Package edu.mssm.crover.util

Provides various tools and APIs.

See:
          Description

Interface Summary
GeneProductPredictor  
ResidueExchangeMatrix  
ScoreEngine Implemented by engines that calculate a score given two sequences.
TmPredictor Engine to predict trans-membrane domains of protein sequences.
 

Class Summary
AlignmentReader Class to read the sequences in a two-sequence alignment, and then find pairs of residues that are conserved or switched between them.
ChunkIterator Uses MultiplePartFileIterator to split a file into chunks containing a predefined number of sections from the input file.
cleanAlignment  
CodonTable  
CommandLineOptions Support for command line options a la UNIX.
CompareSeqSets Scans a set of sequences, taken from a file, for potential TM segments.
DayhoffMatrix  
extract Extracts a subsequence from chromosome long fasta sequence files.
extractMotif Created by IntelliJ IDEA.
FetchURL This bean fetches the text document pointed to by an URL.
FragmentIdentityScoreEngine  
GCContent  
GenScan This implementation wraps around GenScan.
GetCeleraSeq Queries the Celera database for a sequence and writes it to a file.
Inspect Inspect a class with the reflection API.
IRESanalysis Class to calculate the GC content and the loop lengths in the secondary structure of IRES motifs.
Motif Created by IntelliJ IDEA.
MultiplePartFileIterator Divides a multiple XML BlastOutput into several single BlastResults.
MutationsToURLs Converts mutation annotations to URL annotations (bean).
MutationToUrlConverter Converts mutation annotations to URL annotations.
NCBISequences Accesses NCBI formatted sequence databases.
NotAVisualBean A bean which is not intended to represent anything graphic.
PhdHtmTM Should Implements the TmPredictor interface.
RemoveHTMLTags  
ScanForTms Scans a set of sequences, taken from a file, for potential TM segments.
SequenceChunkIterator Uses MultiplePartFileIterator to split a file into chunks containing a predefined number of sections from the input file.
sid Scans a set of sequences, taken from a file, for potential TM segments.
SimpleTM Implements the TmPredictor interface.
smask  
SNOmotif Created by IntelliJ IDEA.
SosuiResult  
splitfile Command line tool to splits a file on lines beginning with boundary-prefix.
strim  
tidyHD  
tidySeq  
 

Exception Summary
UnsupportedOrganism  
 

Package edu.mssm.crover.util Description

Provides various tools and APIs. See for instance a Java API to access Genscan, PhdHTM, etc.

Package Specification

See the sub-packages for a list of available tools.

Related Documentation



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