Download pocketbook Free Java Code

.gitignore/*from w w w  . java 2s .c  om*/
.rspec
Gemfile
Gemfile.lock
README
ROADMAP
Rakefile
app/controllers/application_controller.rb
app/controllers/pages_controller.rb
app/controllers/raw_data_sets_controller.rb
app/controllers/search_controller.rb
app/controllers/users_controller.rb
app/helpers/application_helper.rb
app/helpers/pages_helper.rb
app/helpers/raw_data_sets_helper.rb
app/helpers/search_helper.rb
app/helpers/users_helper.rb
app/models/raw_data_set.rb
app/models/user.rb
app/stylesheets/_font_face.scss
app/stylesheets/application.scss
app/tranche/README.txt
app/tranche/lib/ProteomeCommons.org-IO.jar
app/tranche/lib/bcprov-jdk15-130.jar
app/tranche/lib/commons-codec-1.3.jar
app/tranche/lib/commons-httpclient-3.0-rc4.jar
app/tranche/lib/commons-logging.jar
app/tranche/lib/commons-net-1.4.1.jar
app/tranche/lib/tranche-commons.jar
app/tranche/lib/tranche-gui.jar
app/tranche/lib/tranche.jar
app/tranche/lib/tranche/META-INF/MANIFEST.MF
app/tranche/lib/tranche/META-INF/PRIVATEK.RSA
app/tranche/lib/tranche/META-INF/PRIVATEK.SF
app/tranche/lib/tranche/org/tranche/ConfigureTranche.class
app/tranche/lib/tranche/org/tranche/FileEncoding.class
app/tranche/lib/tranche/org/tranche/LocalDataServer.class
app/tranche/lib/tranche/org/tranche/LocalRoutingServer.class
app/tranche/lib/tranche/org/tranche/TrancheServer.class
app/tranche/lib/tranche/org/tranche/add/AddFileTool$1.class
app/tranche/lib/tranche/org/tranche/add/AddFileTool$ChunkQueueingStream.class
app/tranche/lib/tranche/org/tranche/add/AddFileTool$DataChunk.class
app/tranche/lib/tranche/org/tranche/add/AddFileTool$DataUploadingThread.class
app/tranche/lib/tranche/org/tranche/add/AddFileTool$FileEncodingThread.class
app/tranche/lib/tranche/org/tranche/add/AddFileTool$FileToUpload.class
app/tranche/lib/tranche/org/tranche/add/AddFileTool$MetaChunk.class
app/tranche/lib/tranche/org/tranche/add/AddFileTool$MetaDataUploadingThread.class
app/tranche/lib/tranche/org/tranche/add/AddFileTool.class
app/tranche/lib/tranche/org/tranche/add/AddFileToolAdapter.class
app/tranche/lib/tranche/org/tranche/add/AddFileToolEvent.class
app/tranche/lib/tranche/org/tranche/add/AddFileToolListener.class
app/tranche/lib/tranche/org/tranche/add/AddFileToolPerformanceLog$ChunkType.class
app/tranche/lib/tranche/org/tranche/add/AddFileToolPerformanceLog$ChunkWrapper.class
app/tranche/lib/tranche/org/tranche/add/AddFileToolPerformanceLog.class
app/tranche/lib/tranche/org/tranche/add/AddFileToolReport.class
app/tranche/lib/tranche/org/tranche/add/AddFileToolReportListener.class
app/tranche/lib/tranche/org/tranche/add/AddFileToolUtil.class
app/tranche/lib/tranche/org/tranche/add/CommandLineAddFileToolListener.class
app/tranche/lib/tranche/org/tranche/annotations/Fix.class
app/tranche/lib/tranche/org/tranche/annotations/FixList.class
app/tranche/lib/tranche/org/tranche/annotations/Todo.class
app/tranche/lib/tranche/org/tranche/annotations/TodoList.class
app/tranche/lib/tranche/org/tranche/clc/AddAdministratorItem.class
app/tranche/lib/tranche/org/tranche/clc/ConfigurationItem.class
app/tranche/lib/tranche/org/tranche/clc/HelpItem.class
app/tranche/lib/tranche/org/tranche/clc/KillItem.class
app/tranche/lib/tranche/org/tranche/clc/ServerItem.class
app/tranche/lib/tranche/org/tranche/clc/TrancheServerCommandLineClient.class
app/tranche/lib/tranche/org/tranche/clc/TrancheServerCommandLineClientItem.class
app/tranche/lib/tranche/org/tranche/clc/TrancheServerCommandLineClientItemAttribute.class
app/tranche/lib/tranche/org/tranche/clc/UserZipFileItem.class
app/tranche/lib/tranche/org/tranche/configuration/ConfigKeys$Permissions.class
app/tranche/lib/tranche/org/tranche/configuration/ConfigKeys.class
app/tranche/lib/tranche/org/tranche/configuration/Configuration.class
app/tranche/lib/tranche/org/tranche/configuration/ConfigurationUtil.class
app/tranche/lib/tranche/org/tranche/configuration/ServerModeFlag.class
app/tranche/lib/tranche/org/tranche/default.conf
app/tranche/lib/tranche/org/tranche/delete/DeleteFileTool.class
app/tranche/lib/tranche/org/tranche/delete/DeleteFileToolListener.class
app/tranche/lib/tranche/org/tranche/delete/DeleteFileToolReport.class
