Add ChromosomePositionComparator.

src/main/java/org/pharmgkb/common/comparator/ChromosomePositionComparator.java

@@ -0,0 +1,64 @@
+/*
+ ----- BEGIN LICENSE BLOCK -----
+ This Source Code Form is subject to the terms of the Mozilla Public License, v.2.0.
+ If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ ----- END LICENSE BLOCK -----
+ */
+package org.pharmgkb.common.comparator;
+
+import java.util.Comparator;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+import org.apache.commons.lang3.ObjectUtils;
+
+
+/**
+ * Comparator for chromosomal positions (in the format chrX:1234).
+ *
+ * @author Mark Woon
+ */
+public class ChromosomePositionComparator implements Comparator<String> {
+  public static final Comparator<String> sf_comparator = new ChromosomePositionComparator();
+  private static final Pattern sf_pattern = Pattern.compile("(?:chr)?(\\w{1,2}):(\\d+)");
+
+  /**
+   * Gets an instance of this comparator.
+   *
+   * @return an instance of this comparator
+   */
+  public static Comparator<String> getComparator() {
+    return sf_comparator;
+  }
+
+
+  @Override
+  public int compare(String o1, String o2) {
+
+    //noinspection StringEquality
+    if (o1 == o2) {
+      return 0;
+    }
+    if (o1 == null) {
+      return -1;
+    } else if (o2 == null) {
+      return 1;
+    }
+
+    Matcher m1 = sf_pattern.matcher(o1);
+    if (!m1.matches()) {
+      throw new IllegalArgumentException("'" + o1 + "' is not in the expected chromosomal position format");
+    }
+    Matcher m2 = sf_pattern.matcher(o2);
+    if (!m2.matches()) {
+      throw new IllegalArgumentException("'" + o2 + "' is not in the expected chromosomal position format");
+    }
+
+    int rez = ChromosomeNameComparator.getComparator().compare(m1.group(1), m2.group(1));
+    if (rez != 0) {
+      return rez;
+    }
+    Integer n1 = Integer.parseInt(m1.group(2));
+    Integer n2 = Integer.valueOf(m2.group(2));
+    return ObjectUtils.compare(n1, n2);
+  }
+}

src/test/java/org/pharmgkb/common/comparator/ChromosomePositionComparatorTest.java

@@ -0,0 +1,46 @@
+/*
+ ----- BEGIN LICENSE BLOCK -----
+ This Source Code Form is subject to the terms of the Mozilla Public License, v.2.0.
+ If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ ----- END LICENSE BLOCK -----
+ */
+package org.pharmgkb.common.comparator;
+
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
+
+
+/**
+ * Junit test for {@link ChromosomePositionComparator}.
+ *
+ * @author Mark Woon
+ */
+public class ChromosomePositionComparatorTest {
+
+
+  @Test
+  public void testComparator() {
+
+    assertEquals(0, ChromosomePositionComparator.getComparator().compare(null, null));
+    assertEquals(-1, ChromosomePositionComparator.getComparator().compare(null, "chr1:1"));
+    assertEquals(1, ChromosomePositionComparator.getComparator().compare("chr1:1", null));
+
+    assertEquals(-1, ChromosomePositionComparator.getComparator().compare("chr1:4", "chr1:100"));
+    assertEquals(0, ChromosomePositionComparator.getComparator().compare("chr1:4", "chr1:4"));
+    assertEquals(1, ChromosomePositionComparator.getComparator().compare("chr3:4", "chr1:4"));
+    assertEquals(1, ChromosomePositionComparator.getComparator().compare("chr4:100", "chr1:400"));
+  }
+
+
+  @Test(expected = IllegalArgumentException.class)
+  public void testBadArg1() throws IllegalArgumentException {
+    ChromosomePositionComparator.getComparator().compare("chr1", "chr1:100");
+  }
+
+
+  @Test(expected = IllegalArgumentException.class)
+  public void testBadArg2() throws IllegalArgumentException {
+    ChromosomePositionComparator.getComparator().compare("chr1:1", ":100");
+  }
+}