X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=dfd771a42c9bbb4a0c25c3d3ad8fc9c25f0047cb;hb=64144b92481279aa0aaf11ba05febd65f73cfa30;hp=afc445e5108b4929e877bfaa381fbc6f395afdbf;hpb=3c8a25936a2d805e7e3d7ab82f83b13135406d18;p=jalview.git

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index afc445e..dfd771a 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -34,7 +34,9 @@ import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.Mapping;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceCollectionI;
@@ -45,7 +47,6 @@ import jalview.datamodel.features.FeatureMatcher;
 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.FeatureRenderer;
@@ -86,6 +87,8 @@ import org.testng.AssertJUnit;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 @Test(singleThreaded = true)
 public class Jalview2xmlTests extends Jalview2xmlBase
 {
@@ -147,12 +150,13 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             DataSourceType.FILE);
     assertNotNull(af, "Didn't read input file " + inFile);
     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
-    assertSame(af.getViewport().getGlobalColourScheme().getClass(),
+    AlignViewportI viewport = af.getViewport();
+    assertSame(viewport.getGlobalColourScheme().getClass(),
             TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
     assertNotNull(
-            ColourSchemeProperty.getColourScheme(
-                    af.getViewport().getAlignment(),
-                    af.getViewport().getGlobalColourScheme()
+            ColourSchemeProperty.getColourScheme(viewport,
+                    viewport.getAlignment(),
+                    viewport.getGlobalColourScheme()
                             .getSchemeName()),
             "Recognise T-Coffee score from string");
 
@@ -812,12 +816,13 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
 
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*
      * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
      */
+    av.setColourAppliesToAllGroups(false);
     af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
     assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
     af.abovePIDThreshold_actionPerformed(true);
@@ -899,7 +904,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
    * @throws IOException
    */
   @Test(groups = { "Functional" })
-  public void testSaveLoadFeatureColoursAndFilters() throws IOException
+  public void testStoreAndRecoverFeatureColoursAndFilters()
+          throws IOException
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
@@ -1053,6 +1059,59 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   }
 
   /**
+   * 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.instance.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.instance.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
    */