Work 090612

2015-01-13

azim58 - Work 090612

created createMotifGroupsWithNameIds function in the MotifGrouper class

Next I would like to use the motifgroupswithnameids text file to compare
the most representative motif sequence from each motif and use glam2scan
to look at all the peptides to see how many peptides belong to each motif
group. Then after that I can use bepipred to look at all of the epitope
scores for all of the peptides in a group and get an average. After that
I can start blasting things.

Created MotifGroup class to hold all of the information for a motif
group. I'm thinking I might rewrite how data was written to text files
earlier so that it is all in the form of a motif group (for example with
the createMotifGroupsWithNameIds function; this function should set the
data to a motif group and have the motif group write this data so that it
can be extracted and added to later).

The main information I will have in the MotifGroup class will be as
follows

private int group_number = 0;
private String most_representative_motif = "";
private ArrayList all_motifs = new ArrayList();
private double average_motif_score = 0;
private ArrayList peptides_belonging_to_motif_group = new ArrayList();
private int number_of_peptides_belonging_to_motif_group = 0;
private double average_epitope_score = 0;

this arraylist may just have links to files of the blast results
private ArrayList list_of_blast_results = new ArrayList();

this arraylist may just have links to files of the blast results
private ArrayList bl2seq_with_every_other_blast_result = new ArrayList();

===========================================================================
started working on need_to_find_peptides_with_motif_using_glam2scan
section of Glam2Scan_Handler code
//I need to finish writing this code and actually use the
glam2scan_handler object to scan now!

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