| include/ncbi_pch.hpp [code] | |
| include/ncbi_source_ver.h [code] | |
| include/ncbiconf.h [code] | Front end for a platform-specific configuration summary |
| include/algo/align/contig_assembly/contig_assembly.hpp [code] | |
| include/algo/align/nw/align_exception.hpp [code] | |
| include/algo/align/nw/mm_aligner.hpp [code] | |
| include/algo/align/nw/nw_aligner.hpp [code] | |
| include/algo/align/nw/nw_band_aligner.hpp [code] | |
| include/algo/align/nw/nw_formatter.hpp [code] | |
| include/algo/align/nw/nw_pssm_aligner.hpp [code] | |
| include/algo/align/nw/nw_spliced_aligner.hpp [code] | |
| include/algo/align/nw/nw_spliced_aligner16.hpp [code] | |
| include/algo/align/nw/nw_spliced_aligner32.hpp [code] | |
| include/algo/align/prosplign/compartments.hpp [code] | |
| include/algo/align/prosplign/prosplign.hpp [code] | |
| include/algo/align/prosplign/prosplign_exception.hpp [code] | |
| include/algo/align/splign/splign.hpp [code] | |
| include/algo/align/splign/splign_cmdargs.hpp [code] | |
| include/algo/align/splign/splign_formatter.hpp [code] | |
| include/algo/align/splign/splign_simple.hpp [code] | |
| include/algo/align/util/algo_align_util_exceptions.hpp [code] | |
| include/algo/align/util/align_shadow.hpp [code] | |
| include/algo/align/util/blast_tabular.hpp [code] | |
| include/algo/align/util/compartment_finder.hpp [code] | |
| include/algo/align/util/hit_comparator.hpp [code] | |
| include/algo/align/util/hit_filter.hpp [code] | |
| include/algo/align/util/score_builder.hpp [code] | |
| include/algo/blast/api/bl2seq.hpp [code] | Declares the CBl2Seq (BLAST 2 Sequences) class |
| include/algo/blast/api/blast_advprot_options.hpp [code] | Declares the CBlastAdvancedProteinOptionsHandle class |
| include/algo/blast/api/blast_aux.hpp [code] | Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to convert CSeq_loc to/from BlastMask structures |
| include/algo/blast/api/blast_dbindex.hpp [code] | Declarations for indexed blast databases |
| include/algo/blast/api/blast_exception.hpp [code] | Declares the BLAST exception class |
| include/algo/blast/api/blast_mtlock.hpp [code] | C++ version of the initialization for the mutex locking interface |
| include/algo/blast/api/blast_nucl_options.hpp [code] | Declares the CBlastNucleotideOptionsHandle class |
| include/algo/blast/api/blast_options.hpp [code] | Declares class to encapsulate all BLAST options |
| include/algo/blast/api/blast_options_builder.hpp [code] | Declares the CBlastOptionsBuilder class |
| include/algo/blast/api/blast_options_handle.hpp [code] | Declares the CBlastOptionsHandle and CBlastOptionsFactory classes |
| include/algo/blast/api/blast_prot_options.hpp [code] | Declares the CBlastProteinOptionsHandle class |
| include/algo/blast/api/blast_results.hpp [code] | Definition of classes which constitute the results of running a BLAST search |
| include/algo/blast/api/blast_rps_options.hpp [code] | Declares the CBlastRPSOptionsHandle class |
| include/algo/blast/api/blast_seqinfosrc.hpp [code] | Defines interface for retrieving sequence identifiers |
| include/algo/blast/api/blast_seqinfosrc_aux.hpp [code] | Declarations of auxiliary functions using IBlastSeqInfoSrc to retrieve ids and related sequence information |
| include/algo/blast/api/blast_types.hpp [code] | Definitions of special type used in BLAST |
| include/algo/blast/api/blastx_options.hpp [code] | Declares the CBlastxOptionsHandle class |
| include/algo/blast/api/disc_nucl_options.hpp [code] | Declares the CDiscNucleotideOptionsHandle class |
| include/algo/blast/api/effsearchspace_calc.hpp [code] | Declares auxiliary class to calculate the effective search space |
| include/algo/blast/api/hspstream_queue.hpp [code] | C++ implementation of the BlastHSPStream interface for producing results on the fly |
| include/algo/blast/api/local_blast.hpp [code] | |
| include/algo/blast/api/local_db_adapter.hpp [code] | Declares class which provides internal BLAST database representations to the internal BLAST APIs |
| include/algo/blast/api/local_search.hpp [code] | Implementation of the uniform BLAST search interface for searching locally installed BLAST databases |
| include/algo/blast/api/objmgr_query_data.hpp [code] | NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on them until this notice is removed |
| include/algo/blast/api/objmgrfree_query_data.hpp [code] | NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on them until this notice is removed |
| include/algo/blast/api/phiblast_nucl_options.hpp [code] | Declares the CPHIBlastNuclOptionsHandle class |
| include/algo/blast/api/phiblast_prot_options.hpp [code] | Declares the CPHIBlastProtOptionsHandle class |
| include/algo/blast/api/prelim_stage.hpp [code] | NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on them until this notice is removed |
| include/algo/blast/api/psi_pssm_input.hpp [code] | Defines a concrete strategy to obtain PSSM input data for PSI-BLAST |
| include/algo/blast/api/psibl2seq.hpp [code] | Declares CPsiBl2Seq, the C++ API for the PSI-BLAST 2 Sequences engine |
