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Removed native method call 

and fixed indentation.
This commit is contained in:
Mauricio Carneiro 2013-07-30 13:59:58 -04:00
parent 71eb944e62
commit 7b731dd596
1 changed files with 21 additions and 30 deletions
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51
protected/java/test/org/broadinstitute/sting/utils/pairhmm/CnyPairHMMUnitTest.java
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@ -48,54 +48,45 @@ package org.broadinstitute.sting.utils.pairhmm;
import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.BaseTest;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test; import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.List;
public class CnyPairHMMUnitTest extends BaseTest { public class CnyPairHMMUnitTest extends BaseTest {
private native void puts(String text);
@Test(enabled = true) @Test(enabled = true)
public void testResultQueue() { public void testResultQueue() {
final double[] row1 = new double[] { 4.5, 53.1, 6.4 }; final double[] row1 = new double[] { 4.5, 53.1, 6.4 };
final double[] row2 = new double[] { 1.0, 5.9, 6.9, 6.1, 19.8 }; final double[] row2 = new double[] { 1.0, 5.9, 6.9, 6.1, 19.8 };
final double[] row3 = new double[] { 10.4, 9.101, 89.5, 9.8}; final double[] row3 = new double[] { 10.4, 9.101, 89.5, 9.8};
final double[] row4 = new double[] { 7.3, 1.4, 5.67, 56.32 }; final double[] row4 = new double[] { 7.3, 1.4, 5.67, 56.32 };
CnyPairHMM.ResultQueue queue = new CnyPairHMM.ResultQueue(); CnyPairHMM.ResultQueue queue = new CnyPairHMM.ResultQueue();
// Test inter-mixed push/pop operations produce the correct output // Test inter-mixed push/pop operations produce the correct output
queue.push(row1); queue.push(row1);
queue.push(row2); queue.push(row2);
for (int i=0; i<row1.length; i++) for (double aRow1 : row1) Assert.assertEquals(aRow1, queue.pop());
Assert.assertEquals(row1[i], queue.pop());
for (int i=0; i<2; i++) for (int i=0; i<2; i++)
Assert.assertEquals(row2[i], queue.pop()); Assert.assertEquals(row2[i], queue.pop());
queue.push(row3); queue.push(row3);
for (int i=2; i<row2.length; i++) for (int i=2; i<row2.length; i++)
Assert.assertEquals(row2[i], queue.pop()); Assert.assertEquals(row2[i], queue.pop());
for (int i=0; i<row3.length; i++) for (double aRow3 : row3) Assert.assertEquals(aRow3, queue.pop());
Assert.assertEquals(row3[i], queue.pop());
// Test push/pop after return to empty state // Test push/pop after return to empty state
queue.push(row4); queue.push(row4);
for (int i=0; i<row4.length; i++) for (double aRow4 : row4) Assert.assertEquals(aRow4, queue.pop());
Assert.assertEquals(row4[i], queue.pop());
} }
@Test(enabled = true) @Test(enabled = true)
public void testAddLibraryPath() { public void testAddLibraryPath() {
final String testLibPath = privateTestDir + "testlib"; final String testLibPath = privateTestDir + "testlib";
CnyPairHMM.addLibraryPath(testLibPath); CnyPairHMM.addLibraryPath(testLibPath);
System.loadLibrary("CnyPairHMMUnitTest"); System.loadLibrary("CnyPairHMMUnitTest");
puts("Shared library loaded.");
} }
} }