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Move Goby to org.campagnelab.goby package.
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Former-commit-id: e8c8f311e9dcca5768e00918dd8cadebb4d1705a
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@fac2003
fac2003 committed Aug 28, 2016
1 parent 96837e2 commit e6e083a
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2 changes: 1 addition & 1 deletion CHANGES.txt
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Expand Up @@ -839,7 +839,7 @@
Goby 1.4 (CAC, normalize by the number of alignment record in a sample)
See the --normalization-methods argument. New normalization methods
can be used with Goby by creating an implementation of the
edu.cornell.med.icb.goby.stats.NormalizationMethod interface,
NormalizationMethod interface,
and adding a jar on the classpath that defines a ServiceProvider
(see build.xml goby-jar target for an example of how this is done).
When several normalization methods are given as an argument
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160 changes: 80 additions & 80 deletions build.xml
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Expand Up @@ -54,15 +54,15 @@

<fileset dir="${src}" id="pmd-fileset">
<include name="**/*.java"/>
<exclude name="edu/cornell/med/icb/goby/alignments/Alignments.java"/>
<exclude name="edu/cornell/med/icb/goby/reads/Reads.java"/>
<exclude name="org/campagnelab/goby/alignments/Alignments.java"/>
<exclude name="org/campagnelab/goby/reads/Reads.java"/>
</fileset>

<fileset dir="${src}" id="checkstyle-fileset">
<include name="**/*.java"/>
<exclude name="**/package-info.java"/>
<exclude name="edu/cornell/med/icb/goby/alignments/Alignments.java"/>
<exclude name="edu/cornell/med/icb/goby/reads/Reads.java"/>
<exclude name="org/campagnelab/goby/alignments/Alignments.java"/>
<exclude name="org/campagnelab/goby/reads/Reads.java"/>
</fileset>

<target name="init" depends="buildsupport.init, testsupport.init"/>
Expand Down Expand Up @@ -182,26 +182,26 @@
<attribute name="Implementation-Version" value="${label} (${buildstamp})"/>
<attribute name="Implementation-Vendor"
value="Institute for Computational Biomedicine (ICB), Weill Medical College of Cornell University"/>
<attribute name="Main-Class" value="edu.cornell.med.icb.goby.modes.GobyDriver"/>
<attribute name="Main-Class" value="org.campagnelab.goby.modes.GobyDriver"/>
<attribute name="Built-By" value="${user.name}"/>
</manifest>

<service type="edu.cornell.med.icb.goby.reads.ReadCodec">
<provider classname="edu.cornell.med.icb.goby.reads.ReadCodecImpl"/>
<provider classname="edu.cornell.med.icb.goby.reads.ReadCodec2"/>
<service type="org.campagnelab.goby.reads.ReadCodec">
<provider classname="org.campagnelab.goby.reads.ReadCodecImpl"/>
<provider classname="org.campagnelab.goby.reads.ReadCodec2"/>
</service>
<service type="edu.cornell.med.icb.goby.compression.ChunkCodec">
<provider classname="edu.cornell.med.icb.goby.compression.NullChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.NotCompressedChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.GZipChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.BZip2ChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.HybridChunkCodec1"/>
<provider classname="edu.cornell.med.icb.goby.compression.HybridChunkCodec2"/>
<service type="org.campagnelab.goby.compression.ChunkCodec">
<provider classname="org.campagnelab.goby.compression.NullChunkCodec"/>
<provider classname="org.campagnelab.goby.compression.NotCompressedChunkCodec"/>
<provider classname="org.campagnelab.goby.compression.GZipChunkCodec"/>
<provider classname="org.campagnelab.goby.compression.BZip2ChunkCodec"/>
<provider classname="org.campagnelab.goby.compression.HybridChunkCodec1"/>
<provider classname="org.campagnelab.goby.compression.HybridChunkCodec2"/>
</service>
<!-- define the implementation of NormalizationMethods as Java ServiceProviders: -->
<service type="edu.cornell.med.icb.goby.stats.NormalizationMethod">
<provider classname="edu.cornell.med.icb.goby.stats.BullardUpperQuartileNormalization"/>
<provider classname="edu.cornell.med.icb.goby.stats.AlignedCountNormalization"/>
<service type="org.campagnelab.goby.stats.NormalizationMethod">
<provider classname="org.campagnelab.goby.stats.BullardUpperQuartileNormalization"/>
<provider classname="org.campagnelab.goby.stats.AlignedCountNormalization"/>
</service>
</jar>
<!-- Set executable permissions on the goby wrapper scrip -->
Expand All @@ -224,9 +224,9 @@
<attribute name="Built-By" value="${user.name}"/>
</manifest>
<!-- define the implementation of NormalizationMethods as Java ServiceProviders: -->
<service type="edu.cornell.med.icb.goby.stats.NormalizationMethod">
<provider classname="edu.cornell.med.icb.goby.stats.BullardUpperQuartileNormalization"/>
<provider classname="edu.cornell.med.icb.goby.stats.AlignedCountNormalization"/>
<service type="org.campagnelab.goby.stats.NormalizationMethod">
<provider classname="org.campagnelab.goby.stats.BullardUpperQuartileNormalization"/>
<provider classname="org.campagnelab.goby.stats.AlignedCountNormalization"/>
</service>
</jar>
</target>
Expand All @@ -243,22 +243,22 @@
<attribute name="Built-By" value="${user.name}"/>
</manifest>
<!-- define the implementation of NormalizationMethods as Java ServiceProviders: -->
<service type="edu.cornell.med.icb.goby.stats.NormalizationMethod">
<provider classname="edu.cornell.med.icb.goby.stats.BullardUpperQuartileNormalization"/>
<provider classname="edu.cornell.med.icb.goby.stats.AlignedCountNormalization"/>
<service type="org.campagnelab.goby.stats.NormalizationMethod">
<provider classname="org.campagnelab.goby.stats.BullardUpperQuartileNormalization"/>
<provider classname="org.campagnelab.goby.stats.AlignedCountNormalization"/>
</service>

