import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLocus;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.Mapping;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+import junit.extensions.PA;
+
@Test(singleThreaded = true)
public class Jalview2xmlTests extends Jalview2xmlBase
{
DataSourceType.FILE);
assertNotNull(af, "Didn't read input file " + inFile);
af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
- AlignViewport viewport = af.getViewport();
+ AlignViewportI viewport = af.getViewport();
assertSame(viewport.getGlobalColourScheme().getClass(),
TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
assertNotNull(
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignViewport av = af.getViewport();
+ AlignViewportI av = af.getViewport();
AlignmentI al = av.getAlignment();
/*
}
/**
+ * Load an HMM profile to an alignment, and confirm it is correctly restored
+ * when reloaded from project
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverHmmProfile() throws IOException
+ {
+ Desktop.getInstance().closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+
+ AlignViewportI av = af.getViewport();
+ AlignmentI al = av.getAlignment();
+
+ /*
+ * mimic drag and drop of hmm file on to alignment
+ */
+ AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.hmm", DataSourceType.FILE);
+ al.insertSequenceAt(0,
+ af2.getViewport().getAlignment().getSequenceAt(0));
+
+ /*
+ * check it loaded in
+ */
+ SequenceI hmmSeq = al.getSequenceAt(0);
+ assertTrue(hmmSeq.hasHMMProfile());
+ HiddenMarkovModel hmm = hmmSeq.getHMM();
+ assertSame(hmm.getConsensusSequence(), hmmSeq);
+
+ /*
+ * save project, close windows, reload project, verify
+ */
+ File tfile = File.createTempFile("testStoreAndRecoverHmmProfile",
+ ".jvp");
+ tfile.deleteOnExit();
+ new Jalview2XML(false).saveState(tfile);
+ Desktop.getInstance().closeAll_actionPerformed(null);
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+ Assert.assertNotNull(af, "Failed to reload project");
+
+ hmmSeq = al.getSequenceAt(0);
+ assertTrue(hmmSeq.hasHMMProfile());
+ assertSame(hmm.getConsensusSequence(), hmmSeq);
+ Mapping mapToHmmConsensus = (Mapping) PA.getValue(hmm,
+ "mapToHmmConsensus");
+ assertNotNull(mapToHmmConsensus);
+ assertSame(mapToHmmConsensus.getTo(), hmmSeq.getDatasetSequence());
+ }
+
+ /**
* pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
* view (JAL-3171) this test ensures we can import and merge those views
*/