X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureMatcherSetTest.java;h=47c47a9f674344ee856c27f3c4c114cae1b53a60;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=a98013b6e9d66ed4d1fb0d83db38e31507c63ef0;hpb=1aa039ed9dfe0528cb7b40231734cf3004452c39;p=jalview.git

diff --git a/test/jalview/datamodel/features/FeatureMatcherSetTest.java b/test/jalview/datamodel/features/FeatureMatcherSetTest.java
index a98013b..47c47a9 100644
--- a/test/jalview/datamodel/features/FeatureMatcherSetTest.java
+++ b/test/jalview/datamodel/features/FeatureMatcherSetTest.java
@@ -2,6 +2,7 @@ package jalview.datamodel.features;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 import static org.testng.Assert.fail;
@@ -11,6 +12,7 @@ import jalview.util.matcher.Condition;
 
 import java.util.HashMap;
 import java.util.Iterator;
+import java.util.Locale;
 import java.util.Map;
 
 import org.testng.annotations.Test;
@@ -102,7 +104,8 @@ public class FeatureMatcherSetTest
      * OR failed attribute and score conditions with matched label condition
      */
     fms = new FeatureMatcherSet();
-    fms.or(fm2).or(byScoreFail);
+    fms.or(fm2);
+    fms.or(byScoreFail);
     assertFalse(fms.matches(sf));
     fms.or(byLabelPass);
     assertTrue(fms.matches(sf));
@@ -111,14 +114,14 @@ public class FeatureMatcherSetTest
   @Test(groups = "Functional")
   public void testToString()
   {
+    Locale.setDefault(Locale.ENGLISH);
     FeatureMatcherI fm1 = FeatureMatcher.byAttribute(Condition.LT, "1.2",
             "AF");
     assertEquals(fm1.toString(), "AF < 1.2");
 
     FeatureMatcher fm2 = FeatureMatcher.byAttribute(Condition.NotContains,
-            "path",
-            "CLIN_SIG");
-    assertEquals(fm2.toString(), "CLIN_SIG Does not contain 'PATH'");
+            "path", "CLIN_SIG");
+    assertEquals(fm2.toString(), "CLIN_SIG does not contain 'path'");
 
     /*
      * AND them
@@ -126,10 +129,10 @@ public class FeatureMatcherSetTest
     FeatureMatcherSetI fms = new FeatureMatcherSet();
     assertEquals(fms.toString(), "");
     fms.and(fm1);
-    assertEquals(fms.toString(), "(AF < 1.2)");
+    assertEquals(fms.toString(), "AF < 1.2");
     fms.and(fm2);
     assertEquals(fms.toString(),
-            "(AF < 1.2) AND (CLIN_SIG Does not contain 'PATH')");
+            "(AF < 1.2) and (CLIN_SIG does not contain 'path')");
 
     /*
      * OR them
@@ -137,10 +140,10 @@ public class FeatureMatcherSetTest
     fms = new FeatureMatcherSet();
     assertEquals(fms.toString(), "");
     fms.or(fm1);
-    assertEquals(fms.toString(), "(AF < 1.2)");
+    assertEquals(fms.toString(), "AF < 1.2");
     fms.or(fm2);
     assertEquals(fms.toString(),
-            "(AF < 1.2) OR (CLIN_SIG Does not contain 'PATH')");
+            "(AF < 1.2) or (CLIN_SIG does not contain 'path')");
 
