We fixed a bug in the DNAPhysicalProfile class which made the calculations of upper case sequences incorrect.
This release on adds an implementation of a DefaultConcurrentHashMap. This implementation is like a regular ConcurrentHashMap, except that when a value is requested with a key that does not exist, it will return a default value, instead of null
We have split the FrequencyMap from its utility methods. All utility methods to
manipulate the FrequencyMap now reside in FrequencyMapUtils, while FrequencyMap
is a bare bones implementation.
In this release we have removed the taglets library, as this one is no longer needed.
We added a truncate method and some other utility methods to the FrequencyMap. The requencyMap is now an extension of TreeMap instead of HashMap and we added a DefaultTreeMap implementation
We have split the different GraphicsFileExport formats over different classes, which makes it possible to only use the once you want without needing to include all libraries.
We added a utility class to easily access the MD5 algorithm to calculate the hash from a String and return the result in hexadecimal representation.
We have removed the JMLSourceTaglet, this did not belong is this project and has been moved to the Java-ML machine learning library.
We added FrequencyMap, this class allows you to do quickly count how many of each item occurs.
Added constructor the JIntegerField without arguments
Fixed the output of AutoHelpCmdLineParser when only the long form is supplied
We have added a new utility class called DefaultHashMap to the AJT library. This is an extension of the java.util.HashMap that returns a default value when the key is not present in the map.
The Abeel Java Toolkit version 1.15 has been released, providing SVG export and fixing some bugs in LineIterator and ColumnIterator.
The Abeel Jave Toolkit 1.15 is available for download , with new documentation.
The Abeel Java Toolkit version 1.14 has been released, providing a number of new utilities.
The Abeel Jave Toolkit 1.14 is available for download , with new documentation.
- ColumnIterator class to iterate over columns in a file one line at a time
- Copier class to make deep copies of objects
- AutoHelpCmdLineParser that automatically generates a help option for command line programs.
This release of our tools library mainly extends the functionality of existing classes and fixes some bugs.
The Abeel Jave Toolkit 1.13 is available for download , with new documentation.
Delft University of Technology
Delft Bioinformatics Lab
Van Mourik Broekmanweg 6 (building 28)
2628 XE Delft
The Netherlands
http://bioinformatics.tudelft.nl/
Broad Institute of MIT and Harvard
Genome Sequencing and Analysis Program
7 Cambridge Center
Cambridge, MA, 02142
USA
http://www.broadinstitute.org