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2010-01-25Added MatAssembly commands to write the cached data to the matrix structure.Don Pellegrino1-0/+3
2010-01-25Test of writing a sparse matrix to disk.Don Pellegrino1-0/+10
2010-01-25Added the initialization of a sparse matrix to be used to track theDon Pellegrino6-24/+127
pairwise BLAST scores for all influenza sequences. Modified the Autoconf input so that libraries are automatically added to LIBS rather than manually in Makefile.am. Added the use of the PETSc API which is used for the sparse matrix implementation.
2010-01-24Commented out loading the BLAST file as thing shouldn't have to be done again...Don Pellegrino1-4/+2
2010-01-24Added library dependencies iherited from use of HDF5 on NCBI Cobalt including...Don Pellegrino2-6/+8
2010-01-24Modified to load the blast scores from a text file into the HDF5 file.Don Pellegrino1-8/+45
2010-01-23Added routines for loading BLAST scores.Don Pellegrino2-0/+4
2010-01-23Modified to test loading BLAST scores.Don Pellegrino1-0/+13
2010-01-23Minimized the scope of sequence_data_field_names.Don Pellegrino1-3/+3
2010-01-23Routines to load the results of a BLAST run into the HDF5 file.Don Pellegrino5-0/+208
2010-01-21Removed unused status variable from check_h5_error function.Donald Pellegrino7-31/+35
2010-01-19Ran GNU indent on the code and headers.Don Pellegrino10-93/+99
2010-01-19Cleaned up some of the documentation.Don Pellegrino1-4/+3
2010-01-19Program now fully uses an existing file. The load functions detectDon Pellegrino7-86/+201
their existing target tables and purge them if they exist or create them if they don't. The assign function will reuse existing type values by gi and write a new table that is aligned by gi with influenza.faa.
2010-01-19Removed debugging flag. GNU Autotools is setting default debuggingDon Pellegrino1-1/+1
(-g) and optimization flags (-O2) automatically. To override these exporting CFLAGS at ./configure time is necessary.
2010-01-19Updated to compile. Code fills a new table of type values however it does no...Don Pellegrino1-106/+163
2010-01-18Organzied the functions into assign, error, load and model subdirectories. C...Don Pellegrino22-71/+181
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.
2010-01-16Added 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
2010-01-16Modified to convert the year field from text to numeric during the load.Don Pellegrino1-9/+17
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.
2010-01-15Code compiles and creates an HDF5 file containing a table with oneDon Pellegrino5-0/+208
record of influenza_aa.dat populated.

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