     try
     {
@@ -237,8 +240,8 @@ public class FeatureMatcherSetTest
   }
 
   /**
-   * Tests for the 'compound attribute' key i.e. where first key's value is a map
-   * from which we take the value for the second key, e.g. CSQ : Consequence
+   * Tests for the 'compound attribute' key i.e. where first key's value is a
+   * map from which we take the value for the second key, e.g. CSQ : Consequence
    */
   @Test(groups = "Functional")
   public void testMatches_compoundKey()
@@ -265,7 +268,7 @@ public class FeatureMatcherSetTest
     assertFalse(fms.matches(sf));
     csq.put("Consequence", "junk");
     assertFalse(fms.matches(sf));
-  
+
     /*
      * a string pattern matcher
      */
@@ -281,4 +284,136 @@ public class FeatureMatcherSetTest
     csq.put("Consequence", "Catastrophic");
     assertTrue(fms.matches(sf));
   }
+
+  /**
+   * Tests for toStableString which (unlike toString) does not i18n the
+   * conditions
+   * 
+   * @see FeatureMatcherTest#testToStableString()
+   */
+  @Test(groups = "Functional")
+  public void testToStableString()
+  {
+    FeatureMatcherI fm1 = FeatureMatcher.byAttribute(Condition.LT, "1.2",
+            "AF");
+    assertEquals(fm1.toStableString(), "AF LT 1.2");
+
+    FeatureMatcher fm2 = FeatureMatcher.byAttribute(Condition.NotContains,
+            "path", "CLIN_SIG");
+    assertEquals(fm2.toStableString(), "CLIN_SIG NotContains path");
+
+    /*
+     * AND them
+     */
+    FeatureMatcherSetI fms = new FeatureMatcherSet();
+    assertEquals(fms.toStableString(), "");
+    fms.and(fm1);
+    // no brackets needed if a single condition
+    assertEquals(fms.toStableString(), "AF LT 1.2");
+    // brackets if more than one condition
+    fms.and(fm2);
+    assertEquals(fms.toStableString(),
+            "(AF LT 1.2) AND (CLIN_SIG NotContains path)");
+
+    /*
+     * OR them
+     */
+    fms = new FeatureMatcherSet();
+    assertEquals(fms.toStableString(), "");
+    fms.or(fm1);
+    assertEquals(fms.toStableString(), "AF LT 1.2");
+    fms.or(fm2);
+    assertEquals(fms.toStableString(),
+            "(AF LT 1.2) OR (CLIN_SIG NotContains path)");
+
+    /*
+     * attribute or value including space is quoted
+     */
+    FeatureMatcher fm3 = FeatureMatcher.byAttribute(Condition.NotMatches,
+            "foo bar", "CSQ", "Poly Phen");
+    assertEquals(fm3.toStableString(),
+            "'CSQ:Poly Phen' NotMatches 'foo bar'");
+    fms.or(fm3);
+    assertEquals(fms.toStableString(),
+            "(AF LT 1.2) OR (CLIN_SIG NotContains path) OR ('CSQ:Poly Phen' NotMatches 'foo bar')");
+
+    try
+    {
+      fms.and(fm1);
+      fail("Expected exception");
+    } catch (IllegalStateException e)
+    {
+      // expected
+    }
+  }
+
+  /**
+   * Tests for parsing a string representation of a FeatureMatcherSet
+   * 
+   * @see FeatureMatcherSetTest#testToStableString()
+   */
+  @Test(groups = "Functional")
+  public void testFromString()
+  {
+    String descriptor = "AF LT 1.2";
+    FeatureMatcherSetI fms = FeatureMatcherSet.fromString(descriptor);
+
+    /*
+     * shortcut asserts by verifying a 'roundtrip', 
+     * which we trust if other tests pass :-)
+     */
+    assertEquals(fms.toStableString(), descriptor);
+
+    // brackets optional, quotes optional, condition case insensitive
+    fms = FeatureMatcherSet.fromString("('AF' lt '1.2')");
+    assertEquals(fms.toStableString(), descriptor);
+
+    descriptor = "(AF LT 1.2) AND (CLIN_SIG NotContains path)";
+    fms = FeatureMatcherSet.fromString(descriptor);
+    assertEquals(fms.toStableString(), descriptor);
+
+    // AND is not case-sensitive
+    fms = FeatureMatcherSet
+            .fromString("(AF LT 1.2) and (CLIN_SIG NotContains path)");
+    assertEquals(fms.toStableString(), descriptor);
+
+    descriptor = "(AF LT 1.2) OR (CLIN_SIG NotContains path)";
+    fms = FeatureMatcherSet.fromString(descriptor);
+    assertEquals(fms.toStableString(), descriptor);
+
+    // OR is not case-sensitive
+    fms = FeatureMatcherSet
+            .fromString("(AF LT 1.2) or (CLIN_SIG NotContains path)");
+    assertEquals(fms.toStableString(), descriptor);
+
+    // can get away without brackets on last match condition
+    fms = FeatureMatcherSet
+            .fromString("(AF LT 1.2) or CLIN_SIG NotContains path");
+    assertEquals(fms.toStableString(), descriptor);
+
+    descriptor = "(AF LT 1.2) OR (CLIN_SIG NotContains path) OR ('CSQ:Poly Phen' NotMatches 'foo bar')";
+    fms = FeatureMatcherSet.fromString(descriptor);
+    assertEquals(fms.toStableString(), descriptor);
+
+    // can't mix OR and AND
+    descriptor = "(AF LT 1.2) OR (CLIN_SIG NotContains path) AND ('CSQ:Poly Phen' NotMatches 'foo bar')";
+    assertNull(FeatureMatcherSet.fromString(descriptor));
+
+    // can't mix AND and OR
+    descriptor = "(AF LT 1.2) and (CLIN_SIG NotContains path) or ('CSQ:Poly Phen' NotMatches 'foo bar')";
+    assertNull(FeatureMatcherSet.fromString(descriptor));
+
+    // brackets missing
+    assertNull(FeatureMatcherSet
+            .fromString("AF LT 1.2 or CLIN_SIG NotContains path"));
+
+    // invalid conjunction
+    assertNull(FeatureMatcherSet.fromString("(AF LT 1.2) but (AF GT -2)"));
+
+    // unbalanced quote (1)
+    assertNull(FeatureMatcherSet.fromString("('AF lt '1.2')"));
+
+    // unbalanced quote (2)
+    assertNull(FeatureMatcherSet.fromString("('AF' lt '1.2)"));
+  }
 }