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Fixed README and add Travis-CI
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‎.travis.yml

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language: java
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addons:
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mariadb: '10.0'
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jdk:
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- oraclejdk8
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before_script:
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- mysql -e "use mysql; update user set password=PASSWORD('123456') where User='root'; flush privileges;" -uroot
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- mysql -uroot -p123456 < testsql/unielwin_course.sql
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- mysql -uroot -p123456 < testsql/unielwin_prof.sql
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- mysql -uroot -p123456 < testsql/unielwin_RA.sql
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- mysql -uroot -p123456 < testsql/unielwin_registration.sql
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- mysql -uroot -p123456 < testsql/unielwin_student.sql
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- mysql -uroot -p123456 < testsql/Mutagenesis_std_Atom.sql
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- mysql -uroot -p123456 < testsql/Mutagenesis_std_bond.sql
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- mysql -uroot -p123456 < testsql/Mutagenesis_std_Mole.sql
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- mysql -uroot -p123456 < testsql/Mutagenesis_std_moleatm.sql
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script:
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- cd jar
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- java -jar RunBB.jar > jar.txt
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- tail jar.txt
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- ls -lh
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- tail sort_merge.csv
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- tail Bif_unielwin.xml
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- tail dag_.txt
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- cd ../src
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- javac -cp ".:./lib/*" Config.java BZScriptRunner.java MakeSetup.java
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- javac -cp ".:./lib/*" RunBB.java
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- javac -cp ".:./lib/*" MakeTargetSetup.java
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- javac -cp ".:./lib/*" FunctorWrapper.java
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- mkdir src
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- mv config.cfg src/
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- mv scripts src/
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- java -cp ".:./lib/*" MakeSetup > a.txt
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- java -cp ".:./lib/*" RunBB > b.txt
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- java -cp ".:./lib/*" MakeTargetSetup > c.txt
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- nohup java -cp ".:./lib/*" FunctorWrapper > d.txt &
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- sleep 5m
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- ls -lh d.txt
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- ls -lh
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- tail a.txt
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- tail b.txt
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- tail c.txt
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- tail d.txt
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- tail dag_.txt
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after_script:
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- mysql -e "show databases;" -uroot -p123456
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- mysql -e "use unielwin_BN; show tables;" -uroot -p123456
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- mysql -e "use unielwin_CT; show tables;" -uroot -p123456
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- mysql -e "use Mutagenesis_std_target_final_CT; show tables;" -uroot -p123456
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- mysql -e "use Mutagenesis_std_target_final; show tables;" -uroot -p123456
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- mysql -e "use Mutagenesis_std_target_CT; show tables;" -uroot -p123456
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- mysql -e "use Mutagenesis_std_target_BN; show tables;" -uroot -p123456
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- mysql -e "use Mutagenesis_std_target; show tables;" -uroot -p123456

‎README.md

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# BayesBase
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[![Build Status](https://travis-ci.org/sfu-cl-lab/BayesBase.svg?branch=master)](https://travis-ci.org/sfu-cl-lab/BayesBase)
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The source code repository for the Bayes Base system. Most of the code are classes for CMU's Tetrad system. We may also add datasets if we get around to it.
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For more information about this project, visit our [project website](http://www.cs.sfu.ca/~oschulte/BayesBase/BayesBase.html)
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##How to Use
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First you should import data into your database. We provide two sets of example datasets in `testsql` folder. Then you can either run `.jar` or compile the source yourself.
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###Run .jar
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+ Modify `jar/src/config.cfg` with your own configuration according to format explained [here](http://www.cs.sfu.ca/~oschulte/BayesBase/options.html)
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+ In `jar` folder, run `java -jar RunBB.jar`
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###Compile & Run
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+ Go into `src` folder and modify `config.cfg`
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+ Go into `src/cfg` folder and modify `subsetctcomputation.cfg`
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+ `javac -cp ".:./lib/*" Config.java BZScriptRunner.java MakeSetup.java`
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+ `java -cp ".:./lib/*" MakeSetup`
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+ `javac -cp ".:./lib/*" RunBB.java`
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+ `mkdir src`
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+ `mv scripts src/`
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+ `java -cp ".:./lib/*" MakeSetup`
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+ `java -cp ".:./lib/*" RunBB`
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+ `javac -cp ".:./lib/*" MakeTargetSetup.java`
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+ `java -cp ".:./lib/*" MakeTargetSetup`
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+ `javac -cp ".:./lib/*" FunctorWrapper.java`
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+ `java -cp ".:./lib/*" FunctorWrapper`
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+ Optionally set up the target database and run FunctorWrapper
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+ `javac -cp ".:./lib/*" MakeTargetSetup.java`
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+ `javac -cp ".:./lib/*" FunctorWrapper.java`
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+ `java -cp ".:./lib/*" MakeTargetSetup`
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+ `java -cp ".:./lib/*" FunctorWrapper`
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## Project Specification
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Please visit our [project website](http://www.cs.sfu.ca/~oschulte/BayesBase/BayesBase.html)

