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2010-03-30Added simple print routines as an exercise in navigating the NCBI object stru...masterDon Pellegrino1-0/+10
2010-03-30Added simple print routines as an exercise in navigating the NCBI object stru...Don Pellegrino11-0/+193
2010-03-28Added new load routines for meta-data.Don Pellegrino1-0/+4
2010-03-28Testing options for loading meta-data/features/Entrez into HDF5.Don Pellegrino4-0/+376
2010-03-28Testing the meta-data/feature/Entrez load.Don Pellegrino1-1/+13
2010-03-28Added script for setting environment variables in preparation forDon Pellegrino1-0/+14
2010-03-28Replaced with more generic env-debian.sh which should work on anyDon Pellegrino1-38/+0
2010-03-28Added dependency on the libxml2 library for XML parsing.Don Pellegrino1-0/+9
2010-03-05Modified to take the location of the exp004 directory from anDon Pellegrino4-14/+60
2010-03-04Added dependency on NCBI Toolkit.Don Pellegrino1-0/+3
2010-01-25Added MatAssembly commands to write the cached data to the matrix structure.Don Pellegrino1-0/+3
2010-01-25Added script to build against a custom PETSc build with HDF5 support.Don Pellegrino1-0/+38
2010-01-25Test of writing a sparse matrix to disk.Don Pellegrino1-0/+10
2010-01-25Modified to build using the copy of PETSc already installed on Cobalt.Don Pellegrino5-46/+65
2010-01-25Added the initialization of a sparse matrix to be used to track theDon Pellegrino6-24/+127
2010-01-24Added notes for doing a build on NCSA Cobalt. Using the Intel C Compiler bui...Don Pellegrino1-0/+24
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
2010-01-20Updated the diagram to reflect the recent implementations of the aggregator.Don Pellegrino1-0/+0
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
2010-01-19Updated the merge command to reflect the new table structure in the HDF5 file.Don Pellegrino1-9/+20
2010-01-19Program now fully uses an existing file. The load functions detectDon Pellegrino7-86/+201
2010-01-19Removed debugging flag. GNU Autotools is setting default debuggingDon Pellegrino1-1/+1
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 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
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
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
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
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