| include/algo/blast/api/psiblast.hpp [code] | Declares CPsiBlast, the C++ API for the PSI-BLAST engine |
| include/algo/blast/api/psiblast_iteration.hpp [code] | Defines class which represents the iteration state in PSI-BLAST |
| include/algo/blast/api/psiblast_options.hpp [code] | Declares the CPSIBlastOptionsHandle class |
| include/algo/blast/api/pssm_engine.hpp [code] | C++ API for the PSI-BLAST PSSM engine |
| include/algo/blast/api/pssm_input.hpp [code] | Defines interface for a sequence alignment processor that can populate a multiple alignment data structure used by the PSSM engine |
| include/algo/blast/api/query_data.hpp [code] | NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on them until this notice is removed |
| include/algo/blast/api/remote_blast.hpp [code] | Declares the CRemoteBlast class |
| include/algo/blast/api/remote_search.hpp [code] | Remote implementation of the uniform BLAST search interface |
| include/algo/blast/api/remote_services.hpp [code] | Declares the CRemoteServices class |
| include/algo/blast/api/repeats_filter.hpp [code] | C++ implementation of repeats filtering for C++ BLAST |
| include/algo/blast/api/rps_aux.hpp [code] | Declares auxiliary classes to manage RPS-BLAST related C-structures |
| include/algo/blast/api/rpstblastn_options.hpp [code] | Declares the CRPSTBlastnOptionsHandle class |
| include/algo/blast/api/seqinfosrc_seqdb.hpp [code] | Defines a concrete strategy for the IBlastSeqInfoSrc interface for sequence identifiers retrieval from a CSeqDB class |
| include/algo/blast/api/seqinfosrc_seqvec.hpp [code] | Defines a concrete strategy for the IBlastSeqInfoSrc interface for sequence identifiers retrieval from a CSeqDB class |
| include/algo/blast/api/seqsrc_multiseq.hpp [code] | Implementation of the BlastSeqSrc interface for a vector of sequence locations |
| include/algo/blast/api/seqsrc_seqdb.hpp [code] | Implementation of the BlastSeqSrc interface using the C++ BLAST databases API |
| include/algo/blast/api/setup_factory.hpp [code] | NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on them until this notice is removed |
| include/algo/blast/api/split_query.hpp [code] | Declares CQuerySplitter, a class to split the query sequence(s) |
| include/algo/blast/api/sseqloc.hpp [code] | Definition of SSeqLoc structure |
| include/algo/blast/api/tblastn_options.hpp [code] | Declares the CTBlastnOptionsHandle class |
| include/algo/blast/api/tblastx_options.hpp [code] | Declares the CTBlastxOptionsHandle class |
| include/algo/blast/api/traceback_stage.hpp [code] | NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on them until this notice is removed |
| include/algo/blast/api/uniform_search.hpp [code] | Uniform BLAST Search Interface |
| include/algo/blast/api/version.hpp [code] | |
| include/algo/blast/blastinput/blast_args.hpp [code] | Interface for converting blast-related command line arguments into blast options |
| include/algo/blast/blastinput/blast_fasta_input.hpp [code] | Interface for FASTA files into blast sequence input |
| include/algo/blast/blastinput/blast_input.hpp [code] | Interface for converting sources of sequence data into blast sequence input |
| include/algo/blast/blastinput/blast_input_aux.hpp [code] | Auxiliary classes/functions for BLAST input library |
| include/algo/blast/blastinput/blast_scope_src.hpp [code] | Declares CBlastScopeSource class to create properly configured CScope objects to invoke the BLAST database data loader first and fall back on to the Genbank data loader if the former fails (this is configurable at runtime) |
| include/algo/blast/blastinput/blastn_args.hpp [code] | Main argument class for BLASTN application |
| include/algo/blast/blastinput/blastp_args.hpp [code] | Main argument class for BLASTP application |
| include/algo/blast/blastinput/blastx_args.hpp [code] | Main argument class for BLASTX application |
| include/algo/blast/blastinput/cmdline_flags.hpp [code] | Constant declarations for command line arguments for BLAST programs |
| include/algo/blast/blastinput/psiblast_args.hpp [code] | Main argument class for PSI-BLAST application |
| include/algo/blast/blastinput/rpsblast_args.hpp [code] | Main argument class for RPSBLAST application |
| include/algo/blast/blastinput/rpstblastn_args.hpp [code] | Main argument class for RPS TBLASTN application |
| include/algo/blast/blastinput/tblastn_args.hpp [code] | Main argument class for TBLASTN application |
| include/algo/blast/blastinput/tblastx_args.hpp [code] | Main argument class for TBLASTX application |
| include/algo/blast/composition_adjustment/compo_heap.h [code] | Declares a "heap" data structure that is used to store computed alignments when composition adjustment of scoring matrices is used |
| include/algo/blast/composition_adjustment/compo_mode_condition.h [code] | Declarations of functions used to choose the mode for composition-based statistics |
| include/algo/blast/composition_adjustment/composition_adjustment.h [code] | Definitions used in compositional score matrix adjustment |
