BridgeDb-release_2.0.0.zip
bridgedb-BridgeDb-0750d1d
.gitignore
425 Bytes
LICENSE-2.0.txt
11.4 kB
README.md
2.2 kB
batchmapper.bat
52 Bytes
batchmapper.sh
121 Bytes
benchmarking
IDMapping_En_Test.txt
1.6 kB
IDMapping_Test.cys
17.1 kB
IDMapping_X_Test.txt
1.1 kB
META-INF
MANIFEST.MF
530 Bytes
U133A2-randomset.txt
11.0 kB
build.xml
701 Bytes
src
org
bridgedb
benchmarking
ComparisonScript.java
13.9 kB
Utils.java
849 Bytes
test
org
bridgedb
benchmarking
Base.java
5.6 kB
TestAll.java
4.4 kB
build-common.xml
4.9 kB
build.xml
4.5 kB
common-bundles
com.google.collect_1.0.0.v201105210816.jar
618.4 kB
commons-collections-3.2.1.jar
575.4 kB
javax.activation_1.1.0.v201105071233.jar
54.4 kB
contrib
.project
211 Bytes
README.txt
191 Bytes
src
de
ipk_gatersleben
Test.txt
25 Bytes
dbbuilder
META-INF
MANIFEST.MF
409 Bytes
build.xml
601 Bytes
r-scripts
annot2bridgedb.R
1.1 kB
ec2gene.R
826 Bytes
src
org
bridgedb
README
1.4 kB
build
LinkDatabases.pl
3.4 kB
README
1.8 kB
run.sh
326 Bytes
runALL.sh
439 Bytes
runList
1.1 kB
scripts
PathVisioDerby_BUILD.ij.template
148 Bytes
PathVisioDerby_CREATE.sql
1.1 kB
PathVisioDerby_INDEXES.sql
549 Bytes
PathVisioMySQL_BEEF.sql
721 Bytes
PathVisioMySQL_BUILD.sql.template
3.8 kB
buildPathVisio.sh
5.4 kB
replacePath.pl
509 Bytes
download
NathJohnson_API_patch.txt
1.3 kB
NathJohnson_DB_patch.sql
792 Bytes
ensembl_download.sh
5.6 kB
ensembl_download_release.sh
5.8 kB
genomes_download.sh
3.9 kB
species_list_ensembl
415 Bytes
species_list_genomes
420 Bytes
extract
ArrayList
2.8 kB
Build_ArrayList.pl
6.5 kB
Ensembl_ETL_Device_v18_local.pl
130.8 kB
HashArrayList.pm
950 Bytes
HashSpeciesList.pm
1.4 kB
SpeciesList
2.1 kB
util
Derby2MySQL.java
3.9 kB
hmdb
DownloadMetabocards.java
649 Bytes
Hmdb2Gdb.java
5.9 kB
ParseHmdb.java
5.5 kB
examples
pom.xml
3.1 kB
src
org
bridgedb
examples
ChebiPubchemExample.java
1.1 kB
CounterExampleWithoutBridgedb.java
2.7 kB
ExGuessing.java
1.1 kB
ExHello.java
1.4 kB
ExIDSearch.java
1.1 kB
ExampleWithBridgeDb.java
1.7 kB
PicrUniprotExample.java
1.4 kB
isOSGi.sh
161 Bytes
metric.sh
857 Bytes
org.bridgedb
.classpath
1.3 kB
.project
721 Bytes
META-INF
MANIFEST.MF
315 Bytes
build-lib
checkstyle-all-5.0.jar
1.8 MB
hamcrest-core.jar
19.2 kB
junit.jar
127.5 kB
junit4.jar
217.6 kB
measure.jar
1.4 kB
build.xml
1.1 kB
checks.xml
2.3 kB
pom.xml
1.5 kB
src
buildsystem
Measure.java
757 Bytes
org
bridgedb
AbstractIDMapper.java
1.3 kB
AbstractIDMapperCapabilities.java
2.8 kB
AttributeMapper.java
3.8 kB
BridgeDb.java
2.7 kB
DataSource.java
31.1 kB
DataSourcePatterns.java
2.4 kB
Driver.java
1.8 kB
IDMapper.java
3.7 kB
IDMapperCapabilities.java
2.5 kB
IDMapperException.java
1.7 kB
IDMapperStack.java
15.5 kB
Xref.java
5.2 kB
XrefIterator.java
387 Bytes
file
IDMapperFile.java
5.9 kB
IDMapperText.java
9.9 kB
IDMappingReader.java
1.5 kB
IDMappingReaderFromDelimitedReader.java
7.7 kB
IDMappingReaderFromText.java
6.1 kB
package.html
357 Bytes
impl
InternalUtils.java
11.7 kB
TransitiveGraph.java
11.8 kB
package.html
1.0 kB
webservice
IDMapperWebservice.java
