JAL-2843 read/write feature filters from/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..fd4cad7 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 +34,14 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherI;
+import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.matcher.Condition;
 
 import java.awt.Color;
 import java.io.File;
@@ -44,6 +49,7 @@ 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 +473,10 @@ 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 +485,7 @@ 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
@@ -493,7 +499,7 @@ 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"
             + "\nSTARTGROUP\tuniprot\n"
@@ -508,7 +514,7 @@ 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
      */
@@ -539,8 +545,8 @@ 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 +629,47 @@ 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());
+  }
 }