X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=test%2Fjalview%2Fio%2FPhylipFileTests.java;h=d85335027c59fcd5fdde7bc6f3b3724a88d5ad4a;hb=bd7b3138379c2db8507fe7e8d25f5a921e2d9df7;hp=9db47631a35e4f84076e2b8ab45ad24b3001f405;hpb=c93b9ad2ebfab4cad4608a8890132918589576be;p=jalview.git
diff --git a/test/jalview/io/PhylipFileTests.java b/test/jalview/io/PhylipFileTests.java
index 9db4763..d853350 100644
--- a/test/jalview/io/PhylipFileTests.java
+++ b/test/jalview/io/PhylipFileTests.java
@@ -1,15 +1,37 @@
+/*
+ * 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;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
@@ -25,6 +47,13 @@ import org.testng.annotations.Test;
public class PhylipFileTests
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
// interleaved file from
// http://www.molecularevolution.org/molevolfiles/fileformats/dna.phy.dat
// sequential file is the interleave file converted into sequential format
@@ -79,7 +108,7 @@ public class PhylipFileTests
*
* @throws Exception
*/
- @Test
+ @Test(groups = { "Functional" })
public void testSequentialDataExtraction() throws Exception
{
testDataExtraction(sequentialFile);
@@ -91,7 +120,7 @@ public class PhylipFileTests
*
* @throws Exception
*/
- @Test
+ @Test(groups = { "Functional" })
public void testInterleavedDataExtraction() throws Exception
{
testDataExtraction(interleavedFile);
@@ -106,8 +135,8 @@ public class PhylipFileTests
private void testDataExtraction(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment 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 +153,7 @@ public class PhylipFileTests
*
* @throws Exception
*/
- @Test
+ @Test(groups = { "Functional" })
public void testSequentialIO() throws Exception
{
testIO(sequentialFile);
@@ -136,7 +165,7 @@ public class PhylipFileTests
*
* @throws Exception
*/
- @Test
+ @Test(groups = { "Functional" })
public void testInterleavedIO() throws Exception
{
testIO(interleavedFile);
@@ -151,17 +180,18 @@ public class PhylipFileTests
public void testIO(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment 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);
- Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
- AppletFormatAdapter.PASTE, PhylipFile.FILE_DESC);
+ AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
+ DataSourceType.PASTE, FileFormat.Phylip);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
- StockholmFileTest.testAlignmentEquivalence(al, al_input, false);
+ StockholmFileTest.testAlignmentEquivalence(al, al_input, false, false,
+ false);
}
-}
\ No newline at end of file
+}