| include/algo/blast/composition_adjustment/composition_constants.h [code] | Constants used in compositional score matrix adjustment |
| include/algo/blast/composition_adjustment/matrix_frequency_data.h [code] | Definitions used to get joint probabilities for a scoring matrix |
| include/algo/blast/composition_adjustment/nlm_linear_algebra.h [code] | Declarations for several linear algebra routines |
| include/algo/blast/composition_adjustment/optimize_target_freq.h [code] | Routines for finding an optimal set of target frequencies for the purpose of generating a compositionally adjusted score matrix |
| include/algo/blast/composition_adjustment/redo_alignment.h [code] | Definitions used to redo a set of alignments, using either composition matrix adjustment or the Smith-Waterman algorithm (or both |
| include/algo/blast/composition_adjustment/smith_waterman.h [code] | Definitions for computing Smith-Waterman alignments |
| include/algo/blast/composition_adjustment/unified_pvalues.h [code] | Headers for computing a "composition" p-value of a match, and for computing a unified p-value combining the customary alignment p-value and the new composition p-value |
| include/algo/blast/core/aa_ungapped.h [code] | Protein ungapped extension code |
| include/algo/blast/core/blast_aalookup.h [code] | Routines for creating protein BLAST lookup tables |
| include/algo/blast/core/blast_aascan.h [code] | Routines for creating protein BLAST lookup tables |
| include/algo/blast/core/blast_def.h [code] | Definitions used throughout BLAST |
| include/algo/blast/core/blast_diagnostics.h [code] | Various diagnostics (hit counts, etc |
| include/algo/blast/core/blast_encoding.h [code] | Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent manner by the BLAST engine |
| include/algo/blast/core/blast_engine.h [code] | Function calls to actually perform a BLAST search (high level) |
| include/algo/blast/core/blast_export.h [code] | Defines to provide correct exporting from BLAST DLL in Windows |
| include/algo/blast/core/blast_extend.h [code] | Ungapped extension structures that are common to nucleotide and protein extension routines |
| include/algo/blast/core/blast_filter.h [code] | BLAST filtering functions |
| include/algo/blast/core/blast_gapalign.h [code] | Structures and functions prototypes used for BLAST gapped extension |
| include/algo/blast/core/blast_hits.h [code] | Structures and API used for saving BLAST hits |
| include/algo/blast/core/blast_hspstream.h [code] | Declaration of ADT to save and retrieve lists of HSPs in the BLAST engine |
| include/algo/blast/core/blast_kappa.h [code] | Header file for composition-based statistics |
| include/algo/blast/core/blast_lookup.h [code] | Common definitions for protein and nucleotide lookup tables |
| include/algo/blast/core/blast_message.h [code] | Structures for BLAST messages |
| include/algo/blast/core/blast_nalookup.h [code] | Routines for creating nucleotide BLAST lookup tables |
| include/algo/blast/core/blast_nascan.h [code] | Routines for scanning nucleotide BLAST lookup tables |
| include/algo/blast/core/blast_options.h [code] | The structures and functions in blast_options |
| include/algo/blast/core/blast_parameters.h [code] | Structure and function definitions for BLAST parameter structures, which are internal to the CORE of BLAST |
| include/algo/blast/core/blast_program.h [code] | Definitions for various programs supported by core BLAST |
| include/algo/blast/core/blast_psi.h [code] | High level definitions and declarations for the PSSM engine of PSI-BLAST |
| include/algo/blast/core/blast_query_info.h [code] | Definitions and functions associated with the BlastQueryInfo structure |
| include/algo/blast/core/blast_rps.h [code] | RPS BLAST structure definitions |
| include/algo/blast/core/blast_seg.h [code] | SEG filtering functions |
| include/algo/blast/core/blast_seqsrc.h [code] | Declaration of ADT to retrieve sequences for the BLAST engine |
| include/algo/blast/core/blast_seqsrc_impl.h [code] | Definitions needed for implementing the BlastSeqSrc interface and low level details of the implementation of the BlastSeqSrc framework |
| include/algo/blast/core/blast_setup.h [code] | Utilities initialize/setup BLAST |
| include/algo/blast/core/blast_stat.h [code] | Definitions and prototypes used by blast_stat.c to calculate BLAST statistics |
| include/algo/blast/core/blast_sw.h [code] | Smith-Waterman alignment for use within the infrastructure of BLAST |
| include/algo/blast/core/blast_toolkit.h [code] | Choose C++ basic defines |
| include/algo/blast/core/blast_traceback.h [code] | Functions to do gapped alignment with traceback |
| include/algo/blast/core/blast_tune.h [code] | Compute a blastn word size appropriate for finding, with high probability, alignments with specified length and percent identity |
| include/algo/blast/core/blast_util.h [code] | Various auxiliary BLAST utility functions |
| include/algo/blast/core/gapinfo.h [code] | Definitions of structures used for saving traceback information |
| include/algo/blast/core/gencode_singleton.h [code] | Defines the interface to interact with the genetic code singleton object |
