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mycoSORT: user friendly updated version
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Marie-Jean Meurs
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May 29, 2015
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| # Project source # | ||
| ################### | ||
| *.project | ||
| *.classpath | ||
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| # Package Files # | ||
| ################# | ||
| *.jar |
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| % Weka training file - HIV triage - 2015 | ||
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| @RELATION triage | ||
| @ATTRIBUTE docID REAL %PMID of paper | ||
| @ATTRIBUTE Ngram0trees REAL %trees | ||
| @ATTRIBUTE Ngram1model REAL %model | ||
| @ATTRIBUTE Ngram2triage REAL %triage | ||
| @ATTRIBUTE Ngram3genes REAL %genes | ||
| @ATTRIBUTE Ngram4sampling REAL %sampling | ||
| @ATTRIBUTE Ngram5classification REAL %classification | ||
| @ATTRIBUTE Ngram6processing REAL %processing | ||
| @ATTRIBUTE Ngram7fungal REAL %fungal | ||
| @ATTRIBUTE Ngram8enzymes REAL %enzymes | ||
| @ATTRIBUTE Ngram9manual REAL %manual | ||
| @ATTRIBUTE Ngram10literature REAL %literature | ||
| @ATTRIBUTE Ngram11annotation REAL %annotation | ||
| @ATTRIBUTE Ngram12mycoclapfungalgenomicsca REAL %mycoclapfungalgenomicsca | ||
| @ATTRIBUTE Ngram13machine REAL %machine | ||
| @ATTRIBUTE Ngram14first REAL %first | ||
| @ATTRIBUTE Ngram15features REAL %features | ||
| @ATTRIBUTE Ngram16mycoclap REAL %mycoclap | ||
| @ATTRIBUTE Ngram17results REAL %results | ||
| @ATTRIBUTE Ngram18abstracttext REAL %abstracttext | ||
| @ATTRIBUTE Ngram19task REAL %task | ||
| @ATTRIBUTE Ngram20http REAL %http | ||
| @ATTRIBUTE Ngram21support REAL %support | ||
| @ATTRIBUTE Ngram22learning REAL %learning | ||
| @ATTRIBUTE Ngram23database REAL %database | ||
| @ATTRIBUTE Ngram24curation REAL %curation | ||
| @ATTRIBUTE Ngram25logistic REAL %logistic | ||
| @ATTRIBUTE Ngram26applications REAL %applications | ||
| @ATTRIBUTE Ngram27articletitle REAL %articletitle | ||
| @ATTRIBUTE class {positive, negative} | ||
| @DATA | ||
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| 25754864,0,0,0,2,0,0,2,5,3,1,1,2,2,0,1,0,6,1,0,0,2,2,0,4,2,0,2,0,negative | ||
| 25551575,2,4,3,0,2,2,0,0,0,1,2,0,0,4,1,2,0,1,0,2,0,2,3,0,1,2,0,0,negative | ||
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| Original file line number | Diff line number | Diff line change |
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| % Weka test file - HIV triage - 2015 | ||
|
|
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| @RELATION triage | ||
| @ATTRIBUTE docID REAL %PMID of paper | ||
| @ATTRIBUTE Ngram0trees REAL %trees | ||
| @ATTRIBUTE Ngram1model REAL %model | ||
| @ATTRIBUTE Ngram2triage REAL %triage | ||
| @ATTRIBUTE Ngram3genes REAL %genes | ||
| @ATTRIBUTE Ngram4sampling REAL %sampling | ||
| @ATTRIBUTE Ngram5classification REAL %classification | ||
| @ATTRIBUTE Ngram6processing REAL %processing | ||
| @ATTRIBUTE Ngram7fungal REAL %fungal | ||
| @ATTRIBUTE Ngram8enzymes REAL %enzymes | ||
| @ATTRIBUTE Ngram9manual REAL %manual | ||
| @ATTRIBUTE Ngram10literature REAL %literature | ||
| @ATTRIBUTE Ngram11annotation REAL %annotation | ||
| @ATTRIBUTE Ngram12mycoclapfungalgenomicsca REAL %mycoclapfungalgenomicsca | ||
| @ATTRIBUTE Ngram13machine REAL %machine | ||
