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JAL-2843 unit tests for writing filters to Jalview features file
[jalview.git] / test / jalview / io / FeaturesFileTest.java
diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 152ab84..32ca841 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -23,7 +23,9 @@ package jalview.io;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureRenderer;
@@ -32,11 +34,17 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcher;
+import jalview.datamodel.features.FeatureMatcherI;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
+import jalview.schemes.FeatureColour;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.matcher.Condition;
 
 import java.awt.Color;
 import java.io.File;
@@ -44,6 +52,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
@@ -467,10 +476,10 @@ public class FeaturesFileTest
      */
     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
     Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
-    List<String> visibleGroups = new ArrayList<String>(
+    List<String> visibleGroups = new ArrayList<>(
             Arrays.asList(new String[] {}));
     String exported = featuresFile.printJalviewFormat(
-            al.getSequencesArray(), visible, visibleGroups, false);
+            al.getSequencesArray(), visible, null, visibleGroups, false);
     String expected = "No Features Visible";
     assertEquals(expected, exported);
 
@@ -479,7 +488,7 @@ public class FeaturesFileTest
      */
     visibleGroups.add("uniprot");
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
-            visible, visibleGroups, true);
+            visible, null, visibleGroups, true);
     expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
             + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
             + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n" // NaN is not output
@@ -493,9 +502,9 @@ public class FeaturesFileTest
     fr.setVisible("GAMMA-TURN");
     visible = fr.getDisplayedFeatureCols();
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
-            visible, visibleGroups, false);
+            visible, null, visibleGroups, false);
     expected = "METAL\tcc9900\n"
-            + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
+            + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
             + "\nSTARTGROUP\tuniprot\n"
             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
@@ -508,13 +517,13 @@ public class FeaturesFileTest
     fr.setVisible("Pfam");
     visible = fr.getDisplayedFeatureCols();
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
-            visible, visibleGroups, false);
+            visible, null, visibleGroups, false);
     /*
      * features are output within group, ordered by sequence and by type
      */
     expected = "METAL\tcc9900\n"
             + "Pfam\tff0000\n"
-            + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
+            + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
             + "\nSTARTGROUP\tuniprot\n"
             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
@@ -539,8 +548,8 @@ public class FeaturesFileTest
      */
     FeaturesFile featuresFile = new FeaturesFile();
     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
-    Map<String, FeatureColourI> visible = new HashMap<String, FeatureColourI>();
-    List<String> visibleGroups = new ArrayList<String>(
+    Map<String, FeatureColourI> visible = new HashMap<>();
+    List<String> visibleGroups = new ArrayList<>(
             Arrays.asList(new String[] {}));
     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
             visible, visibleGroups, false);
@@ -623,4 +632,79 @@ public class FeaturesFileTest
             + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
     assertEquals(expected, exported);
   }
+
+  /**
+   * Test for parsing of feature filters as represented in a Jalview features
+   * file
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" })
+  public void testParseFilters() throws Exception
+  {
+    Map<String, FeatureMatcherSetI> filters = new HashMap<>();
+    String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
+            + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
+    FeaturesFile featuresFile = new FeaturesFile(text,
+            DataSourceType.PASTE);
+    featuresFile.parseFilters(filters);
+    assertEquals(filters.size(), 2);
+
+    FeatureMatcherSetI fm = filters.get("sequence_variant");
+    assertNotNull(fm);
+    Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
+    FeatureMatcherI matcher = matchers.next();
+    assertFalse(matchers.hasNext());
+    String[] attributes = matcher.getAttribute();
+    assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
+    assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
+    assertEquals(matcher.getMatcher().getPattern(), "damaging");
+
+    fm = filters.get("missense_variant");
+    assertNotNull(fm);
+    matchers = fm.getMatchers().iterator();
+    matcher = matchers.next();
+    assertTrue(matcher.isByLabel());
+    assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
+    assertEquals(matcher.getMatcher().getPattern(), "foobar");
+    matcher = matchers.next();
+    assertTrue(matcher.isByScore());
+    assertSame(matcher.getMatcher().getCondition(), Condition.LT);
+    assertEquals(matcher.getMatcher().getPattern(), "1.3");
+    assertEquals(matcher.getMatcher().getFloatValue(), 1.3f);
+
+    assertFalse(matchers.hasNext());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testOutputFeatureFilters()
+  {
+    FeaturesFile ff = new FeaturesFile();
+    StringBuilder sb = new StringBuilder();
+    Map<String, FeatureColourI> visible = new HashMap<>();
+    visible.put("pfam", new FeatureColour(Color.red));
+    Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
+
+    // with no filters, nothing is output
+    ff.outputFeatureFilters(sb, visible, featureFilters);
+    assertEquals("", sb.toString());
+
+    // with filter for not visible features only, nothing is output
+    FeatureMatcherSet filter = new FeatureMatcherSet();
+    filter.and(FeatureMatcher.byLabel(Condition.Present, null));
+    featureFilters.put("foobar", filter);
+    ff.outputFeatureFilters(sb, visible, featureFilters);
+    assertEquals("", sb.toString());
+
+    // with filters for visible feature types
+    FeatureMatcherSet filter2 = new FeatureMatcherSet();
+    filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
+            "PolyPhen"));
+    filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
+    featureFilters.put("pfam", filter2);
+    visible.put("foobar", new FeatureColour(Color.blue));
+    ff.outputFeatureFilters(sb, visible, featureFilters);
+    String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n\n";
+    assertEquals(expected, sb.toString());
+  }
 }