app/tranche/lib/tranche/org/tranche/exceptions/AssertionFailedException.class
app/tranche/lib/tranche/org/tranche/exceptions/CantHandleVersionException.class
app/tranche/lib/tranche/org/tranche/exceptions/CantVerifySignatureException.class
app/tranche/lib/tranche/org/tranche/exceptions/ChunkAlreadyExistsSecurityException.class
app/tranche/lib/tranche/org/tranche/exceptions/ChunkDoesNotBelongException.class
app/tranche/lib/tranche/org/tranche/exceptions/ChunkDoesNotMatchHashException.class
app/tranche/lib/tranche/org/tranche/exceptions/CorruptDataException.class
app/tranche/lib/tranche/org/tranche/exceptions/CouldNotFindMetaDataException.class
app/tranche/lib/tranche/org/tranche/exceptions/MetaDataIsCorruptedException.class
app/tranche/lib/tranche/org/tranche/exceptions/NoHostProvidedException.class
app/tranche/lib/tranche/org/tranche/exceptions/NoMatchingServersException.class
app/tranche/lib/tranche/org/tranche/exceptions/NoOnlineServersException.class
app/tranche/lib/tranche/org/tranche/exceptions/OutOfDiskSpaceException.class
app/tranche/lib/tranche/org/tranche/exceptions/PassphraseIncorrectException.class
app/tranche/lib/tranche/org/tranche/exceptions/PassphraseRequiredException.class
app/tranche/lib/tranche/org/tranche/exceptions/PropagationFailedException.class
app/tranche/lib/tranche/org/tranche/exceptions/PropagationUnfulfillableHostException.class
app/tranche/lib/tranche/org/tranche/exceptions/RejectedRequestException.class
app/tranche/lib/tranche/org/tranche/exceptions/ServerIsNotReadableException.class
app/tranche/lib/tranche/org/tranche/exceptions/ServerIsNotWritableException.class
app/tranche/lib/tranche/org/tranche/exceptions/ServerIsOfflineException.class
app/tranche/lib/tranche/org/tranche/exceptions/TodoException.class
app/tranche/lib/tranche/org/tranche/exceptions/TrancheProtocolException.class
app/tranche/lib/tranche/org/tranche/exceptions/UnexpectedEndOfDataBlockException.class
app/tranche/lib/tranche/org/tranche/exceptions/UnexpectedEndOfStreamException.class
app/tranche/lib/tranche/org/tranche/exceptions/UnknownArgumentException.class
app/tranche/lib/tranche/org/tranche/exceptions/UnresponsiveServerException.class
app/tranche/lib/tranche/org/tranche/exceptions/UnsupportedServerOperationException.class
app/tranche/lib/tranche/org/tranche/flatfile/DataBlock.class
app/tranche/lib/tranche/org/tranche/flatfile/DataBlockCache.class
app/tranche/lib/tranche/org/tranche/flatfile/DataBlockCacheEntry.class
app/tranche/lib/tranche/org/tranche/flatfile/DataBlockToMerge.class
app/tranche/lib/tranche/org/tranche/flatfile/DataBlockUtil$1.class
app/tranche/lib/tranche/org/tranche/flatfile/DataBlockUtil.class
app/tranche/lib/tranche/org/tranche/flatfile/DataDirectoryConfiguration.class
app/tranche/lib/tranche/org/tranche/flatfile/FlatFileTrancheServer$1.class
app/tranche/lib/tranche/org/tranche/flatfile/FlatFileTrancheServer.class
app/tranche/lib/tranche/org/tranche/flatfile/FlatFileTrancheServerListener.class
app/tranche/lib/tranche/org/tranche/flatfile/HashSpanFixingThread$1.class
app/tranche/lib/tranche/org/tranche/flatfile/HashSpanFixingThread$ReturnType.class
app/tranche/lib/tranche/org/tranche/flatfile/HashSpanFixingThread$ThreadState.class
app/tranche/lib/tranche/org/tranche/flatfile/HashSpanFixingThread.class
app/tranche/lib/tranche/org/tranche/flatfile/HashSpanFixingThreadPolicyDecider.class
app/tranche/lib/tranche/org/tranche/flatfile/NonceMap.class
app/tranche/lib/tranche/org/tranche/flatfile/ProjectFindingThread.class
app/tranche/lib/tranche/org/tranche/flatfile/ReplaceCorruptedDataBlockThread$ChunkToRetrieve.class
app/tranche/lib/tranche/org/tranche/flatfile/ReplaceCorruptedDataBlockThread.class
app/tranche/lib/tranche/org/tranche/flatfile/ServerConfiguration.class
app/tranche/lib/tranche/org/tranche/flatfile/TargetHashSpanThread.class
app/tranche/lib/tranche/org/tranche/flatfile/logs/DataBlockUtilLog.class
app/tranche/lib/tranche/org/tranche/flatfile/logs/DataBlockUtilLogger.class
app/tranche/lib/tranche/org/tranche/flatfile/logs/DiskBackedTransactionLog.class
app/tranche/lib/tranche/org/tranche/flatfile/logs/InMemoryAggregateLog.class