<service type="edu.cornell.med.icb.goby.reads.ReadCodec">
<provider classname="edu.cornell.med.icb.goby.reads.ReadCodecImpl"/>
<provider classname="edu.cornell.med.icb.goby.reads.ReadCodec2"/>
<service type="org.campagnelab.goby.reads.ReadCodec">
<provider classname="org.campagnelab.goby.reads.ReadCodecImpl"/>
<provider classname="org.campagnelab.goby.reads.ReadCodec2"/>
</service>
<service type="edu.cornell.med.icb.goby.compression.ChunkCodec">
<provider classname="edu.cornell.med.icb.goby.compression.NullChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.NotCompressedChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.GZipChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.BZip2ChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.HybridChunkCodec1"/>
<provider classname="edu.cornell.med.icb.goby.compression.HybridChunkCodec2"/>
<service type="org.campagnelab.goby.compression.ChunkCodec">
<provider classname="org.campagnelab.goby.compression.NullChunkCodec"/>
<provider classname="org.campagnelab.goby.compression.NotCompressedChunkCodec"/>
<provider classname="org.campagnelab.goby.compression.GZipChunkCodec"/>
<provider classname="org.campagnelab.goby.compression.BZip2ChunkCodec"/>
<provider classname="org.campagnelab.goby.compression.HybridChunkCodec1"/>
<provider classname="org.campagnelab.goby.compression.HybridChunkCodec2"/>
</service>

