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2010-01-18Organzied the functions into assign, error, load and model subdirectories. C...Don Pellegrino22-71/+181
2010-01-18Added R history file to the ignore list.Don Pellegrino1-0/+1
2010-01-18Scratch for exploring the HDF5 file in R.Don Pellegrino1-5/+11
2010-01-18Added error handling for the case where a GI record is not found in the BLAST...Don Pellegrino1-16/+57
2010-01-18Implemented updator to calculate and assign protein type values toDon Pellegrino7-96/+188
records which do not have them. This is a re-entrant process that only updates missing records and skips quickly through existing records. In addition premature termination loses at most 999 records of work since every thousand records are written back to the file and flushed to disk. Still to do is to write and flush the last set of records in the final bin under 1000. Also refactored the sequence_data structure so that it can be shared between HDF5 reading and writing operations.
2010-01-18Beginning of implmentation to iterate through and existing HDF5 and add calcu...Don Pellegrino3-14/+59
2010-01-18Moved updating the HDF5 file to a separate driver.Don Pellegrino3-8/+43
2010-01-18Added loading of the influenza.faa file.Don Pellegrino4-8/+126
2010-01-18Ran GNU indent to format the code as per GNU coding conventions.Don Pellegrino13-148/+145
2010-01-17Added error checking routines. Added implementation ofDon Pellegrino12-13/+211
assign_protein_type tested against a single hard-coded sequence input. The next step is to iterate over all records in the HDF5 collection that don't have a type assigned and to assign a type value.
2010-01-16Updated the diagram to remove an aggregator function for converting the year ...Don Pellegrino1-0/+0
2010-01-16Added the assign_protein_type function declaration without implementation.Don Pellegrino1-0/+2
2010-01-16Added the assign_protein_type function declaration without implementation.Don Pellegrino2-0/+20
2010-01-16R worksheet to explore the data from the HDF5 file.Don Pellegrino1-0/+19
2010-01-16Modified to convert the year field from text to numeric during the load.Don Pellegrino1-9/+17
2010-01-16Annotated the inimplemented methods of aggregator. This serves as a todo lis...Don Pellegrino1-0/+0
2010-01-16Added thoughts on the value provided by the HDF5 container.Don Pellegrino1-19/+37
Consideration of the anlaytical tools to be used and their load features should be considered to determine if the HDF5 container adds any value. In general custom C programs should get value out of saving the results of reading and ASCII to binary conversion steps back out to HDF5.
2010-01-16Added function declaration for load_influenza_faa.Don Pellegrino4-3/+31
2010-01-16Implemented the loading of the influenza_aa.dat file. Tested byDon Pellegrino4-41/+145
comparing an export of the data from the HDF5 file and the original file.
2010-01-15Added compilation output to the ignore list.Don Pellegrino1-0/+4
2010-01-15Code compiles and creates an HDF5 file containing a table with oneDon Pellegrino5-0/+208
record of influenza_aa.dat populated.
2010-01-15Added output of GNU Autotools to the ignore list.Don Pellegrino1-0/+15
2010-01-15Added files for initialization and use of the GNU Autotools.Don Pellegrino6-0/+33
2010-01-15Initial check-in.Don Pellegrino3-0/+310

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