X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FPhylipFileTests.java;h=e0f1f684b2c270a702a832d020dfab33ee84e1a4;hb=019a78415854a8c7fbfe0b566174ede7e69f24b8;hp=9c95486dcce25b7c299dfa1021af85578d55875d;hpb=fddf3084802b37e5cee17829e32692a4aac3e60d;p=jalview.git
diff --git a/test/jalview/io/PhylipFileTests.java b/test/jalview/io/PhylipFileTests.java
index 9c95486..e0f1f68 100644
--- a/test/jalview/io/PhylipFileTests.java
+++ b/test/jalview/io/PhylipFileTests.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
import static org.testng.AssertJUnit.assertNotNull;
@@ -79,7 +99,7 @@ public class PhylipFileTests
*
* @throws Exception
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSequentialDataExtraction() throws Exception
{
testDataExtraction(sequentialFile);
@@ -91,7 +111,7 @@ public class PhylipFileTests
*
* @throws Exception
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testInterleavedDataExtraction() throws Exception
{
testDataExtraction(interleavedFile);
@@ -106,8 +126,8 @@ public class PhylipFileTests
private void testDataExtraction(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- AlignmentI al = rf.readFile(file, AppletFormatAdapter.FILE,
- PhylipFile.FILE_DESC);
+ AlignmentI al = rf.readFile(file, DataSourceType.FILE,
+ FileFormat.Phylip);
assertNotNull("Couldn't read supplied alignment data.", al);
Map data = PhylipFileTests.getTestData();
@@ -124,7 +144,7 @@ public class PhylipFileTests
*
* @throws Exception
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSequentialIO() throws Exception
{
testIO(sequentialFile);
@@ -136,7 +156,7 @@ public class PhylipFileTests
*
* @throws Exception
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testInterleavedIO() throws Exception
{
testIO(interleavedFile);
@@ -151,17 +171,17 @@ public class PhylipFileTests
public void testIO(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- AlignmentI al = rf.readFile(file, AppletFormatAdapter.FILE,
- PhylipFile.FILE_DESC);
+ AlignmentI al = rf.readFile(file, DataSourceType.FILE,
+ FileFormat.Phylip);
assertNotNull("Couldn't read supplied alignment data.", al);
- String outputfile = rf.formatSequences(PhylipFile.FILE_DESC, al, true);
+ String outputfile = rf.formatSequences(FileFormat.Phylip, al, true);
AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
- AppletFormatAdapter.PASTE, PhylipFile.FILE_DESC);
+ DataSourceType.PASTE, FileFormat.Phylip);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
StockholmFileTest.testAlignmentEquivalence(al, al_input, false);
}
-}
\ No newline at end of file
+}