</jar>
Expand All @@ -268,23 +268,23 @@
<!-- Standalone jar file. -->
<jar jarfile="${goby-io-jarfile}">
<fileset dir="${classes}">
<include name="edu/cornell/med/icb/goby/algorithmic/compression/**"/>
<include name="edu/cornell/med/icb/goby/compression/**"/>
<include name="edu/cornell/med/icb/goby/reads/**"/>
<include name="edu/cornell/med/icb/goby/readers/**"/>
<include name="edu/cornell/med/icb/goby/alignments/**"/>
<include name="edu/cornell/med/icb/goby/baseinfo/**"/>
<include name="edu/cornell/med/icb/goby/counts/**"/>
<include name="edu/cornell/med/icb/goby/modes/UpgradeMode*"/>
<include name="edu/cornell/med/icb/goby/modes/AbstractGobyMode*"/>
<include name="edu/cornell/med/icb/goby/modes/AbstractCommandLineMode*"/>
<include name="edu/cornell/med/icb/goby/modes/TabToColumnInfoMode*"/>
<include name="edu/cornell/med/icb/goby/modes/GenericToolsDriver*"/>
<include name="edu/cornell/med/icb/goby/util/**"/>
<include name="edu/cornell/med/icb/goby/exception/**"/>
<include name="edu/cornell/med/icb/goby/identifier/**"/>
<include name="edu/cornell/med/icb/goby/counts/**"/>
<include name="edu/cornell/med/icb/goby/GobyVersion*"/>
<include name="org/campagnelab/goby/algorithmic/compression/**"/>
<include name="org/campagnelab/goby/compression/**"/>
<include name="org/campagnelab/goby/reads/**"/>
<include name="org/campagnelab/goby/readers/**"/>
<include name="org/campagnelab/goby/alignments/**"/>
<include name="org/campagnelab/goby/baseinfo/**"/>
<include name="org/campagnelab/goby/counts/**"/>
<include name="org/campagnelab/goby/modes/UpgradeMode*"/>
<include name="org/campagnelab/goby/modes/AbstractGobyMode*"/>
<include name="org/campagnelab/goby/modes/AbstractCommandLineMode*"/>
<include name="org/campagnelab/goby/modes/TabToColumnInfoMode*"/>
<include name="org/campagnelab/goby/modes/GenericToolsDriver*"/>
<include name="org/campagnelab/goby/util/**"/>
<include name="org/campagnelab/goby/exception/**"/>
<include name="org/campagnelab/goby/identifier/**"/>
<include name="org/campagnelab/goby/counts/**"/>
<include name="org/campagnelab/goby/GobyVersion*"/>
</fileset>
<zipgroupfileset dir="${lib}">
<include name="bzip2.jar"/>
Expand Down Expand Up @@ -319,11 +319,11 @@
value="Institute for Computational Biomedicine (ICB), Weill Medical College of Cornell University"/>
<attribute name="Built-By" value="${user.name}"/>
</manifest>
<service type="edu.cornell.med.icb.goby.compression.ChunkCodec">
<provider classname="edu.cornell.med.icb.goby.compression.NullChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.GZipChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.BZip2ChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.HybridChunkCodec1"/>
<service type="org.campagnelab.goby.compression.ChunkCodec">
<provider classname="org.campagnelab.goby.compression.NullChunkCodec"/>
<provider classname="org.campagnelab.goby.compression.GZipChunkCodec"/>
<provider classname="org.campagnelab.goby.compression.BZip2ChunkCodec"/>
<provider classname="org.campagnelab.goby.compression.HybridChunkCodec1"/>
</service>
</jar>
<chmod file="scripts/autojar/run-autojar.sh" perm="744"/>
Expand All @@ -335,22 +335,22 @@
<jar jarfile="${goby-io-api-jarfile}">
<fileset dir="${classes}">

<include name="edu/cornell/med/icb/goby/compression/**"/>
<include name="edu/cornell/med/icb/goby/reads/**"/>
<include name="edu/cornell/med/icb/goby/readers/**"/>
<include name="edu/cornell/med/icb/goby/alignments/**"/>
<include name="edu/cornell/med/icb/goby/baseinfo/**"/>
<include name="edu/cornell/med/icb/goby/counts/**"/>
<include name="edu/cornell/med/icb/goby/modes/UpgradeMode*"/>
<include name="edu/cornell/med/icb/goby/modes/AbstractGobyMode*"/>
<include name="edu/cornell/med/icb/goby/modes/AbstractCommandLineMode*"/>
<include name="edu/cornell/med/icb/goby/modes/TabToColumnInfoMode*"/>
<include name="edu/cornell/med/icb/goby/modes/GenericToolsDriver*"/>
<include name="edu/cornell/med/icb/goby/util/**"/>
<include name="edu/cornell/med/icb/goby/exception/**"/>
<include name="edu/cornell/med/icb/goby/identifier/**"/>
<include name="edu/cornell/med/icb/goby/counts/**"/>
<include name="edu/cornell/med/icb/goby/GobyVersion*"/>
<include name="org/campagnelab/goby/compression/**"/>
<include name="org/campagnelab/goby/reads/**"/>
<include name="org/campagnelab/goby/readers/**"/>
<include name="org/campagnelab/goby/alignments/**"/>
<include name="org/campagnelab/goby/baseinfo/**"/>
<include name="org/campagnelab/goby/counts/**"/>
<include name="org/campagnelab/goby/modes/UpgradeMode*"/>
<include name="org/campagnelab/goby/modes/AbstractGobyMode*"/>
<include name="org/campagnelab/goby/modes/AbstractCommandLineMode*"/>
<include name="org/campagnelab/goby/modes/TabToColumnInfoMode*"/>
<include name="org/campagnelab/goby/modes/GenericToolsDriver*"/>
<include name="org/campagnelab/goby/util/**"/>
<include name="org/campagnelab/goby/exception/**"/>
<include name="org/campagnelab/goby/identifier/**"/>
<include name="org/campagnelab/goby/counts/**"/>
<include name="org/campagnelab/goby/GobyVersion*"/>
</fileset>
<manifest>
<attribute name="Specification-Title" value="Goby IO-API (LGPL compatible)"/>
Expand All @@ -361,15 +361,15 @@
value="Institute for Computational Biomedicine (ICB), Weill Medical College of Cornell University"/>
<attribute name="Built-By" value="${user.name}"/>
</manifest>
<service type="edu.cornell.med.icb.goby.alignments.AlignmentCodec">
<provider classname="edu.cornell.med.icb.goby.alignments.AlignmentCodecDummy"/>
<service type="org.campagnelab.goby.alignments.AlignmentCodec">
<provider classname="org.campagnelab.goby.alignments.AlignmentCodecDummy"/>
</service>
<service type="edu.cornell.med.icb.goby.compression.ChunkCodec">
<provider classname="edu.cornell.med.icb.goby.compression.NullChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.NotCompressedChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.GZipChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.BZip2ChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.HybridChunkCodec1"/>
<service type="org.campagnelab.goby.compression.ChunkCodec">
<provider classname="org.campagnelab.goby.compression.NullChunkCodec"/>
<provider classname="org.campagnelab.goby.compression.NotCompressedChunkCodec"/>
<provider classname="org.campagnelab.goby.compression.GZipChunkCodec"/>
<provider classname="org.campagnelab.goby.compression.BZip2ChunkCodec"/>
<provider classname="org.campagnelab.goby.compression.HybridChunkCodec1"/>
</service>
</jar>
</target>
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2 changes: 1 addition & 1 deletion config/goby-sample.properties
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@@ -1,6 +1,6 @@
#
# Sample configuration for Goby. See
# edu.cornell.med.icb.goby.config.GobyConfiguration for
# GobyConfiguration for
# a list of configurable properties
#

