Junit test submit shivika

build.number

@@ -1,3 +1,3 @@
 #Build Number for ANT. Do not edit!
-#Thu Sep 22 10:10:13 BST 2016
-build.number=203
+#Sat Dec 31 00:30:05 GMT 2016
+build.number=208

build/build.xml

@@ -110,8 +110,9 @@
                 <batchtest todir="${test.home}/results/xml" fork="true">
                     <fileset dir="${test.home}/java">
                     	<include name="**/Test*.java" />
-                    	<include name="**/GolombRiceIntegerCodecTest.java" />
-
+						<include name="**/AlignmentSliceQueryTest.java" />
+						<include name="**/common/UtilsTest.java" />
+						<include name="**/GolombRiceIntegerCodecTest.java" />
                     	<exclude name="**/TestByteArrayStopCodec.java" />
                     	<exclude name="**/TestFZ_B.java" />
                     	<exclude name="**/TestRandomAccess.java" />

src/test/java/net/sf/cram/AlignmentSliceQueryTest.java

@@ -0,0 +1,141 @@
+/***************************************************
+(Test 1)
+Junit Test Cases to test Class AlignmentSliceQuery.java.
+The class is designed to parse and print genome location queries of form:
+sequenceName[:start[-end]]
+where
+sequenceName:    string matching pattern [A-Za-z0-1_-|]+
+start:    an integer [1, 2^31]
+end:    an integer [1, 2^31]
+
+Submitted by: SHIVIKA SHARMA 
+****************************************************/
+
+package net.sf.cram;
+
+import net.sf.cram.AlignmentSliceQuery;
+import org.junit.Test;
+import org.junit.Ignore;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+import static org.junit.Assert.assertTrue;
+
+
+public class AlignmentSliceQueryTest {
+
+	@Test
+	public void testParseSequenceName(){
+
+		AlignmentSliceQuery asq = new AlignmentSliceQuery("chr1");
+
+		assertEquals("Parsed Sequence name is different than expected.", "chr1", asq.sequence);
+		assertEquals("Sequence Start is different than expected default value.",0,asq.start);
+		assertEquals("Sequence End is different than expected default value.",Integer.MAX_VALUE,asq.end);
+	}
+
+
+	@Test
+	public void testParseLocationString1(){
+
+		AlignmentSliceQuery asq = new AlignmentSliceQuery("chr1:10000");
+
+		assertEquals("Parsed Sequence name is different than expected.", "chr1", asq.sequence);
+		assertEquals("Parsed Sequence Start is different than expected.",10000,asq.start);
+		assertEquals("Sequence End is different than expected default value.",Integer.MAX_VALUE,asq.end);
+	}
+
+
+	@Test
+	public void testParseLocationString2(){
+		/*
+		Assuming START and END take integer values between [1-Integer.MAX_VALUE] Inclusive.
+		*/
+		AlignmentSliceQuery asq = new AlignmentSliceQuery("chr1:1");   
+
+		assertEquals("Parsed Sequence name is different than expected.", "chr1", asq.sequence);
+		assertEquals("Parsed Sequence Start is different than expected.",1,asq.start);
+	}
+
+
+	@Test
+	public void testParseLocationString3(){
+
+		AlignmentSliceQuery asq = new AlignmentSliceQuery("ENA|U00096|U00096.3:3000000-3001000");
+
+		assertEquals("Parsed Sequence name is different than expected.", "ENA|U00096|U00096.3", asq.sequence);
+		assertEquals("Parsed Sequence Start is different than expected.",3000000,asq.start);
+		assertEquals("Parsed Sequence End is different than expected.",3001000,asq.end);		  
+
+	}
+
+
+	@Test(expected=NumberFormatException.class)
+	public void testLocationStringWithInvalidInput1(){
+
+		AlignmentSliceQuery asq = new AlignmentSliceQuery("chr1:10a");
+	}
+
+
+	@Test(expected=NumberFormatException.class)
+	public void testLocationStringWithInvalidInput2(){
+		/*
+		When END value is greater than Integer.MAX_VALUE
+		*/
+		AlignmentSliceQuery asq = new AlignmentSliceQuery("ENA|U00096|U00096.3:3000000-2147483648");
+	}
+
+
+	@Test
+	public void testSequenceNameMatchPattern1(){
+		/*
+		Considering Sequence Name must be a string of Regex matching value [A-Za-z0-1_-|]+  (As per provided in the MAIL)
+		*/ 
+		AlignmentSliceQuery asq = new AlignmentSliceQuery("chr1:3000000-3001000");
+
+		String expectedSeq = asq.sequence;
+		assertTrue(expectedSeq.matches("[A-Za-z0-1_-|]+"));
+	}
+
+
+	@Test
+	public void testSequenceNameMatchPattern2(){
+		/*
+		Considering Sequence Name must be a string of Regex matching value [A-Za-z0-1_-|]+  (As per provided in the MAIL)
+		*/
+		AlignmentSliceQuery asq = new AlignmentSliceQuery("ENA|U00096|U00096.3:3000000-3001000");
+
+		String expectedSeq = asq.sequence;
+		assertTrue("Actual Sequence Name does not matches with expected Regular Expression.", expectedSeq.matches("[A-Za-z0-1_-|]+")); 
+	}
+
+
+	@Test
+	public void testToString1(){
+		AlignmentSliceQuery asq = new AlignmentSliceQuery("chr10:1000-30000");
+
+		assertTrue("Expected toString() output is different from Actual String.", "chr10:1000-30000".equals(asq.toString()));			
+	}
+
+
+	@Test
+	public void testToString2(){
+		/*
+		Assuming variable Start can take values between [1 - Integer.MAX_VALUE] inclusive.
+		*/
+		AlignmentSliceQuery asq = new AlignmentSliceQuery("chr1:1");
+
+		assertTrue("Expected toString() output is different from Actual String.", "chr1:1".equals(asq.toString()));			
+	}
+
+
+	@Test
+	public void testEmptyString(){
+
+		AlignmentSliceQuery asq = new AlignmentSliceQuery("");
+
+		assertEquals("",asq.sequence);
+		fail("The Alignment String is empyt");
+
+	}
+
+}