864 Bytes
test
org
bridgedb
DataSourceRegisterTest.java
5.1 kB
DataSourceTest.java
6.4 kB
DataSourceUrnBaseTest.java
8.1 kB
IDMapperCapabilitiesTest.java
3.3 kB
IDMapperStackTest.java
4.2 kB
IDMapperTest.java
9.5 kB
IDMapperTestBase.java
5.9 kB
TestFile.java
4.2 kB
XrefIteratorTest.java
2.7 kB
XrefTest.java
2.8 kB
test-data
AB.csv
22 Bytes
BC.csv
22 Bytes
CD.csv
22 Bytes
DE.csv
22 Bytes
XY.csv
22 Bytes
XZ.csv
10 Bytes
YW.csv
16 Bytes
YZ.csv
16 Bytes
yeast_id_mapping.txt
525.6 kB
version.props
62 Bytes
org.bridgedb.bio
.classpath
1.2 kB
.project
545 Bytes
META-INF
MANIFEST.MF
210 Bytes
build.xml
782 Bytes
pom.xml
1.3 kB
resources
org
bridgedb
bio
datasources.txt
21.4 kB
datasources.xml
441 Bytes
organisms.txt
1.3 kB
src
org
bridgedb
bio
BioDataSource.java
22.2 kB
DataSourceComparator.java
2.1 kB
DataSourceTxt.java
6.5 kB
EnsemblCompatibilityMapper.java
4.9 kB
Organism.java
7.5 kB
package.html
146 Bytes
test
org
bridgedb
bio
BioDataSourceTest.java
7.2 kB
DataSourceTxtTest.java
2.4 kB
OrganismTest.java
3.0 kB
test-data
generatedDatasources.txt
0 Bytes
org.bridgedb.file.orthoxml
META-INF
MANIFEST.MF
281 Bytes
build.xml
811 Bytes
lib
orthoxml-0.1b.jar
36.6 kB
src
org
bridgedb
file
orthoxml
IDMapperOrthoXml.java
5.8 kB
org.bridgedb.gui
META-INF
MANIFEST.MF
670 Bytes
build.xml
911 Bytes
lib
org.pathvisio.jgoodies.forms-1.2.0.jar
111.7 kB
src
org
bridgedb
gui
AbstractParameterModel.java
1.5 kB
BooleanEditor.java
1.8 kB
BridgeDbParameterModel.java
716 Bytes
BridgeRestParameterModel.java
3.8 kB
ConnectionStringParameterModel.java
1.5 kB
Editor.java
928 Bytes
EnumEditor.java
1.8 kB
FileEditor.java
3.1 kB
FileParameter.java
1.5 kB
FileParameterModel.java
1.6 kB
JdbcParameterModel.java
1.9 kB
OrthoXmlParameterModel.java
1.4 kB
ParameterModel.java
2.9 kB
ParameterModelEvent.java
1.7 kB
ParameterPanel.java
2.8 kB
PgdbParameterModel.java
1.6 kB
SimpleFileFilter.java
2.4 kB
SimpleParameterModel.java
1.8 kB
StringEditor.java
2.2 kB
org.bridgedb.rdb
.classpath
1.5 kB
.project
545 Bytes
META-INF
MANIFEST.MF
312 Bytes
build-lib
derbyclient.jar
486.0 kB
build.xml
1.0 kB
lib
derby.jar
2.6 MB
pom.xml
2.0 kB
src
org
bridgedb
rdb
GdbProvider.java
4.7 kB
IDMapperRdb.java
4.2 kB
SimpleGdb.java
7.7 kB
SimpleGdbFactory.java
2.9 kB
SimpleGdbImpl2.java
6.4 kB
SimpleGdbImpl3.java
3.9 kB
SimpleGdbImplCommon.java
12.2 kB
impl
ConfigFile.java
2.8 kB
package.html
377 Bytes
test
org
bridgedb
rdb
Test.java
3.3 kB
Test2.java
5.1 kB
TestStack.java
4.6 kB
test-data
Nugo-hs-custom.txt
184.5 kB
yeast_id_mapping.txt
525.6 kB
org.bridgedb.rdb.construct
.classpath
300 Bytes
.project
385 Bytes
META-INF
MANIFEST.MF
316 Bytes
build.xml
851 Bytes
pom.xml
2.0 kB
src
org
bridgedb
rdb
construct
DBConnector.java
3.9 kB
DBConnectorDerbyServer.java
3.0 kB
DataDerby.java
10.9 kB
DataDerbyDirectory.java
1.6 kB
DataHsqldb.java
4.2 kB
FileUtilsGdb.java
2.6 kB
GdbConstruct.java
2.8 kB
GdbConstructImpl3.java
8.4 kB
org.bridgedb.server
.classpath
1.5 kB
.project
822 Bytes
META-INF
MANIFEST.MF
1.2 kB
build.xml
2.3 kB
contrib