| include/algo/blast/core/greedy_align.h [code] | Prototypes and structures for greedy gapped alignment |
| include/algo/blast/core/hspstream_collector.h [code] | Default implementation of the BlastHSPStream interface to save hits from a BLAST search, and subsequently return them in sorted order |
| include/algo/blast/core/link_hsps.h [code] | Functions to link HSPs using sum statistics |
| include/algo/blast/core/lookup_util.h [code] | Utility functions for lookup table generation |
| include/algo/blast/core/lookup_wrap.h [code] | Wrapper for all lookup tables used in BLAST |
| include/algo/blast/core/mb_indexed_lookup.h [code] | Declarations for functions that extract hits from indexed blast databases (specialized for megablast) |
| include/algo/blast/core/na_ungapped.h [code] | Nucleotide ungapped extension code |
| include/algo/blast/core/ncbi_math.h [code] | Prototypes for portable math library (ported from C Toolkit) |
| include/algo/blast/core/ncbi_std.h [code] | Type and macro definitions from C toolkit that are not defined in C++ toolkit |
| include/algo/blast/core/pattern.h [code] | Functions for finding pattern matches in sequence (PHI-BLAST) |
| include/algo/blast/core/phi_extend.h [code] | Word finder for PHI-BLAST |
| include/algo/blast/core/phi_gapalign.h [code] | Function prototypes used for PHI BLAST gapped extension and gapped extension with traceback |
| include/algo/blast/core/phi_lookup.h [code] | Pseudo lookup table structure and database scanning functions used in PHI-BLAST |
| include/algo/blast/core/split_query.h [code] | |
| include/algo/blast/dbindex/dbindex.hpp [code] | |
| include/algo/blast/dbindex/dbindex_sp.hpp [code] | |
| include/algo/blast/dbindex/sequence_istream.hpp [code] | |
| include/algo/blast/dbindex/sequence_istream_bdb.hpp [code] | |
| include/algo/blast/dbindex/sequence_istream_fasta.hpp [code] | |
| include/algo/blast/dbindex_search/sr_search.hpp [code] | |
| include/algo/cobalt/base.hpp [code] | Definitions used by all COBALT aligner components |
| include/algo/cobalt/clusterer.hpp [code] | |
| include/algo/cobalt/cobalt.hpp [code] | |
| include/algo/cobalt/dist.hpp [code] | Interface for CDistances class |
| include/algo/cobalt/exception.hpp [code] | |
| include/algo/cobalt/hit.hpp [code] | |
| include/algo/cobalt/hitlist.hpp [code] | Interface for CHitList class |
| include/algo/cobalt/kmercounts.hpp [code] | |
| include/algo/cobalt/resfreq.hpp [code] | Interface for CProfileData |
| include/algo/cobalt/seq.hpp [code] | Interface for CSequence class |
| include/algo/cobalt/traceback.hpp [code] | Interface for CEditScript class |
| include/algo/cobalt/tree.hpp [code] | Interface for CTree class |
| include/algo/dustmask/symdust.hpp [code] | |
| include/algo/gnomon/asn1.hpp [code] | |
| include/algo/gnomon/Exon_params.hpp [code] | User-defined methods of the data storage class |
| include/algo/gnomon/Exon_params_.hpp [code] | Data storage class |
| include/algo/gnomon/gnomon.hpp [code] | |
| include/algo/gnomon/gnomon__.hpp [code] | |
| include/algo/gnomon/gnomon_doxygen.h [code] | |
| include/algo/gnomon/gnomon_exception.hpp [code] | |
| include/algo/gnomon/gnomon_model.hpp [code] | |
| include/algo/gnomon/Gnomon_param.hpp [code] | User-defined methods of the data storage class |
| include/algo/gnomon/Gnomon_param_.hpp [code] | Data storage class |
| include/algo/gnomon/Gnomon_params.hpp [code] | User-defined methods of the data storage class |
| include/algo/gnomon/Gnomon_params_.hpp [code] | Data storage class |
| include/algo/gnomon/Intergenic_params.hpp [code] | User-defined methods of the data storage class |
| include/algo/gnomon/Intergenic_params_.hpp [code] | Data storage class |
| include/algo/gnomon/Intron_params.hpp [code] | User-defined methods of the data storage class |
| include/algo/gnomon/Intron_params_.hpp [code] | Data storage class |
| include/algo/gnomon/Length_distribution_params.hpp [code] | User-defined methods of the data storage class |
| include/algo/gnomon/Length_distribution_params_.hpp [code] | Data storage class |
| include/algo/gnomon/Markov_chain_array.hpp [code] | User-defined methods of the data storage class |
| include/algo/gnomon/Markov_chain_array_.hpp [code] | Data storage class |
| include/algo/gnomon/Markov_chain_params.hpp [code] | User-defined methods of the data storage class |
| include/algo/gnomon/Markov_chain_params_.hpp [code] | Data storage class |
| include/algo/gnomon/NCBI_GNOMON_module.hpp [code] | |
| include/algo/gnomon/set.hpp [code] | |
| include/algo/link_reduce/link_reduce.hpp [code] | |
| include/algo/ms/formats/mzdata/AcqSpecification.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/AcqSpecification_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/Acquisition.hpp [code] | |
| include/algo/ms/formats/mzdata/Acquisition_.hpp [code] | |
| include/algo/ms/formats/mzdata/Activation.hpp [code] | |
| include/algo/ms/formats/mzdata/Activation_.hpp [code] | |
