Fix local align score vector #1036
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added 3 commits
July 25, 2022 20:07
Initialize pointers array to dimension (ye,1)
Initialize pointers to size (ye+1,1)
josemduarte
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Aug 26, 2022
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josemduarte
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josemduarte
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Thanks a lot and sorry for the delay. I think this looks good.
I'm not sure why the tests are not running. I'll have a look.
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Could you add a dummy commit to the branch? I'm hoping that will trigger the tests. |
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I've run the tests locally and they pass. I'll merge. |
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Thank you for running that, I missed your comment earlier. |
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Using a local alignment with linear gap penalty resulted in the failure trace below. Setting pointers to dimension (ye+1,1) fixed the error. Added a test "testLinearAlignmentLocal()" in TestDNAAlignment.java to verify results.
java.lang.NullPointerException: Cannot store to object array because "pointers[y]" is null
at org.biojava.nbio.alignment.routines.AlignerHelper.setScoreVector(AlignerHelper.java:587)
at org.biojava.nbio.alignment.routines.AlignerHelper.setScoreVector(AlignerHelper.java:560)
at org.biojava.nbio.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:347)
at org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:114)
at org.biojava.nbio.alignment.TestDNAAlignment.testLinearAlignmentLocal(TestDNAAlignment.java:178)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:577)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:93)
at org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:40)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:529)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:756)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:452)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:210)