A B C D E F G H I J K L M N O P R S T U V W _

D

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

deleteAllFiles(String) - Static method in class compbio.engine.Cleaner

Deprecated.

deleteFiles(ConfiguredExecutable<?>) - Static method in class compbio.engine.Cleaner

Deprecated. 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 - Static variable in class compbio.engine.conf._Key

Deprecated.

DELIM - Static variable in class compbio.engine.conf.DirectoryManager

DIGIT - Static variable in class compbio.data.sequence.SequenceUtil

A digit

DirectoryManager - Class in compbio.engine.conf

DirectoryManager() - Constructor for class compbio.engine.conf.DirectoryManager

disconnect() - 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

DisemblWS - Class in compbio.ws.server

DisemblWS() - Constructor for class compbio.ws.server.DisemblWS

DisorderMethod - Enum in compbio.data.sequence

DisplayStat - Class in compbio.stat.servlet

DisplayStat() - Constructor for class compbio.stat.servlet.DisplayStat

DownloadRedirector - Class in compbio.stat.servlet

DownloadRedirector() - Constructor for class compbio.stat.servlet.DownloadRedirector