app/tranche/lib/tranche/org/tranche/get/CommandLineGetFileToolListener.class
app/tranche/lib/tranche/org/tranche/get/GetFileTool$1.class
app/tranche/lib/tranche/org/tranche/get/GetFileTool$DataChunk.class
app/tranche/lib/tranche/org/tranche/get/GetFileTool$DataChunkBatch.class
app/tranche/lib/tranche/org/tranche/get/GetFileTool$DirectoryDataDownloadingThread.class
app/tranche/lib/tranche/org/tranche/get/GetFileTool$DirectoryMetaDataDownloadingThread.class
app/tranche/lib/tranche/org/tranche/get/GetFileTool$FileDataDownloadingThread.class
app/tranche/lib/tranche/org/tranche/get/GetFileTool$FileDecoding.class
app/tranche/lib/tranche/org/tranche/get/GetFileTool$MetaChunk.class
app/tranche/lib/tranche/org/tranche/get/GetFileTool$MetaChunkBatch.class
app/tranche/lib/tranche/org/tranche/get/GetFileTool.class
app/tranche/lib/tranche/org/tranche/get/GetFileToolAdapter.class
app/tranche/lib/tranche/org/tranche/get/GetFileToolEvent.class
app/tranche/lib/tranche/org/tranche/get/GetFileToolFailedChunksListener.class
app/tranche/lib/tranche/org/tranche/get/GetFileToolListener.class
app/tranche/lib/tranche/org/tranche/get/GetFileToolPerformanceLog$ChunkType.class
app/tranche/lib/tranche/org/tranche/get/GetFileToolPerformanceLog$ChunkWrapper.class
app/tranche/lib/tranche/org/tranche/get/GetFileToolPerformanceLog.class
app/tranche/lib/tranche/org/tranche/get/GetFileToolReport.class
app/tranche/lib/tranche/org/tranche/get/GetFileToolReportListener.class
app/tranche/lib/tranche/org/tranche/get/GetFileToolUtil.class
app/tranche/lib/tranche/org/tranche/get/NotEnoughDiskSpaceException.class
app/tranche/lib/tranche/org/tranche/hash/Base16.class
app/tranche/lib/tranche/org/tranche/hash/Base64$InputStream.class
app/tranche/lib/tranche/org/tranche/hash/Base64$OutputStream.class
app/tranche/lib/tranche/org/tranche/hash/Base64.class
app/tranche/lib/tranche/org/tranche/hash/Base64Util.class
app/tranche/lib/tranche/org/tranche/hash/BigHash.class
app/tranche/lib/tranche/org/tranche/hash/BigHashMaker.class
app/tranche/lib/tranche/org/tranche/hash/DiskBackedBigHashList$DiskBackedHashListIterator.class
app/tranche/lib/tranche/org/tranche/hash/DiskBackedBigHashList$Partition.class
app/tranche/lib/tranche/org/tranche/hash/DiskBackedBigHashList.class
app/tranche/lib/tranche/org/tranche/hash/DiskBackedBigHashSet.class
app/tranche/lib/tranche/org/tranche/hash/span/AbstractHashSpan.class
app/tranche/lib/tranche/org/tranche/hash/span/HashSpan.class
app/tranche/lib/tranche/org/tranche/hash/span/HashSpanCalculator.class
app/tranche/lib/tranche/org/tranche/hash/span/HashSpanCollection.class
app/tranche/lib/tranche/org/tranche/httpd/AbstractHttpHandler.class
app/tranche/lib/tranche/org/tranche/httpd/Formatter.class
app/tranche/lib/tranche/org/tranche/httpd/GetHandler.class
app/tranche/lib/tranche/org/tranche/httpd/Html.class
app/tranche/lib/tranche/org/tranche/httpd/Http.class
app/tranche/lib/tranche/org/tranche/httpd/HttpConstant.class
app/tranche/lib/tranche/org/tranche/httpd/HttpResponseMessages_en_US.properties
app/tranche/lib/tranche/org/tranche/httpd/Httpd.class
app/tranche/lib/tranche/org/tranche/httpd/IFileResources.class
app/tranche/lib/tranche/org/tranche/httpd/IHttpHandler.class
app/tranche/lib/tranche/org/tranche/httpd/IVerbosity.class
app/tranche/lib/tranche/org/tranche/httpd/Main.class
app/tranche/lib/tranche/org/tranche/httpd/Queue.class
app/tranche/lib/tranche/org/tranche/httpd/QueueException.class
app/tranche/lib/tranche/org/tranche/httpd/SocketHandler.class
app/tranche/lib/tranche/org/tranche/httpd/www/error.html
app/tranche/lib/tranche/org/tranche/httpd/www/index.html
app/tranche/lib/tranche/org/tranche/httpd/www/ws/advanced.jnlp
app/tranche/lib/tranche/org/tranche/httpd/www/ws/download.jnlp
app/tranche/lib/tranche/org/tranche/httpd/www/ws/upload.jnlp
app/tranche/lib/tranche/org/tranche/license/CC0-1.0-Universal
app/tranche/lib/tranche/org/tranche/license/License.class
app/tranche/lib/tranche/org/tranche/license/LicenseUtil.class
app/tranche/lib/tranche/org/tranche/logs/ConnectionDiagnosticsLog$1.class
app/tranche/lib/tranche/org/tranche/logs/ConnectionDiagnosticsLog$AggregateRequest.class