| include/algo/ms/formats/mzdata/Additional.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/Additional_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/Admin.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/Admin_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/Analyzer.hpp [code] | |
| include/algo/ms/formats/mzdata/Analyzer_.hpp [code] | |
| include/algo/ms/formats/mzdata/AnalyzerList.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/AnalyzerList_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/Contact.hpp [code] | |
| include/algo/ms/formats/mzdata/Contact_.hpp [code] | |
| include/algo/ms/formats/mzdata/CvLookup.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/CvLookup_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/CvParam.hpp [code] | |
| include/algo/ms/formats/mzdata/CvParam_.hpp [code] | |
| include/algo/ms/formats/mzdata/Data.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/Data_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/DataProcessing.hpp [code] | |
| include/algo/ms/formats/mzdata/DataProcessing_.hpp [code] | |
| include/algo/ms/formats/mzdata/Description.hpp [code] | |
| include/algo/ms/formats/mzdata/Description_.hpp [code] | |
| include/algo/ms/formats/mzdata/Detector.hpp [code] | |
| include/algo/ms/formats/mzdata/Detector_.hpp [code] | |
| include/algo/ms/formats/mzdata/Instrument.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/Instrument_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/IntenArrayBinary.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/IntenArrayBinary_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/IonSelection.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/IonSelection_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/MzArrayBinary.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/MzArrayBinary_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/MzData.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/MzData_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/mzData__.hpp [code] | |
| include/algo/ms/formats/mzdata/mzData_doxygen.h [code] | |
| include/algo/ms/formats/mzdata/mzData_module.hpp [code] | |
| include/algo/ms/formats/mzdata/Precursor.hpp [code] | |
| include/algo/ms/formats/mzdata/Precursor_.hpp [code] | |
| include/algo/ms/formats/mzdata/PrecursorList.hpp [code] | |
| include/algo/ms/formats/mzdata/PrecursorList_.hpp [code] | |
| include/algo/ms/formats/mzdata/ProcessingMethod.hpp [code] | |
| include/algo/ms/formats/mzdata/ProcessingMethod_.hpp [code] | |
| include/algo/ms/formats/mzdata/SampleDescription.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/SampleDescription_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/Software.hpp [code] | |
| include/algo/ms/formats/mzdata/Software_.hpp [code] | |
| include/algo/ms/formats/mzdata/Source.hpp [code] | |
| include/algo/ms/formats/mzdata/Source_.hpp [code] | |
| include/algo/ms/formats/mzdata/SourceFile.hpp [code] | |
| include/algo/ms/formats/mzdata/SourceFile_.hpp [code] | |
| include/algo/ms/formats/mzdata/Spectrum.hpp [code] | |
| include/algo/ms/formats/mzdata/Spectrum_.hpp [code] | |
| include/algo/ms/formats/mzdata/SpectrumDesc.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/SpectrumDesc_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/SpectrumInstrument.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/SpectrumInstrument_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/SpectrumList.hpp [code] | |
| include/algo/ms/formats/mzdata/SpectrumList_.hpp [code] | |
| include/algo/ms/formats/mzdata/SpectrumSettings.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/SpectrumSettings_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/SupDataArray.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/SupDataArray_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/SupDataArrayBinary.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/SupDataArrayBinary_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/SupDataDesc.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/SupDataDesc_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/SupDesc.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/SupDesc_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/SupSourceFile.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzdata/SupSourceFile_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzdata/UserParam.hpp [code] | |
| include/algo/ms/formats/mzdata/UserParam_.hpp [code] | |
| include/algo/ms/formats/mzml/Acquisition.hpp [code] | |
| include/algo/ms/formats/mzml/Acquisition_.hpp [code] | |
| include/algo/ms/formats/mzml/AcquisitionList.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/AcquisitionList_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/AcquisitionSettings.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/AcquisitionSettings_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/AcquisitionSettingsList.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/AcquisitionSettingsList_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/Activation.hpp [code] | |
| include/algo/ms/formats/mzml/Activation_.hpp [code] | |
