Revert "First draft of a parser that loads EMBL MSA data files of the .dat and .aln format into MySQL"

Author Jonathan Bell <jbell@cs.columbia.edu>
Author date 2012-01-10 19:17:00
Author local date 2012-01-10 14:17:00 -0500
Committer Jonathan Bell <jbell@cs.columbia.edu>
Committer date 2012-01-10 19:17:00
Committer local date 2012-01-10 14:17:00 -0500
Commit ad3b78198ee23c24ac11cf26f09a80d2387e14ec
Tree 1052afbb6aa4326a89e1bbb226dddc8c6ec6040b
Parent 8fa75956f0fa2c9b45438cb7df20a6c0783916bd
Revert "First draft of a parser that loads EMBL MSA data files of the .dat and .aln format into MySQL"

This reverts commit 5d121dc3256ab419151022b6f84598de5afd242e.

Conflicts:

	EmblAlignParser/.classpath
	EmblAlignParser/src/META-INF/persistence.xml
	EmblAlignParser/src/coms6901/fall2011/ReadEMBL.java
	EmblAlignParser/src/org/geworkbench/components/genspace/entity/msa/Alignment.java
	genspace-common/.classpath
	genspace-common/makeStubs.sh
	genspace-common/src/org/geworkbench/components/genspace/entity/msa/Alignment.java
	genspace-common/src/org/geworkbench/components/genspace/entity/msa/Reference.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/Alignment.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/FriendFacadeService.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/LazyCycleBreaker.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/NetworkFacadeService.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/ObjectFactory.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/PublicFacadeService.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/Reference.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/ToolUsageInformation.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/ToolUsageInformationService.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/UsageInformationService.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacade.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/UserFacadeService.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/WorkflowRepositoryService.java
	genspace-common/src/org/geworkbench/components/genspace/server/stubs/package-info.java
	genspace-ejb/.classpath
	genspace-ejb/build/classes/META-INF/persistence.xml
	genspace-ejb/build/classes/META-INF/sun-ejb-jar.xml
	genspace-ejb/ejbModule/META-INF/persistence.xml
	genspace-ejb/ejbModule/META-INF/sun-ejb-jar.xml
Affected files:
.gitignore
genspace-common/.classpath
genspace-common/.gitignore
genspace-common/.project
genspace-common/.settings/org.eclipse.jdt.core.prefs
genspace-common/.settings/org.eclipse.wst.common.component
genspace-common/.settings/org.eclipse.wst.common.project.facet.core.xml
genspace-common/bin/META-INF/MANIFEST.MF
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/all-wcprops
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/entries
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEvent.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEventParameter.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Friend.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/IncomingWorkflow.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Network.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Setting.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Tool.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/ToolComment.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/ToolRating.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Transaction.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/User.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/UserNetwork.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/UserWorkflow.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/Workflow.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowComment.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowFolder.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowRating.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowTool.java.svn-base
genspace-common/bin/org/geworkbench/components/genspace/entity/xxxjaxb.properties
genspace-common/lib/javax.ejb.jar
genspace-common/lib/javax.persistence.jar
genspace-common/src/META-INF/MANIFEST.MF
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/all-wcprops
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/entries
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEvent.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/AnalysisEventParameter.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Friend.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/IncomingWorkflow.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Network.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Setting.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Tool.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/ToolComment.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/ToolRating.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Transaction.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/User.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/UserNetwork.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/UserWorkflow.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/Workflow.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowComment.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowFolder.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowRating.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/.svn/text-base/WorkflowTool.java.svn-base
genspace-common/src/org/geworkbench/components/genspace/entity/AnalysisEvent.java
genspace-common/src/org/geworkbench/components/genspace/entity/AnalysisEventParameter.java
genspace-common/src/org/geworkbench/components/genspace/entity/Friend.java
genspace-common/src/org/geworkbench/components/genspace/entity/IncomingWorkflow.java
genspace-common/src/org/geworkbench/components/genspace/entity/LazyCycleBreaker.java
genspace-common/src/org/geworkbench/components/genspace/entity/LogAction.java
genspace-common/src/org/geworkbench/components/genspace/entity/Network.java