app/tranche/lib/tranche/org/tranche/logs/ConnectionDiagnosticsLog$ExceptionRecord.class
app/tranche/lib/tranche/org/tranche/logs/ConnectionDiagnosticsLog$Request.class
app/tranche/lib/tranche/org/tranche/logs/ConnectionDiagnosticsLog$ServerRecord.class
app/tranche/lib/tranche/org/tranche/logs/ConnectionDiagnosticsLog$SocketActivity.class
app/tranche/lib/tranche/org/tranche/logs/ConnectionDiagnosticsLog$SocketActivityWrapper.class
app/tranche/lib/tranche/org/tranche/logs/ConnectionDiagnosticsLog.class
app/tranche/lib/tranche/org/tranche/logs/LogUnit.class
app/tranche/lib/tranche/org/tranche/logs/LogUtil$1.class
app/tranche/lib/tranche/org/tranche/logs/LogUtil.class
app/tranche/lib/tranche/org/tranche/logs/SimpleLog$1.class
app/tranche/lib/tranche/org/tranche/logs/SimpleLog$LogWriterThread.class
app/tranche/lib/tranche/org/tranche/logs/SimpleLog.class
app/tranche/lib/tranche/org/tranche/logs/activity/Activity.class
app/tranche/lib/tranche/org/tranche/logs/activity/ActivityLog$1.class
app/tranche/lib/tranche/org/tranche/logs/activity/ActivityLog$SignatureMap.class
app/tranche/lib/tranche/org/tranche/logs/activity/ActivityLog.class
app/tranche/lib/tranche/org/tranche/logs/activity/ActivityLogEntry.class
app/tranche/lib/tranche/org/tranche/logs/activity/SignatureIndexEntry.class
app/tranche/lib/tranche/org/tranche/meta/AmbiguousFileSelectionException.class
app/tranche/lib/tranche/org/tranche/meta/EditMetaDataTool.class
app/tranche/lib/tranche/org/tranche/meta/EditMetaDataToolListener.class
app/tranche/lib/tranche/org/tranche/meta/EditMetaDataToolReport.class
app/tranche/lib/tranche/org/tranche/meta/MetaData$MetaDataUploader.class
app/tranche/lib/tranche/org/tranche/meta/MetaData.class
app/tranche/lib/tranche/org/tranche/meta/MetaDataAnnotation.class
app/tranche/lib/tranche/org/tranche/meta/MetaDataCache.class
app/tranche/lib/tranche/org/tranche/meta/MetaDataUtil.class
app/tranche/lib/tranche/org/tranche/network/ClientStatusUpdateProcess$1.class
app/tranche/lib/tranche/org/tranche/network/ClientStatusUpdateProcess.class
app/tranche/lib/tranche/org/tranche/network/Connection.class
app/tranche/lib/tranche/org/tranche/network/ConnectionAdapter.class
app/tranche/lib/tranche/org/tranche/network/ConnectionEvent.class
app/tranche/lib/tranche/org/tranche/network/ConnectionListener.class
app/tranche/lib/tranche/org/tranche/network/ConnectionUtil$1.class
app/tranche/lib/tranche/org/tranche/network/ConnectionUtil$2.class
app/tranche/lib/tranche/org/tranche/network/ConnectionUtil$3.class
app/tranche/lib/tranche/org/tranche/network/ConnectionUtil.class
app/tranche/lib/tranche/org/tranche/network/ConnectionUtilStatusTableListener.class
app/tranche/lib/tranche/org/tranche/network/ConnectionsKeepAliveThread.class
app/tranche/lib/tranche/org/tranche/network/MultiServerRequestStrategy$Host.class
app/tranche/lib/tranche/org/tranche/network/MultiServerRequestStrategy.class
app/tranche/lib/tranche/org/tranche/network/NetworkUtil$1.class
app/tranche/lib/tranche/org/tranche/network/NetworkUtil$2.class
app/tranche/lib/tranche/org/tranche/network/NetworkUtil$3.class
app/tranche/lib/tranche/org/tranche/network/NetworkUtil$4$1.class
app/tranche/lib/tranche/org/tranche/network/NetworkUtil$4.class
app/tranche/lib/tranche/org/tranche/network/NetworkUtil.class
app/tranche/lib/tranche/org/tranche/network/ServerStatusTablePerspective.class
app/tranche/lib/tranche/org/tranche/network/ServerStatusUpdateProcess$1.class
app/tranche/lib/tranche/org/tranche/network/ServerStatusUpdateProcess.class
app/tranche/lib/tranche/org/tranche/network/StatusTable.class
app/tranche/lib/tranche/org/tranche/network/StatusTableAdapter.class
app/tranche/lib/tranche/org/tranche/network/StatusTableEvent.class
app/tranche/lib/tranche/org/tranche/network/StatusTableListener.class
app/tranche/lib/tranche/org/tranche/network/StatusTableRow.class
app/tranche/lib/tranche/org/tranche/network/StatusTableRowRange.class
app/tranche/lib/tranche/org/tranche/network/StatusUpdateProcess.class
app/tranche/lib/tranche/org/tranche/project/ArbitraryProjectBuildingTool$ProjectFileCacheItem.class
app/tranche/lib/tranche/org/tranche/project/ArbitraryProjectBuildingTool.class