bridgedb-example.R
703 Bytes
bridgedb-example.php
1.2 kB
bridgedb-example.pl
751 Bytes
bridgedb-example.py
472 Bytes
gdb.config.template
781 Bytes
lib
commons-cli-1.2.jar
41.1 kB
mysql-connector-java-5.1.7-bin.jar
709.9 kB
org.restlet.ext.servlet.jar
21.0 kB
org.restlet.jar
567.4 kB
pom.xml
3.6 kB
src
org
bridgedb
cgi-bin
idLookupCGI.pl
3.1 kB
html
idlookup.html
1.1 kB
server
AttributeSearch.java
2.3 kB
AttributeSet.java
1.4 kB
Attributes.java
2.8 kB
BackPageText.java
3.2 kB
Config.java
930 Bytes
Contents.java
891 Bytes
DataSources.java
339 Bytes
FreeSearch.java
2.0 kB
IDMapperResource.java
3.0 kB
IDMapperService.java
10.4 kB
IsFreeSearchSupported.java
1.2 kB
IsMappingSupported.java
2.0 kB
NoMatch.java
1.1 kB
Properties.java
1.6 kB
Server.java
3.5 kB
SupportedSourceDataSources.java
1.4 kB
SupportedTargetDataSources.java
1.4 kB
XrefExists.java
1.8 kB
Xrefs.java
2.6 kB
test
org
bridgedb
server
Test.java
4.9 kB
web.xml
1.0 kB
org.bridgedb.tools.batchmapper
.classpath
300 Bytes
.project
645 Bytes
META-INF
MANIFEST.MF
271 Bytes
build.xml
1.1 kB
src
org
bridgedb
tools
batchmapper
BatchMapper.java
11.7 kB
Lookup.java
2.3 kB
org.bridgedb.tools.miriam
build.xml
2.5 kB
org.bridgedb.tools.qc
META-INF
MANIFEST.MF
336 Bytes
build.xml
1.2 kB
pom.xml
2.4 kB
src
org
bridgedb
tools
qc
BridgeQC.java
8.4 kB
PatternChecker.java
5.1 kB
org.bridgedb.webservice.biomart
.classpath
1.3 kB
.project
834 Bytes
META-INF
MANIFEST.MF
270 Bytes
build.xml
1.0 kB
pom.xml
1.3 kB
resources
org
bridgedb
webservice
biomart
util
filterconversion.txt
967 Bytes
src
org
bridgedb
webservice
biomart
BiomartStub.java
11.0 kB
IDMapperBiomart.java
12.7 kB
package.html
373 Bytes
util
Attribute.java
1.6 kB
BiomartClient.java
7.7 kB
Database.java
4.1 kB
Dataset.java
6.8 kB
Filter.java
1.4 kB
XMLQueryBuilder.java
4.3 kB
filterconversion.txt
967 Bytes
test
org
bridgedb
webservice
biomart
TestBiomart.java
6.4 kB
org.bridgedb.webservice.bridgerest
.classpath
1.1 kB
.project
563 Bytes
META-INF
MANIFEST.MF
283 Bytes
build.xml
668 Bytes
pom.xml
1.3 kB
src
org
bridgedb
webservice
bridgerest
BridgeRest.java
15.0 kB
org.bridgedb.webservice.cronos
.classpath
2.2 kB
.project
833 Bytes
META-INF
MANIFEST.MF
247 Bytes
WSREADME.txt
5.2 kB
build.xml
2.2 kB
lib
axis-1_4
LICENSE
11.4 kB
NOTICE
416 Bytes
lib
axis-ant.jar
33.2 kB
axis.jar
1.6 MB
commons-discovery-0.2.jar
71.4 kB
commons-logging-1.0.4.jar
38.0 kB
jaxrpc.jar
31.2 kB
log4j-1.2.8.jar
352.7 kB
log4j.properties
921 Bytes
saaj.jar
19.0 kB
wsdl4j-1.5.1.jar
126.8 kB
pom.xml
3.2 kB
resources
cronosws.wsdl
3.4 kB
src
org
bridgedb
webservice
cronos
IDMapperCronos.java
7.0 kB
src-axis
org
bridgedb
webservice
cronos
CronosWS.java
532 Bytes
CronosWSPortBindingStub.java
9.1 kB
CronosWSService.java
555 Bytes
CronosWSServiceLocator.java
5.3 kB
test
org
bridgedb
webservice
cronos
Test.java
1.7 kB
org.bridgedb.webservice.picr
.classpath
2.4 kB
.project
831 Bytes
META-INF
MANIFEST.MF
320 Bytes
build.xml
985 Bytes
lib
jaxb-api-2.1.jar
78.8 kB
jaxb-impl-2.1.2.jar
828.2 kB
jaxb-xjc-2.1.2.jar
3.1 MB
