JAL-2738 extract utility method to MappingUtils

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index abbe139..4adc97c 100644 (file)
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -19,6 +19,7 @@ import jalview.ext.ensembl.EnsemblMap;
 import jalview.ext.htsjdk.VCFReader;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.MapList;
+import jalview.util.MappingUtils;
 
 import java.io.IOException;
 import java.util.HashMap;
@@ -304,6 +305,11 @@ public class VCFLoader
     String alleles = sb.toString(); // e.g. G,A,C
 
     String type = SequenceOntologyI.SEQUENCE_VARIANT;
+
+    /*
+     * extract allele frequency as feature score, but only if
+     * a simple SNP (not for >1 co-located SNPs as each has a score)
+     */
     float score = 0f;
     if (alleleCount == 1)
     {
@@ -434,7 +440,7 @@ public class VCFLoader
           /*
            * mapping is 1:1 in length, so we trust it to have no discontinuities
            */
-          if (rangeContains(fromRange, queryRange))
+          if (MappingUtils.rangeContains(fromRange, queryRange))
           {
             /*
              * fromRange subsumes our query range
@@ -451,23 +457,6 @@ public class VCFLoader
   }
 
   /**
-   * Answers true if range's start-end positions include those of queryRange,
-   * where either range might be in reverse direction, else false
-   * 
-   * @param range
-   * @param queryRange
-   * @return
-   */
-  protected static boolean rangeContains(int[] range, int[] queryRange)
-  {
-    int min = Math.min(range[0], range[1]);
-    int max = Math.max(range[0], range[1]);
-
-    return (min <= queryRange[0] && max >= queryRange[0]
-            && min <= queryRange[1] && max >= queryRange[1]);
-  }
-
-  /**
    * Formats a ranges map lookup key
    * 
    * @param chromosome

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 3682239..d21eac3 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -939,4 +939,32 @@ public final class MappingUtils
     }
     return copy;
   }
+
+  /**
+   * Answers true if range's start-end positions include those of queryRange,
+   * where either range might be in reverse direction, else false
+   * 
+   * @param range
+   *          a start-end range
+   * @param queryRange
+   *          a candidate subrange of range (start2-end2)
+   * @return
+   */
+  public static boolean rangeContains(int[] range, int[] queryRange)
+  {
+    if (range == null || queryRange == null || range.length != 2
+            || queryRange.length != 2)
+    {
+      /*
+       * invalid arguments
+       */
+      return false;
+    }
+
+    int min = Math.min(range[0], range[1]);
+    int max = Math.max(range[0], range[1]);
+  
+    return (min <= queryRange[0] && max >= queryRange[0]
+            && min <= queryRange[1] && max >= queryRange[1]);
+  }
 }

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index d0ec3e8..87070d7 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -1149,4 +1149,93 @@ public class MappingUtilsTest
     assertEquals("[12, 11, 8, 4]", Arrays.toString(ranges));
   }
 
+  @Test(groups = { "Functional" })
+  public void testRangeContains()
+  {
+    /*
+     * both forward ranges
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        1, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        2, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        1, 9 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        4, 5 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        0, 9 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        -10, -9 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        1, 11 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        11, 12 }));
+
+    /*
+     * forward range, reverse query
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        10, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        9, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        10, 2 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        5, 5 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        11, 1 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        10, 0 }));
+
+    /*
+     * reverse range, forward query
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        1, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        1, 9 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        2, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        6, 6 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        6, 11 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        11, 20 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        -3, -2 }));
+
+    /*
+     * both reverse
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        10, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        9, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        10, 2 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        3, 3 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        11, 1 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        10, 0 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        12, 11 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        -5, -8 }));
+
+    /*
+     * bad arguments
+     */
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10, 12 },
+            new int[] {
+        1, 10 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 },
+            new int[] { 1 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, null));
+    assertFalse(MappingUtils.rangeContains(null, new int[] { 1, 10 }));
+  }
+
 }