app/tranche/lib/tranche/org/tranche/project/BackupProjectTool$Partition.class
app/tranche/lib/tranche/org/tranche/project/BackupProjectTool.class
app/tranche/lib/tranche/org/tranche/project/CommandLineProjectReplicationToolListener.class
app/tranche/lib/tranche/org/tranche/project/DiskBackedProjectFilePartSet$1.class
app/tranche/lib/tranche/org/tranche/project/DiskBackedProjectFilePartSet.class
app/tranche/lib/tranche/org/tranche/project/FileReplicationDaemon.class
app/tranche/lib/tranche/org/tranche/project/FileToReplicate.class
app/tranche/lib/tranche/org/tranche/project/ProjectFile.class
app/tranche/lib/tranche/org/tranche/project/ProjectFileCache.class
app/tranche/lib/tranche/org/tranche/project/ProjectFilePart.class
app/tranche/lib/tranche/org/tranche/project/ProjectFileUtil.class
app/tranche/lib/tranche/org/tranche/project/ProjectReplicationTool.class
app/tranche/lib/tranche/org/tranche/project/ProjectReplicationToolListener.class
app/tranche/lib/tranche/org/tranche/project/ProjectSummary.class
app/tranche/lib/tranche/org/tranche/project/ProjectSummaryCache$1.class
app/tranche/lib/tranche/org/tranche/project/ProjectSummaryCache.class
app/tranche/lib/tranche/org/tranche/publish/PublishFileTool.class
app/tranche/lib/tranche/org/tranche/publish/PublishFileToolListener.class
app/tranche/lib/tranche/org/tranche/publish/PublishFileToolReport.class
app/tranche/lib/tranche/org/tranche/remote/ActivityArrayCallback.class
app/tranche/lib/tranche/org/tranche/remote/BooleanArrayCallback.class
app/tranche/lib/tranche/org/tranche/remote/BooleanCallback.class
app/tranche/lib/tranche/org/tranche/remote/CheckForErrorCallback.class
app/tranche/lib/tranche/org/tranche/remote/GetBytesCallback.class
app/tranche/lib/tranche/org/tranche/remote/GetHashesCallback.class
app/tranche/lib/tranche/org/tranche/remote/IntegerCallback.class
app/tranche/lib/tranche/org/tranche/remote/OutGoingBytes.class
app/tranche/lib/tranche/org/tranche/remote/PurgedCallbackException.class
app/tranche/lib/tranche/org/tranche/remote/ReconnectException.class
app/tranche/lib/tranche/org/tranche/remote/RemoteCallback.class
app/tranche/lib/tranche/org/tranche/remote/RemoteCallbackPurgeListener.class
app/tranche/lib/tranche/org/tranche/remote/RemoteCallbackRegistry$CallbackEntry.class
app/tranche/lib/tranche/org/tranche/remote/RemoteCallbackRegistry$ScavengerThread.class
app/tranche/lib/tranche/org/tranche/remote/RemoteCallbackRegistry.class
app/tranche/lib/tranche/org/tranche/remote/RemoteTrancheServer$1.class
app/tranche/lib/tranche/org/tranche/remote/RemoteTrancheServer.class
app/tranche/lib/tranche/org/tranche/remote/RemoteTrancheServerDownloadThread.class
app/tranche/lib/tranche/org/tranche/remote/RemoteTrancheServerListener.class
app/tranche/lib/tranche/org/tranche/remote/RemoteTrancheServerPerformanceListener.class
app/tranche/lib/tranche/org/tranche/remote/RemoteTrancheServerUploadThread.class
app/tranche/lib/tranche/org/tranche/remote/RemoteUtil.class
app/tranche/lib/tranche/org/tranche/remote/StatusTableCallback.class
app/tranche/lib/tranche/org/tranche/remote/Token.class
app/tranche/lib/tranche/org/tranche/remote/UnexpectedTokenException.class
app/tranche/lib/tranche/org/tranche/routing/RoutingTrancheServer.class
app/tranche/lib/tranche/org/tranche/routing/RoutingTrancheServerListener.class
app/tranche/lib/tranche/org/tranche/scripts/BreakApartUserZipFile.class
app/tranche/lib/tranche/org/tranche/scripts/InjectDataIntoTrancheNetwork$ChunkCheckThread.class
app/tranche/lib/tranche/org/tranche/scripts/InjectDataIntoTrancheNetwork$ChunkInjectionThread.class
app/tranche/lib/tranche/org/tranche/scripts/InjectDataIntoTrancheNetwork$ChunkToInject.class
app/tranche/lib/tranche/org/tranche/scripts/InjectDataIntoTrancheNetwork.class
app/tranche/lib/tranche/org/tranche/scripts/ScriptsUtil$ChunkType.class
app/tranche/lib/tranche/org/tranche/scripts/ScriptsUtil$ServerLookupThread.class
app/tranche/lib/tranche/org/tranche/scripts/ScriptsUtil.class
app/tranche/lib/tranche/org/tranche/security/EasySSLProtocolSocketFactory.class
app/tranche/lib/tranche/org/tranche/security/EasyX509TrustManager.class
app/tranche/lib/tranche/org/tranche/security/SecurityUtil.class