| include/algo/ms/formats/mzml/Analyzer.hpp [code] | |
| include/algo/ms/formats/mzml/Analyzer_.hpp [code] | |
| include/algo/ms/formats/mzml/BinaryDataArray.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/BinaryDataArray_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/BinaryDataArrayList.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/BinaryDataArrayList_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/Chromatogram.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/Chromatogram_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/ChromatogramList.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/ChromatogramList_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/ComponentList.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/ComponentList_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/Contact.hpp [code] | |
| include/algo/ms/formats/mzml/Contact_.hpp [code] | |
| include/algo/ms/formats/mzml/Cv.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/Cv_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/CvList.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/CvList_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/CvParam.hpp [code] | |
| include/algo/ms/formats/mzml/CvParam_.hpp [code] | |
| include/algo/ms/formats/mzml/DataProcessing.hpp [code] | |
| include/algo/ms/formats/mzml/DataProcessing_.hpp [code] | |
| include/algo/ms/formats/mzml/DataProcessingList.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/DataProcessingList_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/Detector.hpp [code] | |
| include/algo/ms/formats/mzml/Detector_.hpp [code] | |
| include/algo/ms/formats/mzml/FileContent.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/FileContent_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/FileDescription.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/FileDescription_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/InstrumentConfiguration.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/InstrumentConfiguration_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/InstrumentConfigurationLis.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/InstrumentConfigurationLis_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/IsolationWindow.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/IsolationWindow_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/MzML.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/MzML_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/mzML__.hpp [code] | |
| include/algo/ms/formats/mzml/mzML_doxygen.h [code] | |
| include/algo/ms/formats/mzml/mzML_module.hpp [code] | |
| include/algo/ms/formats/mzml/Precursor.hpp [code] | |
| include/algo/ms/formats/mzml/Precursor_.hpp [code] | |
| include/algo/ms/formats/mzml/PrecursorList.hpp [code] | |
| include/algo/ms/formats/mzml/PrecursorList_.hpp [code] | |
| include/algo/ms/formats/mzml/ProcessingMethod.hpp [code] | |
| include/algo/ms/formats/mzml/ProcessingMethod_.hpp [code] | |
| include/algo/ms/formats/mzml/ReferenceableParamGroup.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/ReferenceableParamGroup_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/ReferenceableParamGroupLis.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/ReferenceableParamGroupLis_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/ReferenceableParamGroupRef.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/ReferenceableParamGroupRef_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/Run.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/Run_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/Sample.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/Sample_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/SampleList.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/SampleList_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/Scan.hpp [code] | |
| include/algo/ms/formats/mzml/Scan_.hpp [code] | |
| include/algo/ms/formats/mzml/ScanWindow.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/ScanWindow_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/ScanWindowList.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/ScanWindowList_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/SelectedIon.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/SelectedIon_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/SelectedIonList.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/SelectedIonList_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/Software.hpp [code] | |
| include/algo/ms/formats/mzml/Software_.hpp [code] | |
| include/algo/ms/formats/mzml/SoftwareList.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/SoftwareList_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/SoftwareParam.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/SoftwareParam_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/SoftwareRef.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/SoftwareRef_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/Source.hpp [code] | |
