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Merge branch 'develop' into features/JAL-2393customMatrices
[jalview.git]
/
test
/
jalview
/
ws
/
jabaws
/
RNAStructExportImport.java
diff --git
a/test/jalview/ws/jabaws/RNAStructExportImport.java
b/test/jalview/ws/jabaws/RNAStructExportImport.java
index
2a111ee
..
4e9741e
100644
(file)
--- a/
test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/
test/jalview/ws/jabaws/RNAStructExportImport.java
@@
-27,8
+27,10
@@
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.Jalview2XML;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile;
import jalview.io.AnnotationFile;
-import jalview.io.FileLoader;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.ws.jws2.Jws2Discoverer;
@@
-53,8
+55,21
@@
import org.testng.annotations.Test;
import compbio.metadata.Argument;
import compbio.metadata.WrongParameterException;
import compbio.metadata.Argument;
import compbio.metadata.WrongParameterException;
+/*
+ * All methods in this class are set to the Network group because setUpBeforeClass will fail
+ * if there is no network.
+ */
+@Test(singleThreaded = true)
public class RNAStructExportImport
{
public class RNAStructExportImport
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private static final String JAR_FILE_NAME = "testRnalifold_param.jar";
public static String testseqs = "examples/RF00031_folded.stk";
private static final String JAR_FILE_NAME = "testRnalifold_param.jar";
public static String testseqs = "examples/RF00031_folded.stk";
@@
-74,6
+89,12
@@
public class RNAStructExportImport
Cache.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
Cache.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
+ while (disc.isRunning())
+ {
+ // don't get services until discoverer has finished
+ Thread.sleep(100);
+ }
+
for (Jws2Instance svc : disc.getServices())
{
for (Jws2Instance svc : disc.getServices())
{
@@
-90,9
+111,9
@@
public class RNAStructExportImport
Assert.fail("no web service");
}
Assert.fail("no web service");
}
- FileLoader fl = new FileLoader(false);
+ jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
- af = fl.LoadFileWaitTillLoaded(testseqs, 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);
@@
-129,7
+150,7
@@
public class RNAStructExportImport
}
}
}
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void testRNAAliFoldValidStructure()
{
public void testRNAAliFoldValidStructure()
{
@@
-162,7
+183,7
@@
public class RNAStructExportImport
}
}
}
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void testRNAStructExport()
{
public void testRNAStructExport()
{
@@
-182,17
+203,17
@@
public class RNAStructExportImport
AlignmentI orig_alig = af.getViewport().getAlignment();
AlignmentI orig_alig = af.getViewport().getAlignment();
- testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
+ verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
}
}
- public static void testAnnotationFileIO(String testname, AlignmentI al)
+ static void verifyAnnotationFileIO(String testname, AlignmentI al)
{
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);
@@
-212,13
+233,13
@@
public class RNAStructExportImport
// 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.Pfam);
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
StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
// test for consistency in io
StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
@@
-232,12
+253,12
@@
public class RNAStructExportImport
+ "\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" })
public void testRnaalifoldSettingsRecovery()
{
List<Argument> opts = new ArrayList<Argument>();
public void testRnaalifoldSettingsRecovery()
{
List<Argument> opts = new ArrayList<Argument>();
- for (Argument rg : (List<Argument>) rnaalifoldws
- .getRunnerConfig().getArguments())
+ for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
+ .getArguments())
{
if (rg.getDescription().contains("emperature"))
{
{
if (rg.getDescription().contains("emperature"))
{