app/tranche/lib/tranche/org/tranche/security/Signature.class
app/tranche/lib/tranche/org/tranche/security/WrongPassphraseException.class
app/tranche/lib/tranche/org/tranche/server/DeleteDataItem$1.class
app/tranche/lib/tranche/org/tranche/server/DeleteDataItem.class
app/tranche/lib/tranche/org/tranche/server/DeleteMetaDataItem$1.class
app/tranche/lib/tranche/org/tranche/server/DeleteMetaDataItem.class
app/tranche/lib/tranche/org/tranche/server/GetActivityLogEntriesCountItem.class
app/tranche/lib/tranche/org/tranche/server/GetActivityLogEntriesItem.class
app/tranche/lib/tranche/org/tranche/server/GetConfigurationItem.class
app/tranche/lib/tranche/org/tranche/server/GetConfigurationNoSigItem.class
app/tranche/lib/tranche/org/tranche/server/GetDataHashesItem.class
app/tranche/lib/tranche/org/tranche/server/GetDataItem.class
app/tranche/lib/tranche/org/tranche/server/GetMetaDataHashesItem.class
app/tranche/lib/tranche/org/tranche/server/GetMetaDataItem.class
app/tranche/lib/tranche/org/tranche/server/GetNetworkStatusItem.class
app/tranche/lib/tranche/org/tranche/server/GetProjectHashesItem.class
app/tranche/lib/tranche/org/tranche/server/HasDataItem.class
app/tranche/lib/tranche/org/tranche/server/HasMetaDataItem.class
app/tranche/lib/tranche/org/tranche/server/HostSignatureNonceWrapper.class
app/tranche/lib/tranche/org/tranche/server/NonceItem$1.class
app/tranche/lib/tranche/org/tranche/server/NonceItem.class
app/tranche/lib/tranche/org/tranche/server/PingItem.class
app/tranche/lib/tranche/org/tranche/server/PropagationExceptionWrapper.class
app/tranche/lib/tranche/org/tranche/server/PropagationReturnWrapper.class
app/tranche/lib/tranche/org/tranche/server/RegisterServerItem$1.class
app/tranche/lib/tranche/org/tranche/server/RegisterServerItem.class
app/tranche/lib/tranche/org/tranche/server/RejectedRequestItem.class
app/tranche/lib/tranche/org/tranche/server/Server.class
app/tranche/lib/tranche/org/tranche/server/ServerItem.class
app/tranche/lib/tranche/org/tranche/server/ServerStartupThread.class
app/tranche/lib/tranche/org/tranche/server/ServerWorkerThread$ServerWorkerKeepAliveThread.class
app/tranche/lib/tranche/org/tranche/server/ServerWorkerThread$ServerWorkerOutputThread.class
app/tranche/lib/tranche/org/tranche/server/ServerWorkerThread$ServerWorkerThreadQueueItem.class
app/tranche/lib/tranche/org/tranche/server/ServerWorkerThread.class
app/tranche/lib/tranche/org/tranche/server/SetConfigurationItem.class
app/tranche/lib/tranche/org/tranche/server/SetDataItem$1.class
app/tranche/lib/tranche/org/tranche/server/SetDataItem.class
app/tranche/lib/tranche/org/tranche/server/SetMetaDataItem$1.class
app/tranche/lib/tranche/org/tranche/server/SetMetaDataItem.class
app/tranche/lib/tranche/org/tranche/server/ShutdownItem.class
app/tranche/lib/tranche/org/tranche/server/logs/ActionByte.class
app/tranche/lib/tranche/org/tranche/server/logs/AutoUploadingBinaryLog$1.class
app/tranche/lib/tranche/org/tranche/server/logs/AutoUploadingBinaryLog$ValidationThread.class
app/tranche/lib/tranche/org/tranche/server/logs/AutoUploadingBinaryLog.class
app/tranche/lib/tranche/org/tranche/server/logs/ChecksumException.class
app/tranche/lib/tranche/org/tranche/server/logs/InternalActionFlag.class
app/tranche/lib/tranche/org/tranche/server/logs/LogEntries.class
app/tranche/lib/tranche/org/tranche/server/logs/LogEntry.class
app/tranche/lib/tranche/org/tranche/server/logs/LogEntryQueueItem.class
app/tranche/lib/tranche/org/tranche/server/logs/LogReader.class
app/tranche/lib/tranche/org/tranche/server/logs/LogSubmitter$LoggerQueueThread.class
app/tranche/lib/tranche/org/tranche/server/logs/LogSubmitter.class
app/tranche/lib/tranche/org/tranche/server/logs/LogUtil.class
app/tranche/lib/tranche/org/tranche/server/logs/LogWriter.class
app/tranche/lib/tranche/org/tranche/server/logs/Submittable.class
app/tranche/lib/tranche/org/tranche/server/logs/UploadFailedException.class
app/tranche/lib/tranche/org/tranche/servers/CommandLineServerListener.class
app/tranche/lib/tranche/org/tranche/servers/ServerAdapter.class
app/tranche/lib/tranche/org/tranche/servers/ServerCallbackEvent.class
app/tranche/lib/tranche/org/tranche/servers/ServerEvent.class
