libMems: Compound Member Index

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a | b | c | d | e | f | g | h | i | k | l | m | n | o | p | q | r | s | t | u | v | w

- a -

adjs : mems::GreedyRemovalScorer, mems::SimpleBreakpointScorer
align_length : mems::AbstractGappedAlignment< AbstractMatchImpl >
align_matrix : mems::GappedAlignment, mems::CompactGappedAlignment< BaseType >
alignedSequenceFileName : mems::gnAlignedSequences
alignedSequences : mems::gnAlignedSequences
alignment_tree : mems::ProgressiveAligner
all_id_remaps : mems::EvenFasterSumOfPairsBreakpointScorer
allocated : mems::MemHash
allocated_aln : mems::ClustalInterface
allocator : mems::MemHash
alpha_map : mems::MatchFinder
alpha_map_size : mems::MatchFinder
alphabet_bits : mems::SMLHeader, mems::MatchFinder, mems::SMLHeader_s
ambiguity_tolerance : mems::MatchFinder

- b -

backbone_filename : mems::GenericIntervalList< MatchType >
base_number : mems::sort_buf_s
bb_cols : mems::bb_entry_s
bb_seq : mems::bb_entry_s
bcount : mems::CompactGappedAlignment< BaseType >
bin : mems::sort_buf_s
binary_seq_len : mems::SortedMerList
bogus_scores : mems::EvenFasterSumOfPairsBreakpointScorer
bp_count : mems::SimpleBreakpointScorer
bp_dist_estimate_score : mems::ProgressiveAligner
bp_dist_scale : mems::ProgressiveAligner
bp_distance : mems::ProgressiveAligner
bp_penalty : mems::SimpleBreakpointScorer, mems::EvenFasterSumOfPairsBreakpointScorer
bp_weights : mems::EvenFasterSumOfPairsBreakpointScorer
breakpoint_penalty : mems::ProgressiveAligner
buf : mems::sort_buf_s, mems::iodevice_s, mems::_aIORec
bufpos : mems::seqbuf_s
bufs : mems::seqbuf_s, mems::bin_s, mems::working_set_s
busy : mems::_aFILE

- c -

c1_siv : mems::SuperInterval
c2_siv : mems::SuperInterval
children : TreeNode
children_aligned : mems::AlignmentTreeNode
circular : mems::SMLHeader, mems::SMLHeader_s
clustal_score_cutoff : mems::ClustalInterface
collinear : mems::SimpleBreakpointScorer
collinear_genomes : mems::Aligner
comp : mems::CgaBsComp< CompType >
consensus : mems::gnAlignedSequences
conservation_dist_scale : mems::ProgressiveAligner
conservation_distance : mems::ProgressiveAligner
conservation_weights : mems::EvenFasterSumOfPairsBreakpointScorer
count : mems::_aIORec
cur_leftend : mems::AlnProgressTracker
cur_min_coverage : mems::Aligner
cur_position : mems::sort_buf_s
cur_ptr_offsets : mems::sort_buf_s
currently_recursing : mems::Aligner

- d -

data : mems::SlotAllocator< T >, mems::SeedOccurrenceList, genome::gnRAWSequence
data_ : Matrix< T >
debug : mems::ProgressiveAligner, mems::Aligner
deleted_tracking_matches : mems::EvenFasterSumOfPairsBreakpointScorer
description : mems::SMLHeader, mems::SMLHeader_s
dev : mems::seqbuf_s, mems::bin_s, mems::device_s, mems::sort_buf_s
device : mems::buffer_s
devname : mems::device_s
distance : TreeNode
distance_matrix : mems::ClustalInterface
divisor : mems::sort_buf_s

- e -

extend_lcbs : mems::Aligner
extra_muscle_arguments : mems::MuscleInterface

- f -

file : mems::seqbuf_s, mems::bin_s, mems::buffer_s
filename : genome::gnRAWSequence, mems::FileSML
fileop : mems::buffer_s
filep_high : mems::_aFILE
filep_low : mems::_aFILE
first_time : mems::EvenFasterSumOfPairsBreakpointScorer
fixed_seq_ids : mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >
fixed_starts : mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >
fname : mems::bin_s
free_list : mems::SlotAllocator< T >
full_impact_list : mems::EvenFasterSumOfPairsBreakpointScorer