‎jar/src/config.cfg

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dbname = 1
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dbusername = 1
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dbpassword = 1
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dbaddress = mysql://xxx.sfu.ca
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dbname = unielwin
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dbusername = root
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dbpassword = 123456
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dbaddress = mysql://127.0.0.1
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AutomaticSetup = 1
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LinkCorrelations = 1
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ComputeKLD = 0
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Continuous = 0
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Continuous = 0

‎src/cfg/fmtconfig.cfg

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Address = mysql://xx.sfu.ca
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User = 1
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Password = 1
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Address = mysql://127.0.0.1
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User = root
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Password = 123456
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SetupDBName = unielwin_fmt_setup
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DataDBName = unielwin_fmt
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OutDBName = unielwin_fmt_CT

‎src/cfg/scorecomputation.cfg

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dbaddress = mysql://xxx.sfu.ca
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dbusername = 1
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dbpassword = 1
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dbaddress = mysql://127.0.0.1
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dbusername = root
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dbpassword = 123456
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dbschema = unielwin_BN
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dbcounts = unielwin_db
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dbcondprob = unielwin_db

‎src/cfg/subsetctcomputation.cfg

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dbaddress = mysql://xxx.sfu.ca
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dbusername = 1
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dbpassword = 1
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dbBNschema = Financial_std_Training2_BN
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dbDataSchema = Financial_std_Training2
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dbOutputSchema = Financial_std_Training2_db
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dbaddress = mysql://127.0.0.1
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dbusername = root
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dbpassword = 123456
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dbBNschema = Mutagenesis_std_BN
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dbDataSchema = Mutagenesis_std
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dbOutputSchema = Mutagenesis_std_db
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pathBayesNet = Path_BayesNets
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LinkAnalysis = 1
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Grounded = 0
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/* real data for FunctorWrapper, cross validation: Financial_std_Training2*/
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dbname = Financial_std_Training2
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dbname = Mutagenesis_std
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AutomaticSetup = 1
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LinkCorrelations = 1
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ComputeKLD = 0
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dbschema = Financial_std_Training2_BN
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dbcounts = Financial_std_Training2_db
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dbcondprob = Financial_std_Training2_db
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dbschema = Mutagenesis_std_BN
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dbcounts = Mutagenesis_std_db
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dbcondprob = Mutagenesis_std_db
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/* FunctorWrapper should be 0; For TestScoreComputation should be 1, or the program will compute the parameters twice*/
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UseLocal_CT = 0
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/*For Propositionalization, generating the subCT tables based on each family configuration, add one option to control the spliting; Sep 11, 2014, zqian */
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CrossValidation = 1
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CrossValidation = 0
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‎src/config.cfg

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dbname = Hepatitis_std
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dbusername = 1
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dbpassword = 1
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dbaddress = mysql://xxx.sfu.ca
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dbname = Mutagenesis_std
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dbusername = root
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dbpassword = 123456
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dbaddress = mysql://127.0.0.1
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AutomaticSetup = 0
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LinkCorrelations = 1
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ComputeKLD = 0

‎testsql/Mutagenesis_std_Atom.sql

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‎testsql/Mutagenesis_std_Mole.sql