app/tranche/lib/tranche/org/tranche/servers/ServerMessageDownEvent.class
app/tranche/lib/tranche/org/tranche/servers/ServerMessageEvent.class
app/tranche/lib/tranche/org/tranche/servers/ServerMessageUpEvent.class
app/tranche/lib/tranche/org/tranche/servers/ServerUtil$1.class
app/tranche/lib/tranche/org/tranche/servers/ServerUtil.class
app/tranche/lib/tranche/org/tranche/streams/AESEncodingStream.class
app/tranche/lib/tranche/org/tranche/streams/DeleteFileOnExitFileInputStream.class
app/tranche/lib/tranche/org/tranche/streams/GZIPEncodingStream.class
app/tranche/lib/tranche/org/tranche/streams/PrettyPrintStream.class
app/tranche/lib/tranche/org/tranche/streams/StringPrintStream$StringOutputStream.class
app/tranche/lib/tranche/org/tranche/streams/StringPrintStream.class
app/tranche/lib/tranche/org/tranche/streams/WrappedOutputStream.class
app/tranche/lib/tranche/org/tranche/tasks/CSVFile.class
app/tranche/lib/tranche/org/tranche/tasks/CSVReader.class
app/tranche/lib/tranche/org/tranche/tasks/CSVWriter.class
app/tranche/lib/tranche/org/tranche/tasks/ExcelSavvyLineSplitter.class
app/tranche/lib/tranche/org/tranche/tasks/TaskUtil.class
app/tranche/lib/tranche/org/tranche/time/TimeUtil$1.class
app/tranche/lib/tranche/org/tranche/time/TimeUtil.class
app/tranche/lib/tranche/org/tranche/timeestimator/ContextualTimeEstimator.class
app/tranche/lib/tranche/org/tranche/timeestimator/TimeEstimator.class
app/tranche/lib/tranche/org/tranche/users/InvalidSignInException.class
app/tranche/lib/tranche/org/tranche/users/MakeRepositoryCertsTool.class
app/tranche/lib/tranche/org/tranche/users/MakeUserZipFileTool.class
app/tranche/lib/tranche/org/tranche/users/User.class
app/tranche/lib/tranche/org/tranche/users/UserCertificateUtil.class
app/tranche/lib/tranche/org/tranche/users/UserZipFile.class
app/tranche/lib/tranche/org/tranche/users/UserZipFileUtil.class
app/tranche/lib/tranche/org/tranche/util/AssertionUtil.class
app/tranche/lib/tranche/org/tranche/util/CompressionUtil.class
app/tranche/lib/tranche/org/tranche/util/EmailUtil.class
app/tranche/lib/tranche/org/tranche/util/IOUtil.class
app/tranche/lib/tranche/org/tranche/util/OperatingSystem.class
app/tranche/lib/tranche/org/tranche/util/OperatingSystemUtil$1.class
app/tranche/lib/tranche/org/tranche/util/OperatingSystemUtil$CommandStreamHandler.class
app/tranche/lib/tranche/org/tranche/util/OperatingSystemUtil$StreamType.class
app/tranche/lib/tranche/org/tranche/util/OperatingSystemUtil.class
app/tranche/lib/tranche/org/tranche/util/PersistentServerFileUtil.class
app/tranche/lib/tranche/org/tranche/util/PreferencesUtil$1.class
app/tranche/lib/tranche/org/tranche/util/PreferencesUtil.class
app/tranche/lib/tranche/org/tranche/util/TempFileUtil.class
app/tranche/lib/tranche/org/tranche/util/TestUtil.class
app/tranche/lib/tranche/org/tranche/util/TestUtilListener.class
app/tranche/pc-tranche-add.jar
app/tranche/pc-tranche-get.jar
app/tranche/pc-tranche-gui.jar
app/tranche/pc-tranche-server.jar
app/tranche/pc-tranche-server/META-INF/MANIFEST.MF
app/tranche/pc-tranche-server/org/proteomecommons/tranche/AddFileTool.class
app/tranche/pc-tranche-server/org/proteomecommons/tranche/AddFileToolWizard.class
app/tranche/pc-tranche-server/org/proteomecommons/tranche/AdvancedGUI.class
app/tranche/pc-tranche-server/org/proteomecommons/tranche/ArbitraryProjectBuildingTool.class
app/tranche/pc-tranche-server/org/proteomecommons/tranche/CreateUserZipFileFrame.class
app/tranche/pc-tranche-server/org/proteomecommons/tranche/GetFileTool.class
app/tranche/pc-tranche-server/org/proteomecommons/tranche/GetFileToolWizard.class
app/tranche/pc-tranche-server/org/proteomecommons/tranche/InjectDataIntoTrancheNetwork.class
app/tranche/pc-tranche-server/org/proteomecommons/tranche/LocalDataServer.class
app/tranche/pc-tranche-server/org/proteomecommons/tranche/Main.class
app/tranche/pc-tranche-server/org/proteomecommons/tranche/MakeRepositoryCertsTool.class
app/tranche/pc-tranche-server/org/proteomecommons/tranche/ProjectToolGUI.class
app/tranche/pc-tranche-server/org/proteomecommons/tranche/ProteomeCommonsTrancheConfig.class
app/tranche/pc-tranche-server/org/proteomecommons/tranche/admin.public.certificate
