- DATE_TIME - Static variable in class compbio.stat.collector.JobStat
-
- deepClean() - Method in class compbio.engine.cluster.drmaa.ClusterRunner
-
- deepClean() - Method in class compbio.engine.cluster.drmaa.JobRunner
-
- deepCleanSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
-
Removes all special characters and digits as well as whitespace chars
from the sequence
- DEFAULT_COLUMN_SCORE - Static variable in enum compbio.data.sequence.SMERFSConstraints
-
Default column scoring schema
- DEFAULT_GAP_THRESHOLD - Static variable in enum compbio.data.sequence.SMERFSConstraints
-
Default gap threshold value for SMERFS algorithm
- DEFAULT_WINDOW_SIZE - Static variable in enum compbio.data.sequence.SMERFSConstraints
-
Default window size value for SMERFS algorithm
- defaultDelay - Static variable in class compbio.engine.FilePuller
-
- defaultValue - Variable in class compbio.metadata.Option
-
- delay - Variable in class compbio.engine.FilePuller
-
- deleteAllFiles(String) - Static method in class compbio.engine.Cleaner
-
- deleteDirectory(String) - Static method in class compbio.engine.Cleaner
-
- deleteFiles(ConfiguredExecutable<?>) - Static method in class compbio.engine.Cleaner
-
This method returns true if all files specified by List files were
successfully removed or there was no files to remove (files list was
empty)
- DELIM - Variable in class compbio.data.sequence.FastaReader
-
Delimiter for the scanner
- DELIM - Static variable in class compbio.engine.conf.DirectoryManager
-
- description - Variable in class compbio.metadata.Option
-
- description - Variable in class compbio.metadata.Preset
-
- details - Variable in class compbio.stat.servlet.ServiceTestResult
-
- DF - Static variable in class compbio.stat.collector.ExecutionStatCollector
-
- DIGIT - Static variable in class compbio.data.sequence.SequenceUtil
-
A digit
- dir - Variable in class compbio.engine.conf.RunnerConfigMarshaller.MySchemaOutputResolver
-
- DirCleaner - Class in compbio.stat.collector
-
Number of runs of each WS = number of folders with name
Number of successful runs = all runs with no result file
Per period of time = limit per file creating time Runtime (avg/max) =
started time - finished time
Task & result size = result.size
Abandoned runs - not collected runs
Cancelled runs - cancelled
Cluster vs local runs
Reasons for failure = look in the err out?
Metadata required:
work directory for local and cluster tasks = from Helper or cmd parameter.
- DirCleaner(String, int) - Constructor for class compbio.stat.collector.DirCleaner
-
- directories - Static variable in class compbio.stat.collector.DirCleaner
-
- directories - Static variable in class compbio.stat.collector.ExecutionStatCollector
-
- DirectoryManager - Class in compbio.engine.conf
-
- DirectoryManager() - Constructor for class compbio.engine.conf.DirectoryManager
-
- disconnect() - Method in class compbio.engine.FilePuller
-
- disconnected() - Method in class compbio.engine.FilePuller
-
- Disembl - Class in compbio.runner.disorder
-
DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops
fold_rem465 sequence_file print
'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'
This version of DisEMBL is 1.4 (latest available for download in Feb 2011)
capable of outputting raw values
The values of the parameters are hard coded in DisEMBL.py script.
- Disembl() - Constructor for class compbio.runner.disorder.Disembl
-
- DISEMBL_INFO - Static variable in enum compbio.ws.client.Services
-
- DisemblResult - Enum in compbio.data.sequence
-
- DisemblResult() - Constructor for enum compbio.data.sequence.DisemblResult
-
- DisemblWS - Class in compbio.ws.server
-
- DisemblWS() - Constructor for class compbio.ws.server.DisemblWS
-
- DisorderMethod - Enum in compbio.data.sequence
-
- DisorderMethod() - Constructor for enum compbio.data.sequence.DisorderMethod
-
- DisplayStat - Class in compbio.stat.servlet
-
- DisplayStat() - Constructor for class compbio.stat.servlet.DisplayStat
-
- doCleaning() - Method in class compbio.stat.collector.DirCleaner
-
- doGet(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.AnnualStat
-
- doGet(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.DisplayStat
-
- doGet(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.DownloadRedirector
-
- doGet(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.HttpCodeResponseServiceStatus
-
- doGet(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.Joblist
-
Input:
ws=${ws.key}
where=everywhere cluster local
type=cancelled all incomplete
from=${startDate}
to=${stopDate}
- doGet(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.ServiceStatus
-
- doHead(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.HttpCodeResponseServiceStatus
-
- doPost(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.DownloadRedirector
-
- DownloadRedirector - Class in compbio.stat.servlet
-
- DownloadRedirector() - Constructor for class compbio.stat.servlet.DownloadRedirector
-
- driver - Static variable in class compbio.stat.collector.StatDB
-