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CREATE DATABASE IF NOT EXISTS `Mutagenesis_std` /*!40100 DEFAULT CHARACTER SET latin1 */;
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USE `Mutagenesis_std`;
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-- MySQL dump 10.13 Distrib 5.1.69, for redhat-linux-gnu (x86_64)
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--
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-- Host: kripke.cs.sfu.ca Database: Mutagenesis_std
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-- ------------------------------------------------------
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-- Server version 5.0.95
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/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
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/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
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/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
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/*!40101 SET NAMES utf8 */;
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/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
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/*!40103 SET TIME_ZONE='+00:00' */;
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/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */;
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/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */;
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/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */;
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/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
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--
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-- Not dumping tablespaces as no INFORMATION_SCHEMA.FILES table on this server
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--
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--
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-- Table structure for table `Mole`
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--
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DROP TABLE IF EXISTS `Mole`;
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/*!40101 SET @saved_cs_client = @@character_set_client */;
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/*!40101 SET character_set_client = utf8 */;
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CREATE TABLE `Mole` (
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`m_id` smallint(8) NOT NULL,
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`ind1` varchar(45) default NULL,
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`inda` varchar(45) default NULL,
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`lumo` varchar(45) default NULL,
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`logp` varchar(45) default NULL,
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`label` varchar(45) default NULL,
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PRIMARY KEY USING BTREE (`m_id`),
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KEY `Mole_ind1` USING HASH (`ind1`),
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KEY `Mole_inda` USING HASH (`inda`),
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KEY `Mole_lumo` USING HASH (`lumo`),
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KEY `Mole_logp` USING HASH (`logp`),
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KEY `Mole_label` USING HASH (`label`)
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) ENGINE=InnoDB DEFAULT CHARSET=latin1;
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/*!40101 SET character_set_client = @saved_cs_client */;
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--
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-- Dumping data for table `Mole`
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--
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LOCK TABLES `Mole` WRITE;
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/*!40000 ALTER TABLE `Mole` DISABLE KEYS */;
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INSERT INTO `Mole` VALUES (1,'1','0','7','5','1'),(2,'0','0','7','1','2'),(3,'0','0','7','2','2'),(4,'1','0','6','5','1'),(5,'0','0','6','2','2'),(6,'1','0','1','5','1'),(7,'0','0','8','5','2'),(8,'1','0','7','4','1'),(9,'0','0','8','2','2'),(10,'1','0','7','5','1'),(11,'1','0','7','5','1'),(12,'1','0','6','4','1'),(13,'1','0','4','5','1'),(14,'0','0','7','2','2'),(15,'1','0','6','5','1'),(16,'1','0','4','5','1'),(17,'0','0','9','1','2'),(18,'1','0','5','3','1'),(19,'0','0','7','2','2'),(20,'1','0','6','4','1'),(21,'0','0','6','4','1'),(22,'1','0','6','6','1'),(23,'1','1','4','6','1'),(24,'1','0','6','8','1'),(25,'1','0','7','4','1'),(26,'0','0','5','2','1'),(27,'1','0','6','7','1'),(28,'1','0','6','5','1'),(29,'1','0','2','3','1'),(30,'1','1','5','6','1'),(31,'1','0','5','5','1'),(32,'0','0','3','3','1'),(33,'1','0','6','5','1'),(34,'0','0','7','4','