app/tranche/pc-tranche-server/org/proteomecommons/tranche/anonymous.private.key
app/tranche/pc-tranche-server/org/proteomecommons/tranche/anonymous.public.certificate
app/tranche/pc-tranche-server/org/proteomecommons/tranche/autocert.public.certificate
app/tranche/pc-tranche-server/org/proteomecommons/tranche/email.private.key
app/tranche/pc-tranche-server/org/proteomecommons/tranche/email.public.certificate
app/tranche/pc-tranche-server/org/proteomecommons/tranche/pc-tranche.conf
app/tranche/pc-tranche-server/org/proteomecommons/tranche/read.public.certificate
app/tranche/pc-tranche-server/org/proteomecommons/tranche/user.public.certificate
app/tranche/pc-tranche-server/org/proteomecommons/tranche/write.public.certificate
app/views/devise/confirmations/new.html.haml
app/views/devise/mailer/confirmation_instructions.html.haml
app/views/devise/mailer/reset_password_instructions.html.haml
app/views/devise/mailer/unlock_instructions.html.haml
app/views/devise/passwords/edit.html.haml
app/views/devise/passwords/new.html.haml
app/views/devise/registrations/edit.html.haml
app/views/devise/registrations/new.html.haml
app/views/devise/sessions/new.html.haml
app/views/devise/shared/_links.haml
app/views/devise/unlocks/new.html.haml
app/views/layouts/_footer.html.haml
app/views/layouts/_header.html.haml
app/views/layouts/_sign_in_out_up.html.haml
app/views/layouts/_stylesheets_and_scripts.html.haml
app/views/layouts/application.html.haml
app/views/pages/about.html.haml
app/views/pages/help.html.haml
app/views/pages/home.html.haml
app/views/raw_data_sets/_raw_data_sets_table.html.haml
app/views/raw_data_sets/create.html.haml
app/views/raw_data_sets/download.html.haml
app/views/raw_data_sets/index.html.haml
app/views/raw_data_sets/new.html.haml
app/views/raw_data_sets/show.html.haml
app/views/search/search.html.haml
app/views/users/index.html.haml
app/views/users/show.html.haml
autotest/discover.rb
config.ru
config/application.rb
config/boot.rb
config/database.yml
config/environment.rb
config/environments/development.rb
config/environments/production.rb
config/environments/test.rb
config/initializers/backtrace_silencers.rb
config/initializers/delayed_job_config.rb
config/initializers/devise.rb
config/initializers/inflections.rb
config/initializers/mime_types.rb
config/initializers/secret_token.rb
config/initializers/session_store.rb
config/locales/devise.en.yml
config/locales/en.yml
config/routes.rb
db/schema.rb
db/seeds.rb
doc/README_FOR_APP
lib/modules/filesystem_helpers.rb
lib/modules/std_lib_extentions.rb
lib/modules/tranche_helpers.rb
lib/tasks/.gitkeep
public/404.html
public/422.html
public/500.html
public/favicon.ico
public/images/rails.png
public/javascripts/.gitkeep
public/javascripts/application.js
public/javascripts/controls.js
public/javascripts/dragdrop.js
public/javascripts/effects.js
public/javascripts/prototype.js
public/javascripts/rails.js
public/robots.txt
public/stylesheets/.gitkeep
public/stylesheets/compiled/Museo_Slab_500.otf
public/stylesheets/compiled/application.css
public/stylesheets/scaffold.css
script/delayed_job
script/rails
spec/controllers/pages_controller_spec.rb
spec/controllers/raw_data_sets_controller_spec.rb
spec/controllers/search_controller_spec.rb
spec/controllers/users_controller_spec.rb
spec/factories.rb
spec/helpers/pages_helper_spec.rb
spec/helpers/raw_data_sets_helper_spec.rb
spec/helpers/search_helper_spec.rb
spec/helpers/users_helper_spec.rb
spec/models/raw_data_set_spec.rb
spec/models/user_spec.rb
spec/modules/filesystem_helpers_spec.rb
spec/modules/std_lib_extensions.rb
spec/modules/tranche_helpers_spec.rb
spec/spec_helper.rb
spec/views/pages/about.html.haml_spec.rb
spec/views/pages/help.html.haml_spec.rb
spec/views/pages/home.html.haml_spec.rb
spec/views/raw_data_sets/create.html.haml_spec.rb
spec/views/raw_data_sets/download.html.haml_spec.rb
spec/views/raw_data_sets/index.html.haml_spec.rb
spec/views/raw_data_sets/new.html.haml_spec.rb
spec/views/raw_data_sets/show.html.haml_spec.rb
spec/views/search/search.html.haml_spec.rb
spec/views/users/index.html.haml_spec.rb
spec/views/users/show.html.haml_spec.rb
vendor/plugins/.gitkeep