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Added a test+fix for isotope pattern generation for C10000 #190

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merged 3 commits into from Feb 1, 2016
Merged

Added a test+fix for isotope pattern generation for C10000 #190

merged 3 commits into from Feb 1, 2016

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tomas-pluskal
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The test is failing at the moment due to NullPointerException somewhere in IsotopePatternManipulator

java.lang.NullPointerException
    at org.openscience.cdk.formula.IsotopePatternManipulator.sortByMass(IsotopePatternManipulator.java:131)
    at org.openscience.cdk.formula.IsotopePatternGenerator.getIsotopes(IsotopePatternGenerator.java:113)
    at org.openscience.cdk.formula.IsotopePatternGeneratorTest.testCalculateIsotopesC10000(IsotopePatternGeneratorTest.java:266)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
    at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
    at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
    at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
    at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
    at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
    at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
    at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
    at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
    at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
    at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
    at org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:86)
    at org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
    at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:459)
    at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:675)
    at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:382)
    at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:192)

@tomas-pluskal
Added a test for isotope pattern generation for C10000.
fed836f 
The test is failing at the moment due to NullPointerException
@johnmay
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johnmay commented Jan 26, 2016

Can you help with the fix, don't like adding tests for stuff without a fix otherwise they just ignored.

I can fix the the NPE by making this value Double.Max.

But then the assertion on number of isotopes fails...

java.lang.AssertionError: 
Expected :98
Actual   :44

Any ideas?

@johnmay
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johnmay commented Jan 26, 2016

Also ouch that N^2 sort... in sortByMass

@tomas-pluskal
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I guess 44 is the correct result. I didn't realize the intensities were in the scale 0 to 1.
I will commit a fix.

@tomas-pluskal
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Fix added

@tomas-pluskal tomas-pluskal changed the title Added a test for isotope pattern generation for C10000. Added a test+fix for isotope pattern generation for C10000. Jan 26, 2016
@tomas-pluskal tomas-pluskal changed the title Added a test+fix for isotope pattern generation for C10000. Added a test+fix for isotope pattern generation for C10000 Jan 26, 2016
@johnmay
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johnmay commented Feb 1, 2016

Looks good, don't see any failures. Thanks

johnmay added a commit that referenced this pull request Feb 1, 2016
@johnmay
Merge pull request #190 from tomas-pluskal/master
35e874e 
Added a test+fix for isotope pattern generation for C10000
@johnmay johnmay merged commit 35e874e into cdk:master Feb 1, 2016
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@tomas-pluskal @johnmay