2'),(35,'1','0','7','3','1'),(36,'0','0','7','4','2'),(37,'0','0','7','5','1'),(38,'0','0','7','4','2'),(39,'0','0','7','2','2'),(40,'0','0','7','4','2'),(41,'1','0','6','6','1'),(42,'0','0','7','2','2'),(43,'1','0','6','5','1'),(44,'1','0','7','5','1'),(45,'0','0','4','1','1'),(46,'1','0','6','8','1'),(47,'1','0','5','6','1'),(48,'1','0','6','5','1'),(49,'1','0','2','2','1'),(50,'0','0','5','3','1'),(51,'1','0','4','7','1'),(52,'1','0','4','7','1'),(53,'1','0','4','4','1'),(54,'1','0','7','7','1'),(55,'0','0','7','4','2'),(56,'1','0','4','3','1'),(57,'0','0','4','4','1'),(58,'1','0','5','3','1'),(59,'1','1','5','6','1'),(60,'0','0','4','2','1'),(61,'1','0','6','5','1'),(62,'0','0','8','1','2'),(63,'0','0','2','3','1'),(64,'1','0','4','3','1'),(65,'0','0','5','3','2'),(66,'0','0','8','3','2'),(67,'1','0','6','5','1'),(68,'1','0','6','7','1'),(69,'1','0','5','4','1'),(70,'0','0','6','0','2'),(71,'1','0','5','7','1'),(72,'1','0','7','4','1'),(73,'0','0','9','3','2'),(74,'1','0','6','7','1'),(75,'0','0','5','4','1'),(76,'0','0','8','2','2'),(77,'0','0','8','3','2'),(78,'0','0','7','5','2'),(79,'1','0','7','6','1'),(80,'1','0','7','5','1'),(81,'0','0','5','1','1'),(82,'1','0','3','5','1'),(83,'1','0','8','4','1'),(84,'0','0','7','3','2'),(85,'1','1','5','6','1'),(86,'1','1','5','6','1'),(87,'1','0','7','4','1'),(88,'0','0','6','1','2'),(89,'0','0','8','2','2'),(90,'1','0','6','7','1'),(91,'1','0','5','3','1'),(92,'1','0','7','6','1'),(93,'1','0','6','7','1'),(94,'1','0','6','5','1'),(95,'0','0','4','3','1'),(96,'1','0','2','5','1'),(97,'1','0','7','5','1'),(98,'0','0','6','2','2'),(99,'1','0','4','3','1'),(100,'0','0','8','3','2'),(101,'1','0','6','7','1'),(102,'1','0','1','3','1'),(103,'1','0','7','5','1'),(104,'1','0','6','7','1'),(105,'1','0','6','2','1'),(106,'1','0','6','5','1'),(107,'1','0','2','5','1'),(108,'1','0','6','5','1'),(109,'1','0','4','7','1'),(110,'0','0','5','3','2'),(111,'0','0','6','2','2'),(112,'1','0','7','4','1'),(113,'0','0','7','2','2'),(114,'0','0','8','3','2'),(115,'0','0','8','3','1'),(116,'0','0','7','2','2'),(117,'0','0','5','4','1'),(118,'1','0','6','8','1'),(119,'0','0','5','4','2'),(120,'0','0','8','2','2'),(121,'1','0','3','5','1'),(122,'1','0','6','6','1'),(123,'0','0','8','5','2'),(124,'0','0','6','2','2'),(125,'1','0','7','6','1'),(126,'1','0','3','2','1'),(127,'0','0','4','4','1'),(128,'1','0','5','4','1'),(129,'0','0','6','1','2'),(130,'0','0','8','2','2'),(131,'0','0','6','3','2'),(132,'0','0','7','2','2'),(133,'1','0','7','9','2'),(134,'1','0','5','6','1'),(135,'0','0','6','3','2'),(136,'1','0','6','5','1'),(137,'1','0','4','5','1'),(138,'0','0','8','2','2'),(139,'0','0','8','3','2'),(140,'0','0','6','3','1'),(141,'0','0','7','3','2'),(142,'1','0','7','8','2'),(143,'0','0','8','3','2'),(144,'0','0','7','3','2'),(145,'0','0','7','3','1'),(146,'0','0','8','3','1'),(147,'0','0','8','2','2'),(148,'1','0','4','4','1'),(149,'1','0','2','2','1'),(150,'0','0','8','0','2'),(151,'0','0','7','2','1'),(152,'1','0','4','5','1'),(153,'1','0','8','4','1'),(154,'0','0','7','2','2'),(155,'0','0','6','2','2'),(156,'0','0','8','2','2'),(157,'1','0','6','5','1'),(158,'1','0','7','3','1'),(159,'1','0','6','5','1'),(160,'0','0','6','3','2'),(161,'1','0','4','7','1'),(162,'0','0','3','3','1'),(166,'1','0','6','5','1'),(167,'1','0','4','5','1'),(168,'0','0','8','2','2'),(169,'0','0','4','1','1'),(170,'1','0','5','3','1'),(171,'0','0','3','3','1'),(172,'0','0','7','2','1'),(173,'0','0','4','4','1'),(174,'1','0','4','5','1'),(175,'1','0','6','9','2'),(176,'0','0','7','3','1'),(177,'1','0','3','2','1'),(178,'0','0','7','2','1'),(179,'0','0','5','3','2'),(180,'1','0','4','7','1'),(181,'0','0','9','0','2'),(182,'0','0','7','2','2'),(183,'1','0','4','5','1'),(184,'1','0','5','5','1'),(185,'0','0','5','2','2'),(186,'0','0','9','2','2'),(187,'1','0','7','6','1'),(188,'1','0','8','4','2');
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/*!40000 ALTER TABLE `Mole` ENABLE KEYS */;
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UNLOCK TABLES;
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/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
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/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
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/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */;
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/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */;
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/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
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/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
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/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
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/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
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-- Dump completed on 2013-08-29 15:44:12

‎testsql/Mutagenesis_std_bond.sql

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