| @ATTRIBUTE Ngram14first REAL %first | ||
| @ATTRIBUTE Ngram15features REAL %features | ||
| @ATTRIBUTE Ngram16mycoclap REAL %mycoclap | ||
| @ATTRIBUTE Ngram17results REAL %results | ||
| @ATTRIBUTE Ngram18abstracttext REAL %abstracttext | ||
| @ATTRIBUTE Ngram19task REAL %task | ||
| @ATTRIBUTE Ngram20http REAL %http | ||
| @ATTRIBUTE Ngram21support REAL %support | ||
| @ATTRIBUTE Ngram22learning REAL %learning | ||
| @ATTRIBUTE Ngram23database REAL %database | ||
| @ATTRIBUTE Ngram24curation REAL %curation | ||
| @ATTRIBUTE Ngram25logistic REAL %logistic | ||
| @ATTRIBUTE Ngram26applications REAL %applications | ||
| @ATTRIBUTE Ngram27articletitle REAL %articletitle | ||
| @ATTRIBUTE class {positive, negative} | ||
| @DATA | ||
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| 25754864,0,0,0,2,0,0,2,5,3,1,1,2,2,0,1,0,6,1,0,0,2,2,0,4,2,0,2,0,negative | ||
| 25551575,2,4,3,0,2,2,0,0,0,1,2,0,0,4,1,2,0,1,0,2,0,2,3,0,1,2,0,0,negative | ||
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <project name="mycoSORTtriage.makejar" basedir="." default="makejar"> | ||
| <path id="build.classpath"> | ||
| <fileset dir="jars"> | ||
| <include name="*.jar"/> | ||
| </fileset> | ||
| </path> | ||
| <manifestclasspath property="jar.classpath" jarfile="executables/*.jar"> | ||
| <classpath refid="build.classpath"/> | ||
| </manifestclasspath> | ||
| <target name="clean"> | ||
| <delete dir="bin" /> | ||
| <mkdir dir="bin" /> | ||
| </target> | ||
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| <target name="copy"> | ||
| <copy todir="bin" includeemptydirs="false"> | ||
| <fileset dir="." includes="*.cfg, *.txt" /> | ||
| </copy> | ||
| </target> | ||
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| <target name="compile" depends="clean,copy"> | ||
| <javac srcdir="src" destdir="bin" debug="true" | ||
| includes="analyse/**, arffmatrix/**, | ||
| arffvector/**, classifier/**, | ||
| configure/**, filter/**, preprocessing/**" | ||
| classpathref="build.classpath" | ||
| /> | ||
| </target> | ||
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| <target name ="makejar" depends="compile" description="Create jars for the mycoSORT Triage project."> | ||
| <jar destfile="executables/CorpusHandler.jar"> | ||
| <fileset dir="bin/"> | ||
| <include name="preprocessing/CorpusHandler*.class"/> | ||
| <include name="configure/ConfigConstants.class"/> | ||
| <include name="config.cfg"/> | ||
| </fileset> | ||
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| <manifest> | ||
| <attribute name="Main-Class" value="preprocessing.CorpusHandler"/> | ||
| <attribute name="Class-Path" value="${jar.classpath}"/> | ||
| </manifest> | ||
| </jar> | ||
| <jar destfile="executables/SampleCorpus.jar"> | ||
| <fileset dir="bin/"> | ||
| <include name="preprocessing/SampleCorpus*.class"/> | ||
| <include name="configure/ConfigConstants.class"/> | ||
| <include name="config.cfg"/> | ||
| </fileset> | ||
| <manifest> | ||
| <attribute name="Main-Class" value="preprocessing.SampleCorpus"/> | ||
| <attribute name="Class-Path" value="${jar.classpath}"/> | ||
| </manifest> | ||
| </jar> | ||
| <jar destfile="executables/NgramExtractor.jar"> | ||
| <fileset dir="bin/"> | ||
| <include name="analyse/Extractor.class"/> | ||
| <include name="analyse/NgramExtractor.class"/> | ||
| <include name="filter/NaiveFilter.class"/> | ||