| include/algo/ms/formats/mzml/Source_.hpp [code] | |
| include/algo/ms/formats/mzml/SourceFile.hpp [code] | |
| include/algo/ms/formats/mzml/SourceFile_.hpp [code] | |
| include/algo/ms/formats/mzml/SourceFileList.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/SourceFileList_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/SourceFileRef.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/SourceFileRef_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/SourceFileRefList.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/SourceFileRefList_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/Spectrum.hpp [code] | |
| include/algo/ms/formats/mzml/Spectrum_.hpp [code] | |
| include/algo/ms/formats/mzml/SpectrumDescription.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/SpectrumDescription_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/SpectrumList.hpp [code] | |
| include/algo/ms/formats/mzml/SpectrumList_.hpp [code] | |
| include/algo/ms/formats/mzml/Target.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/Target_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/TargetList.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzml/TargetList_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzml/UserParam.hpp [code] | |
| include/algo/ms/formats/mzml/UserParam_.hpp [code] | |
| include/algo/ms/formats/mzxml/DataProcessing.hpp [code] | |
| include/algo/ms/formats/mzxml/DataProcessing_.hpp [code] | |
| include/algo/ms/formats/mzxml/Index.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/Index_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/Maldi.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/Maldi_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/MaldiMatrix.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/MaldiMatrix_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/MsDetector.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/MsDetector_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/MsInstrument.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/MsInstrument_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/MsIonisation.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/MsIonisation_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/MsManufacturer.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/MsManufacturer_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/MsMassAnalyzer.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/MsMassAnalyzer_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/MsModel.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/MsModel_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/MsResolution.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/MsResolution_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/MsRun.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/MsRun_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/MzXML.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/MzXML_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/mzXML__.hpp [code] | |
| include/algo/ms/formats/mzxml/mzXML_doxygen.h [code] | |
| include/algo/ms/formats/mzxml/mzXML_module.hpp [code] | |
| include/algo/ms/formats/mzxml/NameValue.hpp [code] | |
| include/algo/ms/formats/mzxml/NameValue_.hpp [code] | |
| include/algo/ms/formats/mzxml/Offset.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/Offset_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/Operator.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/Operator_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/Orientation.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/Orientation_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/ParentFile.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/ParentFile_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/Pattern.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/Pattern_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/Peaks.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/Peaks_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/Plate.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/Plate_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/PlateManufacturer.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/PlateManufacturer_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/PlateModel.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/PlateModel_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/PrecursorMz.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/PrecursorMz_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/ProcessingOperation.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/ProcessingOperation_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/Robot.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/Robot_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/RobotManufacturer.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/RobotManufacturer_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/RobotModel.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/RobotModel_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/Scan.hpp [code] | |