jaxws-api-2.1.jar
35.8 kB
jaxws-rt-2.1.jar
1.1 MB
jaxws-tools-2.1.jar
491.2 kB
jsr173_api-1.0.jar
49.7 kB
jsr181-api-1.0-MR1.jar
8.0 kB
jsr250-api-1.0.jar
5.8 kB
resolver.jar
68.2 kB
saaj-api-1.3.jar
18.8 kB
saaj-impl-1.3.2.jar
278.1 kB
sjsxp-SNAPSHOT.jar
330.8 kB
stax-api-1.0.jar
26.3 kB
stax-ex-1.0.jar
13.1 kB
streambuffer-0.4.jar
67.8 kB
xfire-jsr181-api-1.0-M1.jar
8.1 kB
pom.xml
1.3 kB
src
org
bridgedb
webservice
picr
IDMapperPicr.java
7.8 kB
IDMapperPicrRest.java
9.5 kB
uk
ac
ebi
demo
picr
business
PICRClient.java
4.2 kB
soap
AccessionMapperInterface.java
4.3 kB
AccessionMapperService.java
2.4 kB
CrossReference.java
7.5 kB
GetMappedDatabaseNames.java
831 Bytes
GetMappedDatabaseNamesResponse.java
2.1 kB
GetUPIForAccession.java
4.5 kB
GetUPIForAccessionResponse.java
2.1 kB
GetUPIForSequence.java
3.8 kB
GetUPIForSequenceResponse.java
1.7 kB
ObjectFactory.java
2.6 kB
UPEntry.java
6.4 kB
package-info.java
206 Bytes
swing
PICRAccessionDemo.java
9.4 kB
PICRSequenceDemo.java
9.0 kB
test
org
bridgedb
webservice
picr
Test.java
2.5 kB
TestRest.java
2.8 kB
org.bridgedb.webservice.synergizer
.classpath
1.2 kB
.project
837 Bytes
META-INF
MANIFEST.MF
240 Bytes
build.xml
1.0 kB
lib
synergizer.jar
51.2 kB
pom.xml
1.7 kB
src
org
bridgedb
webservice
synergizer
IDMapperSynergizer.java
10.2 kB
SynergizerStub.java
8.1 kB
test
org
bridgedb
webservice
synergizer
Test.java
4.4 kB
org.bridgedb.webservice.uniprot
META-INF
MANIFEST.MF
417 Bytes
build.xml
894 Bytes
lib
commons-codec-1.4.jar
58.2 kB
commons-httpclient-3.1.jar
305.0 kB
commons-logging-1.0.4.jar
38.0 kB
src
org
bridgedb
webservice
uniprot
IDMapperUniprot.java
10.6 kB
test
org
bridgedb
webservice
uniprot
Test.java
1.7 kB
pom.xml
3.6 kB
qc.sh
56 Bytes
start-server-derby.sh
158 Bytes
start-server.sh
110 Bytes
taverna-bridgedb
bridgedb-activity
pom.xml
1.6 kB
src
main
java
org
bridgedb
util
taverna
BridgeDbActivity.java
6.3 kB
BridgeDbActivityConfigurationBean.java
1.6 kB
BridgeDbActivityHealthChecker.java
2.0 kB
resources
META-INF
services
net.sf.taverna.t2.workflowmodel.health.HealthChecker
56 Bytes
test
java
org
bridgedb
util
taverna
BridgeDbActivityTest.java
4.3 kB
bridgedb-activity-ui
pom.xml
4.2 kB
src
main
java
org
bridgedb
util
taverna
ui
config
BridgeDbConfigurationPanel.java
3.4 kB
BridgeDbConfigureAction.java
1.4 kB
menu
BridgeDbConfigureMenuAction.java
746 Bytes
serviceprovider
BridgeDbServiceDesc.java
3.0 kB
BridgeDbServiceIcon.java
773 Bytes
BridgeDbServiceProvider.java
2.0 kB
view
BridgeDbActivityContextViewFactory.java
692 Bytes
BridgeDbContextualView.java
1.8 kB
resources
META-INF
services
net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
68 Bytes
net.sf.taverna.t2.ui.menu.MenuComponent
62 Bytes
net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
65 Bytes
net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
71 Bytes
exampleIcon.png
3.7 kB
test
java
org
bridgedb
util
taverna
ui
TavernaWorkbenchWithExamplePlugin.java
551 Bytes
pom.xml
2.3 kB
test-data
Nugo-hs-custom.txt
184.5 kB
yeast_id_mapping.txt
525.6 kB