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8 changes: 4 additions & 4 deletions config/log4j-sample.properties
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Expand Up @@ -2,10 +2,10 @@

################################################################
log4j.rootLogger=INFO, console
log4j.logger.edu.cornell.med.icb.goby.stats.EmpiricalPValueEstimator=INFO
log4j.logger.edu.cornell.med.icb.goby.stats.AnnotationAveragingWriter=INFO
log4j.logger.edu.cornell.med.icb.goby.alignments.SortIterateAlignments=DEBUG
log4j.logger.edu.cornell.med.icb.goby.modes.SortMode=DEBUG
log4j.logger.EmpiricalPValueEstimator=INFO
log4j.logger.AnnotationAveragingWriter=INFO
log4j.logger.SortIterateAlignments=DEBUG
log4j.logger.SortMode=DEBUG
log4j.logger.org.reflections=WARN

log4j.appender.CHAINSAW_CLIENT=org.apache.log4j.net.SocketAppender
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8 changes: 4 additions & 4 deletions config/log4j.properties
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Expand Up @@ -2,10 +2,10 @@

################################################################
log4j.rootLogger=INFO, console
log4j.logger.edu.cornell.med.icb.goby.stats.EmpiricalPValueEstimator=INFO
log4j.logger.edu.cornell.med.icb.goby.stats.AnnotationAveragingWriter=INFO
log4j.logger.edu.cornell.med.icb.goby.alignments.SortIterateAlignments=DEBUG
log4j.logger.edu.cornell.med.icb.goby.modes.SortMode=DEBUG
log4j.logger.EmpiricalPValueEstimator=INFO
log4j.logger.AnnotationAveragingWriter=INFO
log4j.logger.SortIterateAlignments=DEBUG
log4j.logger.SortMode=DEBUG
log4j.logger.org.reflections=WARN

log4j.appender.CHAINSAW_CLIENT=org.apache.log4j.net.SocketAppender
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8 changes: 4 additions & 4 deletions release.xml
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Expand Up @@ -110,10 +110,10 @@
<!-- Remove any files that should not be included in the formal release -->
<!-- NOTE: These files should probably be on a branch or something -->
<delete dir="${exportdir}/${tag}">
<include name="src/edu/cornell/med/icb/goby/algorithmic/data/AnnotationRPKM.java"/>
<include name="src/edu/cornell/med/icb/goby/modes/AggregatePeaks*"/>
<include name="src/edu/cornell/med/icb/goby/modes/AnnotationPenaltyMode*"/>
<include name="src/edu/cornell/med/icb/goby/modes/CountsArchiveToUnionPeaksAnnotationMode*"/>
<include name="src/org/campagnelab/goby/algorithmic/data/AnnotationRPKM.java"/>
<include name="src/org/campagnelab/goby/modes/AggregatePeaks*"/>
<include name="src/org/campagnelab/goby/modes/AnnotationPenaltyMode*"/>
<include name="src/org/campagnelab/goby/modes/CountsArchiveToUnionPeaksAnnotationMode*"/>
</delete>

<!-- Create a "version" file which contains the release number -->
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