annotation.processing.enabled=true
annotation.processing.enabled.in.editor=false
annotation.processing.run.all.processors=true
application.desc=JFITOM is a computer program written in Java for the detection of binding sites in DNA or RNA sequences. It implements several methods described in the literature to compute an approximation of binding affinity for a particular site based on a collection of binding sequences provided by the user. Using this method, FITOM scans a sequence file looking for putative binding sites across the DNA/RNA sequence in both strands, and filters the results according to a user-specified threshold. If sequence annotation is provided in the sequence file, FITOM will also link the identified sites with annotated genes and it will infer their role from their location in the vicinity of genes.
application.homepage=http://userpages.umbc.edu/~erill/7399/
application.splash=C:\\Documents and Settings\\Shehab\\My Documents\\My Pictures\\erilllabsplash.JPG
application.title=JFitom - Alpha
application.vendor=The Erill Lab, University of Maryland, Baltimore County
build.classes.dir=${build.dir}/classes
build.classes.excludes=**/*.java,**/*.form
# This directory is removed when the project is cleaned:
build.dir=build
build.generated.dir=${build.dir}/generated
build.generated.sources.dir=${build.dir}/generated-sources
# Only compile against the classpath explicitly listed here:
build.sysclasspath=ignore
build.test.classes.dir=${build.dir}/test/classes
build.test.results.dir=${build.dir}/test/results
debug.classpath=\
    ${run.classpath}
debug.test.classpath=\
    ${run.test.classpath}
# This directory is removed when the project is cleaned:
dist.dir=dist
dist.jar=${dist.dir}/GUI.jar
dist.javadoc.dir=${dist.dir}/javadoc
endorsed.classpath=
excludes=
file.reference.biojava.jar=C:\\Documents and Settings\\Shehab\\My Documents\\softwares\\combio\\biojava\\biojava.jar
file.reference.bytecode.jar=C:\\Documents and Settings\\Shehab\\My Documents\\softwares\\combio\\biojava\\bytecode.jar
file.reference.commons-cli.jar=C:\\Documents and Settings\\Shehab\\My Documents\\softwares\\combio\\biojava\\commons-cli.jar
file.reference.commons-collections-2.1.jar=C:\\Documents and Settings\\Shehab\\My Documents\\softwares\\combio\\biojava\\commons-collections-2.1.jar
file.reference.commons-dbcp-1.1.jar=C:\\Documents and Settings\\Shehab\\My Documents\\softwares\\combio\\biojava\\commons-dbcp-1.1.jar
file.reference.commons-pool-1.1.jar=C:\\Documents and Settings\\Shehab\\My Documents\\softwares\\combio\\biojava\\commons-pool-1.1.jar
file.reference.jfitom.jar=C:\\Documents and Settings\\Shehab\\My Documents\\softwares\\combio\\development\\workspace\\jFITOM\\output\\jfitom.jar
file.reference.jgrapht-jdk1.5.jar=C:\\Documents and Settings\\Shehab\\My Documents\\softwares\\combio\\biojava\\jgrapht-jdk1.5.jar
file.reference.log4j-1.2.16.jar=C:\\Documents and Settings\\Shehab\\My Documents\\softwares\\utils\\log4j\\apache-log4j-1.2.16\\log4j-1.2.16.jar
includes=**
jar.archive.disabled=${jnlp.enabled}
jar.compress=false
jar.index=${jnlp.enabled}
javac.classpath=\
    ${libs.swing-app-framework.classpath}:\
    ${file.reference.biojava.jar}:\
    ${file.reference.bytecode.jar}:\
    ${file.reference.commons-cli.jar}:\
    ${file.reference.commons-collections-2.1.jar}:\
    ${file.reference.commons-dbcp-1.1.jar}:\
    ${file.reference.commons-pool-1.1.jar}:\
    ${file.reference.jgrapht-jdk1.5.jar}:\
    ${file.reference.log4j-1.2.16.jar}:\
    ${file.reference.jfitom.jar}
# Space-separated list of extra javac options
javac.compilerargs=
javac.deprecation=false
javac.processorpath=\
    ${javac.classpath}:\
    ${file.reference.biojava.jar}:\
    ${file.reference.jfitom.jar}:\
    ${file.reference.bytecode.jar}:\
    ${file.reference.commons-cli.jar}:\
    ${file.reference.commons-collections-2.1.jar}:\
    ${file.reference.commons-dbcp-1.1.jar}:\
    ${file.reference.commons-pool-1.1.jar}:\
    ${file.reference.jgrapht-jdk1.5.jar}:\
    ${file.reference.log4j-1.2.16.jar}
javac.source=1.5
javac.target=1.5
javac.test.classpath=\
    ${javac.classpath}:\
    ${build.classes.dir}:\
    ${libs.junit.classpath}:\
    ${libs.junit_4.classpath}
javadoc.additionalparam=
javadoc.author=false
javadoc.encoding=${source.encoding}
javadoc.noindex=false
javadoc.nonavbar=false
javadoc.notree=false
javadoc.private=false
javadoc.splitindex=true
javadoc.use=true
javadoc.version=false
javadoc.windowtitle=
jnlp.codebase.type=no.codebase
jnlp.descriptor=application
jnlp.enabled=false
jnlp.mixed.code=defaut
jnlp.offline-allowed=false
jnlp.signed=false
main.class=edu.umbc.combio.erilllab.jfitom.gui.Main
manifest.file=manifest.mf
meta.inf.dir=${src.dir}/META-INF
platform.active=default_platform
run.classpath=\
    ${javac.classpath}:\
    ${build.classes.dir}:\
    ${file.reference.biojava.jar}:\
    ${file.reference.bytecode.jar}:\
    ${file.reference.commons-cli.jar}:\
    ${file.reference.commons-collections-2.1.jar}:\
    ${file.reference.commons-dbcp-1.1.jar}:\
    ${file.reference.commons-pool-1.1.jar}:\
    ${file.reference.jgrapht-jdk1.5.jar}:\
    ${file.reference.log4j-1.2.16.jar}
# Space-separated list of JVM arguments used when running the project
# (you may also define separate properties like run-sys-prop.name=value instead of -Dname=value
# or test-sys-prop.name=value to set system properties for unit tests):
run.jvmargs=
run.test.classpath=\
    ${javac.test.classpath}:\
    ${build.test.classes.dir}
source.encoding=UTF-8
src.dir=src
test.src.dir=test
