public class Jalview2xmlTests extends Jalview2xmlBase
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJalviewSynchonization()
+ {
+ Jalview.setSynchronous(true);
+ }
+
@Override
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- Jalview.setSynchronous(true);
}
@Test(groups = { "Functional" })
String inFile = "examples/RF00031_folded.stk";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
- // Jalview.setSynchronous(true);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
DataSourceType.FILE);
assertNotNull(af, "Didn't read input file " + inFile);
inAnnot = "examples/uniref50.score_ascii";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
- // Jalview.setSynchronous(true);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
DataSourceType.FILE);
assertNotNull(af, "Didn't read input file " + inFile);
assertNotNull(
ColourSchemeProperty.getColourScheme(viewport,
viewport.getAlignment(),
- viewport.getGlobalColourScheme()
- .getSchemeName()),
+ viewport.getGlobalColourScheme().getSchemeName()),
"Recognise T-Coffee score from string");
af.saveAlignment(tfile, FileFormat.Jalview);
inAnnot = "examples/testdata/uniref50_iupred.jva";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
- // Jalview.setSynchronous(true);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
DataSourceType.FILE);
assertNotNull(af, "Didn't read input file " + inFile);
{
int origCount = Desktop.getAlignFrames() == null ? 0
: Desktop.getAlignFrames().length;
- // Jalview.setSynchronous(true);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
{
StructureImportSettings.setProcessSecondaryStructure(true);
StructureImportSettings.setVisibleChainAnnotation(true);
- // Jalview.setSynchronous(true);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
StructureMapping[] x = af.getCurrentView()
.getStructureSelectionManager()//
.getMapping(pdbFile);
- assertEquals(x.length,
- 2, "Expected only two mappings for 1A70");
+ assertEquals(x.length, 2, "Expected only two mappings for 1A70");
}
{
StructureImportSettings.setProcessSecondaryStructure(true);
StructureImportSettings.setVisibleChainAnnotation(true);
- // Jalview.setSynchronous(true);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
@Test(groups = { "Functional" })
public void testCopyViewSettings() throws Exception
{
- // Jalview.setSynchronous(true);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
public void testStoreAndRecoverExpandedviews() throws Exception
{
Desktop.getInstance().closeAll_actionPerformed(null);
- // Jalview.setSynchronous(true);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
Assert.assertEquals(Desktop.getAlignFrames().length, 1);
Assert.assertEquals(Desktop.getAlignFrames().length,
Desktop.getAlignmentPanels(
af.getViewport().getSequenceSetId()).length);
- Assert.assertEquals(
- Desktop.getAlignmentPanels(
- af.getViewport().getSequenceSetId()).length,
+ Assert.assertEquals(Desktop
+ .getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
oldviews);
}
public void testStoreAndRecoverReferenceSeqSettings() throws Exception
{
Desktop.getInstance().closeAll_actionPerformed(null);
- // Jalview.setSynchronous(true);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
public void testStoreAndRecoverGroupRepSeqs() throws Exception
{
Desktop.getInstance().closeAll_actionPerformed(null);
- // Jalview.setSynchronous(true);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
{
Desktop.getInstance().closeAll_actionPerformed(null);
String exampleFile = "examples/3W5V.pdb";
- // Jalview.setSynchronous(true);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
public void testStoreAndRecoverColourThresholds() throws IOException
{
Desktop.getInstance().closeAll_actionPerformed(null);
- // Jalview.setSynchronous(true);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
@Test(groups = { "Functional" })
public void testSaveLoadFeatureColoursAndFilters() throws IOException
{
- // Jalview.setSynchronous(true);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
public void testMergeDatasetsforViews() throws IOException
{
// simple project - two views on one alignment
- // Jalview.setSynchronous(true);
AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
"examples/testdata/projects/twoViews.jvp", DataSourceType.FILE);
assertNotNull(af);
{
Desktop.getInstance().closeAll_actionPerformed(null);
- // complex project - one dataset, several views on several alignments
- // Jalview.setSynchronous(true);
+ // complex project - one dataset, several views on several alignment
AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
"examples/testdata/projects/manyViews.jvp",
DataSourceType.FILE);
public void testPcaViewAssociation() throws IOException
{
Desktop.getInstance().closeAll_actionPerformed(null);
- // Jalview.setSynchronous(true);
final String PCAVIEWNAME = "With PCA";
// create a new tempfile
File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp");