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Merge branch 'features/JAL-2447experimentalFlag' into develop
[jalview.git]
/
test
/
jalview
/
ws
/
jabaws
/
JpredJabaStructExportImport.java
diff --git
a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
index
7f94b6b
..
dc157e2
100644
(file)
--- a/
test/jalview/ws/jabaws/JpredJabaStructExportImport.java
+++ b/
test/jalview/ws/jabaws/JpredJabaStructExportImport.java
@@
-26,7
+26,10
@@
import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.gui.Jalview2XML;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile;
import jalview.io.AnnotationFile;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.ws.jws2.JPred301Client;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.ws.jws2.JPred301Client;
@@
-46,6
+49,7
@@
import javax.swing.JMenuItem;
import org.testng.Assert;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.Assert;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeGroups;
import org.testng.annotations.Test;
import compbio.metadata.Argument;
import org.testng.annotations.Test;
import compbio.metadata.Argument;
@@
-53,6
+57,14
@@
import compbio.metadata.WrongParameterException;
public class JpredJabaStructExportImport
{
public class JpredJabaStructExportImport
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
public static String testseqs = "examples/uniref50.fa";
public static Jws2Discoverer disc;
public static String testseqs = "examples/uniref50.fa";
public static Jws2Discoverer disc;
@@
-63,7
+75,7
@@
public class JpredJabaStructExportImport
public static jalview.gui.AlignFrame af = null;
public static jalview.gui.AlignFrame af = null;
- @BeforeClass(alwaysRun = true)
+ @BeforeGroups(groups = { "Network" })
public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
@@
-81,7
+93,7
@@
public class JpredJabaStructExportImport
System.out.println("State of jpredws: " + jpredws);
Assert.assertNotNull(jpredws, "jpredws is null!");
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
System.out.println("State of jpredws: " + jpredws);
Assert.assertNotNull(jpredws, "jpredws is null!");
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
- af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
+ af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
}
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
}
@@
-95,7
+107,7
@@
public class JpredJabaStructExportImport
}
}
}
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" }, enabled = false)
public void testJPredStructOneSeqOnly()
{
af.selectAllSequenceMenuItem_actionPerformed(null);
public void testJPredStructOneSeqOnly()
{
af.selectAllSequenceMenuItem_actionPerformed(null);
@@
-147,7
+159,7
@@
public class JpredJabaStructExportImport
}
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" }, enabled = false)
public void testJPredStructExport()
{
public void testJPredStructExport()
{
@@
-177,8
+189,8
@@
public class JpredJabaStructExportImport
try
{
// what format would be appropriate for RNAalifold annotations?
try
{
// what format would be appropriate for RNAalifold annotations?
- String aligfileout = new FormatAdapter().formatSequences("PFAM",
- al.getSequencesArray());
+ String aligfileout = FileFormat.Pfam.getWriter(null).print(
+ al.getSequencesArray(), true);
String anfileout = new AnnotationFile()
.printAnnotationsForAlignment(al);
String anfileout = new AnnotationFile()
.printAnnotationsForAlignment(al);
@@
-198,16
+210,17
@@
public class JpredJabaStructExportImport
// again what format would be appropriate?
AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
// again what format would be appropriate?
AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
- FormatAdapter.PASTE, "PFAM");
+ DataSourceType.PASTE, FileFormat.Fasta);
assertTrue(
"Test "
+ testname
+ "\nregenerated annotation file did not annotate alignment.",
new AnnotationFile().readAnnotationFile(al_new, anfileout,
assertTrue(
"Test "
+ testname
+ "\nregenerated annotation file did not annotate alignment.",
new AnnotationFile().readAnnotationFile(al_new, anfileout,
- FormatAdapter.PASTE));
+ DataSourceType.PASTE));
// test for consistency in io
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+ false);
return;
} catch (Exception e)
{
return;
} catch (Exception e)
{
@@
-218,7
+231,7
@@
public class JpredJabaStructExportImport
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" }, enabled = false)
public void testJpredwsSettingsRecovery()
{
Assert.fail("not implemnented");
public void testJpredwsSettingsRecovery()
{
Assert.fail("not implemnented");