The database listener interface is used for receiving database information events, including database connection and database sample change.
Provide the database event handler; add several operation to the table.
A dialog to select the database and sample relative to a data set. It is worth to say that data sets must be imported first to RED and user should know what they should select with a given data set.
Provide a tree model which describes the RNA editing detected mode and samples in database.
Provide a tree model which describes the RNA editing detected mode and samples in database.
Add a method to retrieve a site set from the database by a given sample name.
Separate the table creating operation into a single class file, including the reference file table and filter table.
A table node which uses in DatabaseTreeMode.
A database connection dialog, providing host, port, user and password field.
The Class AnnotationCollection is the main object through which annotation objects can be accessed
AnnotationSet represents a set of genome annotations deriving from a single source (i.e., file). They are combined in an AnnotationCollection to provide the full set of genome annotations used by the program.
The Class CoreAnnotationSet is an extension of AnnotationSet reserved for use by the core genome annotation files which are not stored with the user data but are assumed to be available from the online repositories.
The Cytoband file format is used to specify the cytobands for an imported genome. We uses this file to draw the chromosome ideograms for the genome, with the idea put forward by IGV.
Add comments.
A Feature represents a strip of information obtained from UCSC gene annotation file(i.e., gene.gtf).
The FeatureLocation class is a wrap class for feature to parse location by a given string. It is only used in REDParser.
The Class Chromosome represents a single chromosome in a genome.
The Class Genome represents an entire annotated genome assembly
Describe a genome and its relative resources.
Delete the old files we didn't need any more.