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Ensure deterministic order in toConciseAlignmentString #908
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This line fixes an error I was getting compiling with Java 1.8:
The second form isn't documented, so it could be that this change will cause a warning with different JDKs.
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@sbliven
I did initially try to fix this error with the same change. However the TreeMap here, is not fixing this flaky error. The tool still marks it as flaky with error of the sort -
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@sbliven @josemduarte
Would like to link the Nondex tool here : https://github.com/TestingResearchIllinois/NonDex
The tool requires :
Adding the plugin as specified in the documentation which applies if you want to run NonDex mutliple times.
Run for the test -
mvn -pl biojava-integrationtest nondex:nondex -Dtest=AlignmentToolsTest#testToConciseAlignmentString
Run for the whole module -
mvn -pl biojava-integrationtest nondex:nondex
.Otherwise, one need not add the plugin to
pom.xml
file(s) and can run just runmvn edu.illinois:nondex-maven-plugin:1.1.2:nondex
instead ofmvn test
. Please check that the command does work for you.This could be added into travis.yml, so it can be run on new tests too.
It also has the debug feature that can be used to point to the file(s) that could require changes. The link to the tool has all the documentation.