc / compbio / data / sequence / ClustalAlignmentUtilTester.java

diff --git a/testsrc/compbio/data/sequence/ClustalAlignmentUtilTester.java b/testsrc/compbio/data/sequence/ClustalAlignmentUtilTester.java
index addba28..812cd6f 100644 (file)
--- a/testsrc/compbio/data/sequence/ClustalAlignmentUtilTester.java
+++ b/testsrc/compbio/data/sequence/ClustalAlignmentUtilTester.java
@@ -25,8 +25,9 @@ import static org.testng.AssertJUnit.fail;
 \r
 import java.io.FileInputStream;\r
 import java.io.FileNotFoundException;\r
-import java.io.FileOutputStream;\r
+import java.io.FileWriter;\r
 import java.io.IOException;\r
+import java.io.Writer;\r
 \r
 import org.testng.annotations.Test;\r
 \r
@@ -34,68 +35,68 @@ import compbio.metadata.AllTestSuit;
 \r
 public class ClustalAlignmentUtilTester {\r
 \r
-    @Test()\r
-    public void testReadClustalFile() {\r
-       try {\r
-           readWriteClustal("TO1381.aln");\r
-       } catch (FileNotFoundException e) {\r
-           e.printStackTrace();\r
-           fail(e.getMessage());\r
-       } catch (Exception e) {\r
-           e.printStackTrace();\r
-           fail(e.getMessage());\r
+       @Test()\r
+       public void testReadClustalFile() {\r
+               try {\r
+                       readWriteClustal("TO1381.aln");\r
+               } catch (FileNotFoundException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               } catch (Exception e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               }\r
        }\r
-    }\r
 \r
-    static void readWriteClustal(String fname) throws IOException,\r
-           UnknownFileFormatException {\r
-       FileInputStream fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
-               + fname);\r
-       Alignment seqAl = ClustalAlignmentUtil.readClustalFile(fio);\r
-       assertTrue(seqAl != null);\r
-       assertTrue(seqAl.getSize() == 3);\r
-       assertNotNull(seqAl.getSequences());\r
-       assertEquals(3, seqAl.getSequences().size());\r
+       static void readWriteClustal(String fname) throws IOException,\r
+                       UnknownFileFormatException {\r
+               FileInputStream fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
+                               + fname);\r
+               Alignment seqAl = ClustalAlignmentUtil.readClustalFile(fio);\r
+               assertTrue(seqAl != null);\r
+               assertTrue(seqAl.getSize() == 3);\r
+               assertNotNull(seqAl.getSequences());\r
+               assertEquals(3, seqAl.getSequences().size());\r
 \r
-       // Now try to write the alignment read\r
-       FileOutputStream os = new FileOutputStream(AllTestSuit.TEST_DATA_PATH\r
-               + fname + ".written");\r
-       ClustalAlignmentUtil.writeClustalAlignment(os, seqAl);\r
-       fio.close();\r
-       os.close();\r
+               // Now try to write the alignment read\r
+               Writer os = new FileWriter(AllTestSuit.TEST_DATA_PATH + fname\r
+                               + ".written");\r
+               ClustalAlignmentUtil.writeClustalAlignment(os, seqAl);\r
+               fio.close();\r
+               os.close();\r
 \r
-       fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + fname\r
-               + ".written");\r
-       Alignment readseqs = ClustalAlignmentUtil.readClustalFile(fio);\r
-       assertTrue(readseqs != null);\r
-       assertTrue(readseqs.getSize() == 3);\r
-       fio.close();\r
-    }\r
+               fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + fname\r
+                               + ".written");\r
+               Alignment readseqs = ClustalAlignmentUtil.readClustalFile(fio);\r
+               assertTrue(readseqs != null);\r
+               assertTrue(readseqs.getSize() == 3);\r
+               fio.close();\r
+       }\r
 \r
-    @Test()\r
-    public void testReadClustalFileShortNames() {\r
-       try {\r
-           readWriteClustal("TO1381s.aln");\r
-       } catch (FileNotFoundException e) {\r
-           e.printStackTrace();\r
-           fail(e.getMessage());\r
-       } catch (Exception e) {\r
-           e.printStackTrace();\r
-           fail(e.getMessage());\r
+       @Test()\r
+       public void testReadClustalFileShortNames() {\r
+               try {\r
+                       readWriteClustal("TO1381s.aln");\r
+               } catch (FileNotFoundException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               } catch (Exception e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               }\r
        }\r
-    }\r
 \r
-    @Test()\r
-    public void testReadClustalFileLongNames() {\r
-       try {\r
-           readWriteClustal("TO1381L.aln");\r
-       } catch (FileNotFoundException e) {\r
-           e.printStackTrace();\r
-           fail(e.getMessage());\r
-       } catch (Exception e) {\r
-           e.printStackTrace();\r
-           fail(e.getMessage());\r
+       @Test()\r
+       public void testReadClustalFileLongNames() {\r
+               try {\r
+                       readWriteClustal("TO1381L.aln");\r
+               } catch (FileNotFoundException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               } catch (Exception e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               }\r
        }\r
-    }\r
 \r
 }\r