monarch-initiative/owlsim-v3

use guice

fixed missing import

Merge branch 'master' of github.com:cmungall/owlsim-v3 …

Conflicts:
	owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/matcher/perf/PhenodigmMatcherPerfIT.java

documentation changes

Adding informative fail message, see #18

Updates coveralls status icon

Restricts JVMs

Adds JDK8 and fixes coveralls plugin

Reduces "writeToStdout" and also removes manual log level setting in … …

…favor of log4.properties

Fixes Travis badge

Reduces logging in test

Increases ulimit

Adds travis and coveralls to README

added docs. Also made an executable jar

suppressing

Adding runner

Merge branch 'master' of github.com:cmungall/owlsim-v3

organizing imports

Adds make to travis

Refactors MatcherMapModule for #16

Cleans up unused imports

Merge branch 'master' of github.com:cmungall/owlsim-v3

Moves state references into array declaration.

Renames MatcherModule

Updates to Guice 4.0

saving intermediate work, still needs revision

tweaking params

required for MicaTest

ensuring all tests pass

new

Allow use of annotation property to indicate opposing classes

adding missing files

Merge branch 'master' of github.com:cmungall/owlsim-v3

First version of 3state NaiveBayes

NaiveBayes: intermediate commit pre refactoring into two classes …

Changes to other probabilistic methods