| Interface | Description |
|---|---|
| BitSet | |
| GeneralAnnotation |
Provide generalized annotations (descriptors).
|
| Graph<T> |
Created by Eli Rodgers-Melnick on 7/2/2014 This interface is implemented by graphs, both directed and undirected. The design is inspired by the Python networkx library (https://networkx.github.io/)
|
| ProgressListener | |
| SuperByteMatrix | |
| TableReport |
Interface for classes with data that can be presented in tables
|
| Class | Description |
|---|---|
| AbstractTableReport | |
| ArgsEngine |
A reusable solution for Command Line Arguments Parsing in Java.
|
| BasicFileFilter |
Title:
|
| BitUtil |
A variety of high efficiency bit twiddling routines.
|
| BuilderFromVCFUtil | |
| ChangeLog |
This outputs the change logs messages in HTML for tassel-5-source since this last
"New Build Date" message. The results can be added to Tassel5ChangeHistory.html on
the website.
|
| CheckSum | |
| ColumnMatrix | |
| ConvertOldFastqToModernFormatPlugin |
This plugin takes a single fastq or a directory of fastq files in the "old" format and converts them to the "modern" illumina format. The old format had multiple taxa combined in a single file, with barcodes attaached to each read sequence. The new fastQ format has the taxa (samples) each in individual files. THis method takes the old fastq and for each read block, subsets the sequence to start after the barcode (but including the initial cut site) and end after the ending cut site. The quality score is subsetted identically to the sequence so the 2 match. Files are written to a user defined directory.
|
| DirectedGraph<T> |
Class used to represent a directed graph The design is inspired by the Python networkx library (https://networkx.github.io/)
|
| DirectoryCrawler |
Directory crawler that matches REGEX or Glob patterns. Glob patterns are indicated by using the syntax:pattern approach that is used by PathMatcher. So to use glob "glob:*.{hmp,hmp.gz}"
|
| DoubleFormat | |
| ExceptionUtils | |
| FormattedInput |
tools to simplify formatted input from an input stream
|
| FormattedOutput |
tools to simplify formatted output to a stream
|
| GeneralAnnotationStorage | |
| GraphBuilder<T> |
Builder for graphs, directed and undirected
|
| GraphUtils<T> |
Functions used for Graph traversal and analysis
|
| HDF5TableReport | |
| HDF5Utils | |
| InputSource |
convenience class to open input streams linked to files, stdin, and strings
|
| LoggingUtils | |
| MultiMemberGZIPInputStream | |
| OpenBitSet |
An "open" BitSet implementation that allows direct access to the array of words storing the bits.
|
| SMTPClient |
This class can be used to send email. When the host is "appsmtp.mail.cornell.edu", any machine within the Cornell network can be used to send an email. Reference: https://confluence.cornell.edu/login.action?os_destination=https%3A%2F%2Fconfluence.cornell.edu%2Fdisplay%2Fcitapps%2FHow%2Bto%2Bconfigure%2Bapplications%2Bto%2Bsend%2Bmail%2Bthrough%2Bthe%2BCornell%2Bmail%2Bservers.
|
| SimpleTableReport |
Created by IntelliJ IDEA. User: ed Date: Sep 28, 2006 Time: 9:37:46 PM
|
| Sizeof | |
| StringNumberComparator |
Title: TASSEL Description: A java program to deal with diversity Copyright: Copyright (c) 2000 Company: USDA-ARS/NCSU
|
| SuperByteMatrixBuilder | |
| SuperByteMatrixMultiple | |
| SuperByteMatrixSingle | |
| SuperByteMatrixSingleValue | |
| SuperByteMatrixTranspose | |
| TableReportBuilder | |
| TableReportUtils | |
| Tassel5HDF5Constants |
Definition of attributes and paths for Tassel HDF5 file format.
|
| Tuple<X,Y> |
Based on response in http://stackoverflow.com/questions/2670982/using-pairs-or-2-tuples-in-java
|
| UndirectedGraph<T> |
Class used to represent an undirected graph. The design is inspired by the Python networkx library (https://networkx.github.io/)
|
| UnmodifiableBitSet | |
| Utils |