| <include name="configure/ConfigConstants.class"/> | ||
| <include name="config.cfg"/> | ||
| <include name="stopList.txt"/> | ||
| </fileset> | ||
| <manifest> | ||
| <attribute name="Main-Class" value="analyse.NgramExtractor"/> | ||
| <attribute name="Class-Path" value="${jar.classpath}"/> | ||
| </manifest> | ||
| </jar> | ||
| <jar destfile="executables/FeatureExtractor.jar"> | ||
| <fileset dir="bin/"> | ||
| <include name="analyse/Extractor.class"/> | ||
| <include name="analyse/FeatureExtractor.class"/> | ||
| <include name="filter/NaiveFilter.class"/> | ||
| <include name="configure/ConfigConstants.class"/> | ||
| <include name="config.cfg"/> | ||
| <include name="stopList.txt"/> | ||
| </fileset> | ||
| <manifest> | ||
| <attribute name="Main-Class" value="analyse.FeatureExtractor"/> | ||
| <attribute name="Class-Path" value="${jar.classpath}"/> | ||
| </manifest> | ||
| </jar> | ||
| <jar destfile="executables/BuildModel.jar"> | ||
| <fileset dir="bin/"> | ||
| <include name="arffmatrix/BuildModel.class"/> | ||
| <include name="arffvector/CreateVector.class"/> | ||
| <include name="analyse/Extractor.class"/> | ||
| <include name="configure/ConfigConstants.class"/> | ||
| <include name="config.cfg"/> | ||
| </fileset> | ||
| <manifest> | ||
| <attribute name="Main-Class" value="arffmatrix.BuildModel"/> | ||
| <attribute name="Class-Path" value="${jar.classpath}"/> | ||
| </manifest> | ||
| </jar> | ||
| <jar destfile="executables/Trainer.jar"> | ||
| <fileset dir="bin/"> | ||
| <include name="classifier/Trainer.class"/> | ||
| <include name="filter/InformedFilter.class"/> | ||
| <include name="configure/ConfigConstants.class"/> | ||
| <include name="config.cfg"/> | ||
| </fileset> | ||
| <manifest> | ||
| <attribute name="Main-Class" value="classifier.Trainer"/> | ||
| <attribute name="Class-Path" value="${jar.classpath}"/> | ||
| </manifest> | ||
| </jar> | ||
| </target> | ||
| <target name="corpus-handler"> | ||
| <java fork="true" classname="preprocessing/CorpusHandler"> | ||
| <classpath> | ||
| <path location="executables/CorpusHandler.jar"/> | ||
| </classpath> | ||
| <arg value="${options}"/> | ||
| </java> | ||
| </target> | ||
| <target name="sample-corpus"> | ||
| <java fork="true" classname="preprocessing/SampleCorpus"> | ||
| <classpath> | ||
| <path location="executables/SampleCorpus.jar"/> | ||
| </classpath> | ||
| </java> | ||
| </target> | ||
| <target name="ngram-extractor"> | ||
| <java fork="true" classname="analyse/NgramExtractor"> | ||
| <classpath> | ||
| <path location="executables/NgramExtractor.jar"/> | ||
| </classpath> | ||
| </java> | ||
| </target> | ||
| <target name="annotation-extractor"> | ||
| <java fork="true" classname="analyse/FeatureExtractor"> | ||
| <classpath> | ||
| <path location="executables/FeatureExtractor.jar"/> | ||
| </classpath> | ||
| </java> | ||
| </target> | ||
| <target name="build-model"> | ||
| <java fork="true" classname="arffmatrix/BuildModel"> | ||
| <classpath> | ||
| <path location="executables/BuildModel.jar"/> | ||
| </classpath> | ||
| </java> | ||
| </target> | ||
| <target name="trainer"> | ||
| <java fork="true" classname="classifier/Trainer"> | ||
| <classpath> | ||
| <path location="executables/Trainer.jar"/> | ||
| </classpath> | ||
| <arg value="${classifier}"/> | ||
| </java> | ||
| </target> | ||
| </project> |
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