| include/algo/ms/formats/mzxml/Scan_.hpp [code] | |
| include/algo/ms/formats/mzxml/ScanOrigin.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/ScanOrigin_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/Separation.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/Separation_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/Software.hpp [code] | |
| include/algo/ms/formats/mzxml/Software_.hpp [code] | |
| include/algo/ms/formats/mzxml/Spot.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/Spot_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/Spotting.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/Spotting_.hpp [code] | Data storage class |
| include/algo/ms/formats/mzxml/SpottingPattern.hpp [code] | User-defined methods of the data storage class |
| include/algo/ms/formats/mzxml/SpottingPattern_.hpp [code] | Data storage class |
| include/algo/ms/formats/unimod/Mod.hpp [code] | |
| include/algo/ms/formats/unimod/Unimod.hpp [code] | User-defined methods of the data storage class |
| include/algo/phy_tree/bio_tree.hpp [code] | Things for representing and manipulating bio trees |
| include/algo/phy_tree/bio_tree_conv.hpp [code] | |
| include/algo/phy_tree/dist_methods.hpp [code] | |
| include/algo/phy_tree/phy_node.hpp [code] | |
| include/algo/phy_tree/tree_to_dist_mat.hpp [code] | |
| include/algo/seqqa/blastp_tests.hpp [code] | |
| include/algo/seqqa/prot_prod_tests.hpp [code] | |
| include/algo/seqqa/seq_id_tests.hpp [code] | |
| include/algo/seqqa/seqtest.hpp [code] | |
| include/algo/seqqa/single_aln_tests.hpp [code] | |
| include/algo/seqqa/xcript_tests.hpp [code] | |
| include/algo/sequence/align_cleanup.hpp [code] | |
| include/algo/sequence/align_group.hpp [code] | |
| include/algo/sequence/annot_compare.hpp [code] | |
| include/algo/sequence/antigenic.hpp [code] | |
| include/algo/sequence/coiled_coil.hpp [code] | |
| include/algo/sequence/compare_feats.hpp [code] | |
| include/algo/sequence/consensus_splice.hpp [code] | |
| include/algo/sequence/cpg.hpp [code] | |
| include/algo/sequence/find_pattern.hpp [code] | |
| include/algo/sequence/gene_model.hpp [code] | |
| include/algo/sequence/loc_mapper.hpp [code] | |
| include/algo/sequence/make_cdr_prods.hpp [code] | |
| include/algo/sequence/masking_delta.hpp [code] | |
| include/algo/sequence/nuc_prop.hpp [code] | |
| include/algo/sequence/orf.hpp [code] | |
| include/algo/sequence/polya.hpp [code] | |
| include/algo/sequence/prot_prop.hpp [code] | |
| include/algo/sequence/regexp_loc.hpp [code] | Header file for creating CSeq_locs from CRegexps |
| include/algo/sequence/restriction.hpp [code] | |
| include/algo/sequence/seq_match.hpp [code] | |
| include/algo/sequence/signal_seq.hpp [code] | |
| include/algo/sequence/util.hpp [code] | |
| include/algo/structure/MSAAInterface.hpp [code] | |
| include/algo/structure/bma_refine/AlignRefineScorer.hpp [code] | |
| include/algo/structure/bma_refine/BlockBoundaryAlgorithm.hpp [code] | |
| include/algo/structure/bma_refine/BlockEditor.hpp [code] | |
| include/algo/structure/bma_refine/BMAUtils.hpp [code] | |
| include/algo/structure/bma_refine/ColumnScorer.hpp [code] | |
| include/algo/structure/bma_refine/diagnosticDefs.hpp [code] | |
| include/algo/structure/bma_refine/Interface.hpp [code] | |
| include/algo/structure/bma_refine/InterfaceGUI.hpp [code] | |
| include/algo/structure/bma_refine/RefinerCycle.hpp [code] | |
| include/algo/structure/bma_refine/RefinerDefs.hpp [code] | |
| include/algo/structure/bma_refine/RefinerEngine.hpp [code] | |
| include/algo/structure/bma_refine/RefinerPhase.hpp [code] | |
| include/algo/structure/bma_refine/RefinerTrial.hpp [code] | |
| include/algo/structure/bma_refine/RowSelector.hpp [code] | |
| include/algo/structure/cd_utils/cuAlign.hpp [code] | |
| include/algo/structure/cd_utils/cuAlignedDM.hpp [code] | |
| include/algo/structure/cd_utils/cuAlignmentCollection.hpp [code] | |
| include/algo/structure/cd_utils/cuBaseClusterer.hpp [code] | |
| include/algo/structure/cd_utils/cuBlast2Seq.hpp [code] | |
| include/algo/structure/cd_utils/cuBlock.hpp [code] | |
| include/algo/structure/cd_utils/cuBlockExtender.hpp [code] | |
| include/algo/structure/cd_utils/cuBlockFormater.hpp [code] | |
| include/algo/structure/cd_utils/cuBlockIntersector.hpp [code] | |
| include/algo/structure/cd_utils/cuCD.hpp [code] | |
| include/algo/structure/cd_utils/cuCdBlaster.hpp [code] | |
| include/algo/structure/cd_utils/cuCdCore.hpp [code] | |
| include/algo/structure/cd_utils/cuCdFamily.hpp [code] | |
| include/algo/structure/cd_utils/cuCdFromFasta.hpp [code] | |
| include/algo/structure/cd_utils/cuCdReadWriteASN.hpp [code] | |
| include/algo/structure/cd_utils/cuCdUpdateParameters.hpp [code] | |
| include/algo/structure/cd_utils/cuCdUpdater.hpp [code] | |
| include/algo/structure/cd_utils/cuConsensusMaker.hpp [code] | |
| include/algo/structure/cd_utils/cuCppNCBI.hpp [code] | |
| include/algo/structure/cd_utils/cuDistmat.hpp [code] |