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Alvin
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.gitignore

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/nbproject/private/
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/build/

PMID-9619918.a1

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T1 Protein 0 4 IL-2
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T2 Protein 101 120 IL-2 receptor alpha
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T3 Protein 149 162 interleukin-2
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T4 Protein 164 168 IL-2
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T5 Protein 287 320 IL-2 receptor (IL-2R) alpha chain
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T6 Protein 584 594 IL-2Ralpha
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T7 Protein 599 603 beta
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T8 Protein 677 687 IL-2Ralpha
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T9 Protein 726 730 IL-2
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T10 Protein 772 776 IL-2
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T11 Protein 799 803 IL-2
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T12 Protein 907 911 IL-2
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T13 Protein 1031 1035 IL-2
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T14 Protein 1103 1108 c-Rel
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T15 Protein 1113 1117 KBF1
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T16 Protein 1134 1138 IL-2
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T17 Protein 1174 1178 IL-2
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T18 Protein 1336 1340 IL-2

PMID-9619918.a2

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* Equiv T4 T3
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T19 Gene_expression 121 131 expression
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T20 Binding 138 145 binding
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T21 Positive_regulation 204 211 induces
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T22 Positive_regulation 269 279 activation
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T23 Gene_expression 574 583 expressed
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T24 Positive_regulation 665 673 increase
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T25 Gene_expression 688 698 expression
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T26 Transcription 765 771 detect
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T27 Positive_regulation 1036 1045 increased
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T28 Transcription 1050 1068 abundance of mRNAs
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T29 Binding 1139 1146 binding
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E1 Gene_expression:T19 Theme:T2
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E2 Binding:T20 Theme:T4
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E3 Positive_regulation:T21 Theme:E4 Cause:E2
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E4 Positive_regulation:T22 Theme:T5
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E5 Gene_expression:T23 Theme:T7
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E6 Gene_expression:T23 Theme:T6
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E7 Positive_regulation:T24 Theme:E8 Cause:T9
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E8 Gene_expression:T25 Theme:T8
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E9 Transcription:T26 Theme:T10
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E10 Positive_regulation:T27 Theme:E13 Cause:T13
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E11 Positive_regulation:T27 Theme:E12 Cause:T13
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E12 Transcription:T28 Theme:T14
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E13 Transcription:T28 Theme:T15
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E14 Binding:T29 Theme:T16
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M1 Negation E9
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M2 Speculation E14

README.md

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This file was deleted.

build.xml

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<?xml version="1.0" encoding="UTF-8"?>
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<!-- You may freely edit this file. See commented blocks below for -->
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<!-- some examples of how to customize the build. -->
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<!-- (If you delete it and reopen the project it will be recreated.) -->
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<!-- By default, only the Clean and Build commands use this build script. -->
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<!-- Commands such as Run, Debug, and Test only use this build script if -->
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<!-- the Compile on Save feature is turned off for the project. -->
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<!-- You can turn off the Compile on Save (or Deploy on Save) setting -->
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<!-- in the project's Project Properties dialog box.-->
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<project name="AnnotationParser" default="default" basedir=".">
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<description>Builds, tests, and runs the project AnnotationParser.</description>
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<import file="nbproject/build-impl.xml"/>
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<!--
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There exist several targets which are by default empty and which can be
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used for execution of your tasks. These targets are usually executed
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before and after some main targets. They are:
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-pre-init: called before initialization of project properties
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-post-init: called after initialization of project properties
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-pre-compile: called before javac compilation
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-post-compile: called after javac compilation
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-pre-compile-single: called before javac compilation of single file
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-post-compile-single: called after javac compilation of single file
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-pre-compile-test: called before javac compilation of JUnit tests
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-post-compile-test: called after javac compilation of JUnit tests
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-pre-compile-test-single: called before javac compilation of single JUnit test
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-post-compile-test-single: called after javac compilation of single JUunit test
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-pre-jar: called before JAR building
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-post-jar: called after JAR building
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-post-clean: called after cleaning build products
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(Targets beginning with '-' are not intended to be called on their own.)
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Example of inserting an obfuscator after compilation could look like this:
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<target name="-post-compile">
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<obfuscate>
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<fileset dir="${build.classes.dir}"/>
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</obfuscate>
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</target>
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For list of available properties check the imported
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nbproject/build-impl.xml file.
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Another way to customize the build is by overriding existing main targets.
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The targets of interest are:
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-init-macrodef-javac: defines macro for javac compilation
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-init-macrodef-junit: defines macro for junit execution
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-init-macrodef-debug: defines macro for class debugging
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-init-macrodef-java: defines macro for class execution
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-do-jar-with-manifest: JAR building (if you are using a manifest)
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-do-jar-without-manifest: JAR building (if you are not using a manifest)
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run: execution of project
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-javadoc-build: Javadoc generation
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test-report: JUnit report generation
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An example of overriding the target for project execution could look like this:
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<target name="run" depends="AnnotationParser-impl.jar">
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<exec dir="bin" executable="launcher.exe">
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<arg file="${dist.jar}"/>
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</exec>
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</target>
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Notice that the overridden target depends on the jar target and not only on
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the compile target as the regular run target does. Again, for a list of available
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properties which you can use, check the target you are overriding in the
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nbproject/build-impl.xml file.
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-->
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</project>

manifest.mf

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Manifest-Version: 1.0
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X-COMMENT: Main-Class will be added automatically by build
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