genspace-common/src/org/geworkbench/components/genspace/entity/Setting.java
genspace-common/src/org/geworkbench/components/genspace/entity/TasteUser.java
genspace-common/src/org/geworkbench/components/genspace/entity/Tool.java
genspace-common/src/org/geworkbench/components/genspace/entity/ToolComment.java
genspace-common/src/org/geworkbench/components/genspace/entity/ToolRating.java
genspace-common/src/org/geworkbench/components/genspace/entity/Transaction.java
genspace-common/src/org/geworkbench/components/genspace/entity/UsageEvent.java
genspace-common/src/org/geworkbench/components/genspace/entity/User.java
genspace-common/src/org/geworkbench/components/genspace/entity/UserNetwork.java
genspace-common/src/org/geworkbench/components/genspace/entity/UserWorkflow.java
genspace-common/src/org/geworkbench/components/genspace/entity/Workflow.java
genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowComment.java
genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowFolder.java
genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowRating.java
genspace-common/src/org/geworkbench/components/genspace/entity/WorkflowTool.java
genspace-common/src/org/geworkbench/components/genspace/entity/xxxjaxb.properties
genspace-common/src/org/geworkbench/components/genspace/server/FriendFacadeRemote.java
genspace-common/src/org/geworkbench/components/genspace/server/NetworkFacadeRemote.java
genspace-common/src/org/geworkbench/components/genspace/server/PublicFacadeRemote.java
genspace-common/src/org/geworkbench/components/genspace/server/ToolInformationProvider.java
genspace-common/src/org/geworkbench/components/genspace/server/UsageInformationRemote.java
genspace-common/src/org/geworkbench/components/genspace/server/UserFacadeRemote.java
genspace-common/src/org/geworkbench/components/genspace/server/WorkflowRepositoryRemote.java
genspace-common/src/org/geworkbench/components/genspace/server/task/ManualRunnerRemote.java
genspace-common/src/org/geworkbench/components/genspace/server/task/Test.java
genspace-common/src/org/geworkbench/components/genspace/server/task/WorkflowStatisticsMaintainerLocal.java
genspace-ejb/.classpath
genspace-ejb/.gitignore
genspace-ejb/.project
genspace-ejb/.settings/org.eclipse.jdt.core.prefs
genspace-ejb/.settings/org.eclipse.wst.common.component
genspace-ejb/.settings/org.eclipse.wst.common.project.facet.core.xml
genspace-ejb/INSTALL.txt
genspace-ejb/NOTES
genspace-ejb/bin/.classpath
genspace-ejb/bin/.project
genspace-ejb/bin/.settings/org.eclipse.jdt.core.prefs
genspace-ejb/bin/.settings/org.eclipse.jst.j2ee.ejb.annotations.xdoclet.prefs
genspace-ejb/bin/.settings/org.eclipse.ltk.core.refactoring.prefs
genspace-ejb/bin/.settings/org.eclipse.wst.common.component
genspace-ejb/bin/.settings/org.eclipse.wst.common.project.facet.core.xml
genspace-ejb/bin/.settings/org.eclipse.wst.ws.service.policy.prefs
genspace-ejb/bin/INSTALL.txt
genspace-ejb/bin/NOTES
genspace-ejb/bin/build/classes/META-INF/MANIFEST.MF
genspace-ejb/bin/build/classes/META-INF/ejb-jar.xml
genspace-ejb/bin/build/classes/META-INF/login.conf
genspace-ejb/bin/build/classes/META-INF/mysql-resource.xml
genspace-ejb/bin/build/classes/META-INF/persistence.xml
genspace-ejb/bin/build/classes/META-INF/sun-application.xml
genspace-ejb/bin/build/classes/META-INF/sun-ejb-jar.xml
genspace-ejb/bin/ejbModule/META-INF/MANIFEST.MF
genspace-ejb/bin/ejbModule/META-INF/ejb-jar.xml
genspace-ejb/bin/ejbModule/META-INF/login.conf
genspace-ejb/bin/ejbModule/META-INF/mysql-resource.xml
genspace-ejb/bin/ejbModule/META-INF/persistence.xml
genspace-ejb/bin/ejbModule/META-INF/sun-application.xml
genspace-ejb/bin/ejbModule/META-INF/sun-ejb-jar.xml
genspace-ejb/bin/lib/mahout-core-0.5-job.jar
genspace-ejb/bin/lib/mahout-core-0.5.jar
genspace-ejb/bin/lib/mahout-math-0.5.jar
genspace-ejb/bin/lib/mahout-utils-0.5.jar
genspace-ejb/build/classes/META-INF/MANIFEST.MF
genspace-ejb/build/classes/META-INF/ejb-jar.xml
genspace-ejb/build/classes/META-INF/login.conf
genspace-ejb/build/classes/META-INF/mysql-resource.xml
genspace-ejb/build/classes/META-INF/persistence.xml
genspace-ejb/build/classes/META-INF/sun-application.xml
genspace-ejb/build/classes/META-INF/sun-ejb-jar.xml
genspace-ejb/ejbModule/META-INF/MANIFEST.MF
genspace-ejb/ejbModule/META-INF/ejb-jar.xml
genspace-ejb/ejbModule/META-INF/login.conf
genspace-ejb/ejbModule/META-INF/mysql-resource.xml
genspace-ejb/ejbModule/META-INF/persistence.xml
genspace-ejb/ejbModule/META-INF/sun-application.xml
genspace-ejb/ejbModule/META-INF/sun-ejb-jar.xml
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/AbstractFacade.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/FriendFacade.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/GenericUsageInformation.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/MahoutRecommender.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/MahoutRecommenderLocal.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/NetworkFacade.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/PublicFacade.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/ToolUsageInformation.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/UsageInformation.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/UserFacade.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/WorkflowRepository.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceItemRecommender.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceItemSimilarity.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceMySQLJDBCDataModel.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceSimilarWorkflowRecommender.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/mahout/GenspaceUserSimilarity.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/stubs/Tool.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/task/ManualRunner.java
genspace-ejb/ejbModule/org/geworkbench/components/genspace/server/task/WorkflowStatisticsMaintainer.java
genspace-ejb/lib/mahout-core-0.5-job.jar
genspace-ejb/lib/mahout-core-0.5.jar
genspace-ejb/lib/mahout-math-0.5.jar
genspace-ejb/lib/mahout-utils-0.5.jar