- g -

gal : mems::Aligner
gap_extend : mems::PairwiseScoringScheme
gap_mh : mems::Aligner
gap_open : mems::PairwiseScoringScheme
gapped_alignment : mems::Aligner

- h -

head : mems::buffer_list_s
header : mems::SortedMerList
histogram : mems::sort_buf_s
histogram_size : mems::sort_buf_s

- i -

id : mems::SMLHeader, mems::idmer, mems::SMLHeader_s
indexPositions : mems::gnAlignedSequences
input_guide_tree_fname : mems::ProgressiveAligner
input_pos : mems::buffer_s
internal_lcb_removed_count : mems::EvenFasterSumOfPairsBreakpointScorer
internal_lcb_score_diff : mems::EvenFasterSumOfPairsBreakpointScorer
inverted : mems::PairwiseMatchAdapter
io_pos : mems::buffer_s
io_size : mems::buffer_s
iter : mems::PlacementMatch
iv : mems::bb_entry_s

- k -

key : mems::sml_s, mems::record_s

- l -

label : mems::LabeledMem
last : mems::buffer_s, mems::_aIORec
lcb_id : mems::LCB, mems::TrackingLCB< MatchType >
lcb_ids : mems::EvenFasterSumOfPairsBreakpointScorer
LCB_minimum_density : mems::Aligner
LCB_minimum_range : mems::Aligner
left_adjacency : mems::LCB, mems::TrackingLCB< MatchType >
left_col : mems::HssCols
left_end : mems::SuperInterval, mems::LCB, mems::TrackingLCB< MatchType >
leftend : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >
leftI : mems::Island
leftJ : mems::Island
length : genome::gnRAWSequence, mems::SuperInterval, mems::SMLHeader, mems::SMLHeader_s, mems::AbstractGappedAlignment< AbstractMatchImpl >
little_endian : mems::SMLHeader, mems::SMLHeader_s
log_stream : mems::MatchFinder
lrc_zeros : mems::EvenFasterSumOfPairsBreakpointScorer
lsd_zeros : mems::EvenFasterSumOfPairsBreakpointScorer

- m -

m : mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter
m_collision_count : mems::MemHash
m_enumeration_tolerance : mems::MemHash
m_extended : mems::MatchHashEntry
m_length : mems::UngappedLocalAlignment< AbstractMatchImpl >
m_mem_count : mems::MemHash
m_mersize : mems::MatchHashEntry
m_multiplicity : mems::DenseAbstractMatch< MAX_SEQS >
m_offset : mems::MatchHashEntry
m_progress : mems::MatchFinder
m_repeat_tolerance : mems::MemHash
m_seq : mems::GenericMatchSeqManipulator< MatchType >, mems::LCBLeftComparator, mems::PlacementMatchComparator, mems::LabeledMemComparator, mems::MatchLeftEndComparator, mems::SSC< MatchType >, mems::SingleStartComparator< MatchType >, mems::MatchStartComparator< MatchType >, mems::AbstractMatchSingleStartComparator< MatchType >, mems::AbstractMatchStartComparator< MatchType >
m_seq_count : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >
m_seq_id : mems::RepeatMatch
mask_size : mems::SortedMerList
match_id : mems::LcbTrackingMatch< MatchType >
match_log : mems::MemHash
matches : mems::GenericInterval< GappedBaseImpl >, mems::TrackingLCB< MatchType >
matrix : mems::PairwiseScoringScheme
max_alignment_length : mems::GappedAligner
max_extension_iters : mems::Aligner
max_gapped_alignment_length : mems::ProgressiveAligner
mem : mems::PlacementMatch, mems::LabeledMem
mem_table : mems::MemHash
mem_table_count : mems::MemHash
mer : mems::bmer, mems::idmer
mer_mask : mems::SortedMerList
mer_size : mems::MatchFinder
mers_processed : mems::MatchFinder
mhecomp : mems::MemHash
min_breakpoint_penalty : mems::ProgressiveAligner, mems::EvenFasterSumOfPairsBreakpointScorer
min_flank_size : mems::ClustalInterface
min_recursive_gap_length : mems::Aligner
min_weight : mems::GreedyRemovalScorer
mode : mems::_aFILE
msc : mems::SearchCacheComparator
muscle_arguments : mems::MuscleInterface
muscle_cmdline : mems::MuscleInterface
muscle_path : mems::MuscleInterface
my_del_lcbs : mems::EvenFasterSumOfPairsBreakpointScorer

