JAL-1483 basic test of sequence similarity score model (also gives the refactored...

diff --git a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
new file mode 100644 (file)
index 0000000..1dbaa4a
--- /dev/null
+++ b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
@@ -0,0 +1,74 @@
+package jalview.analysis.scoremodels;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+public class FeatureScoreModelTest
+{
+  public static String alntestFile = "FER1_MESCR/72-76 DVYIL\nFER1_SPIOL/71-75 DVYIL\nFER3_RAPSA/21-25 DVYVL\nFER1_MAIZE/73-77 DVYIL\n";
+
+  int[] sf1 = new int[]
+  { 74, 74, 73, 73, 23, 23, -1, -1 };
+
+  int[] sf2 = new int[]
+  { -1, -1, 74, 75, -1, -1, 76, 77 };
+
+  int[] sf3 = new int[]
+  { -1, -1, -1, -1, -1, -1, 76, 77 };
+
+  @Test
+  public void testFeatureScoreModel() throws Exception
+  {
+    AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(alntestFile,
+            FormatAdapter.PASTE);
+    AlignmentI al = alf.getViewport().getAlignment();
+    Assert.assertEquals(4, al.getHeight());
+    Assert.assertEquals(5, al.getWidth());
+    for (int i = 0; i < 4; i++)
+    {
+      SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
+      if (sf1[i * 2] > 0)
+      {
+        ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", "sf1",
+                sf1[i * 2], sf1[i * 2 + 1], "sf1"));
+      }
+      if (sf2[i * 2] > 0)
+      {
+        ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", "sf2",
+                sf2[i * 2], sf2[i * 2 + 1], "sf2"));
+      }
+      if (sf3[i * 2] > 0)
+      {
+        ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", "sf3",
+                sf3[i * 2], sf3[i * 2 + 1], "sf3"));
+      }
+    }
+    alf.setShowSeqFeatures(true);
+    alf.getFeatureRenderer().setVisible("sf1");
+    alf.getFeatureRenderer().setVisible("sf2");
+    alf.getFeatureRenderer().setVisible("sf3");
+    alf.getFeatureRenderer().findAllFeatures(true);
+    Assert.assertEquals("Number of feature types", 3, alf
+            .getFeatureRenderer().getDisplayedFeatureTypes().length);
+    Assert.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
+    FeatureScoreModel fsm = new FeatureScoreModel();
+    Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
+            .getAlignPanel()));
+    alf.selectAllSequenceMenuItem_actionPerformed(null);
+    float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
+            true));
+    Assert.assertTrue("FER1_MESCR should be identical with RAPSA (2)",
+            dm[0][2] == 0f);
+    Assert.assertTrue(
+            "FER1_MESCR should be further from SPIOL (1) than it is from RAPSA (2)",
+            dm[0][1] > dm[0][2]);
+
+  }
+}