- n -

n1_des : mems::EvenFasterSumOfPairsBreakpointScorer
n2_des : mems::EvenFasterSumOfPairsBreakpointScorer
n_elems : mems::SlotAllocator< T >
name : TreeNode
names : mems::gnAlignedSequences
nbufs : mems::working_set_s
ncols_ : Matrix< T >
next : mems::buffer_s, mems::_aIORec
nitems : mems::buffer_list_s
NO_SEQ : mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >
node_match : mems::LcbTrackingMatch< MatchType >
node_sequence_map : mems::ProgressiveAligner
nodes : PhyloTree< T >
nrecs : mems::bin_s
nrows_ : Matrix< T >
num : mems::record_s
numrecs : mems::buffer_s
nway_mh : mems::Aligner

- o -

offset_stream : mems::MatchFinder
op : mems::iodevice_s, mems::_aFILE
operation : mems::buffer_s, mems::_aIORec
operator= : mems::SuperInterval, mems::PairwiseScoringScheme, mems::SortedMerList, mems::SlotAllocator< T >, mems::SeedOccurrenceList, mems::ProgressiveAligner, PhyloTree< T >, NumericMatrix< T >, mems::MuscleInterface, mems::MemorySML, mems::MemHash, Matrix< T >, mems::MatchProjectionAdapter, mems::GenericMatchList< MatchPtrType >, mems::MatchHashEntry, mems::MaskedMemHash, mems::GenericIntervalList< MatchType >, mems::GenericInterval< GappedBaseImpl >, mems::TrackingLCB< MatchType >, mems::GappedAligner, mems::FileSML, mems::DNAMemorySML, mems::DNAFileSML, mems::ClustalInterface, mems::Aligner, mems::SSC< MatchType >, mems::SingleStartComparator< MatchType >, mems::MatchStartComparator< MatchType >, mems::AbstractMatchSingleStartComparator< MatchType >, mems::AbstractMatchStartComparator< MatchType >, mems::ParallelMemHash
ordering : mems::AlignmentTreeNode
orient : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::DenseAbstractMatch< MAX_SEQS >
original_match : mems::LcbTrackingMatch< MatchType >
original_ml : mems::ProgressiveAligner
output_guide_tree_fname : mems::ProgressiveAligner

- p -

pairwise_adjacencies : mems::EvenFasterSumOfPairsBreakpointScorer
pairwise_lcb_count : mems::EvenFasterSumOfPairsBreakpointScorer
pairwise_lcb_score : mems::EvenFasterSumOfPairsBreakpointScorer
parent_siv : mems::SuperInterval
parents : TreeNode
parents_aligned : mems::AlignmentTreeNode
path : mems::device_s
payload : mems::record_s
permutation_filename : mems::Aligner
permutation_weight : mems::Aligner
pos : mems::sml_s, mems::_aIORec
position : mems::bmer, mems::idmer
positions : mems::MemorySML, mems::gnAlignedSequences
prev_progress : mems::AlnProgressTracker

- q -

queuehead : mems::_aFILE
queuetail : mems::_aFILE

- r -

radix_tmp : mems::sort_buf_s
rec_ptrs : mems::sort_buf_s
recs : mems::buffer_s
recursive : mems::Aligner
reference_iv : mems::SuperInterval
refine : mems::ProgressiveAligner
refined : mems::AlignmentTreeNode
right_adjacency : mems::LCB, mems::TrackingLCB< MatchType >
right_col : mems::HssCols
right_end : mems::LCB, mems::TrackingLCB< MatchType >
rightI : mems::Island
rightJ : mems::Island
root : PhyloTree< T >

- s -

sar : mems::MerCompare
sar_table : mems::MatchFinder
sardata : mems::FileSML
sarfile : mems::FileSML
sarray_start_offset : mems::FileSML
scores : mems::GreedyRemovalScorer, mems::SimpleBreakpointScorer
scoring_scheme : mems::ProgressiveAligner
search_cache : mems::Aligner
seed : mems::SMLHeader, mems::MatchHashEntry, mems::SMLHeader_s
seed_length : mems::SMLHeader, mems::SMLHeader_s
seed_mask : mems::SortedMerList
seed_weight : mems::SMLHeader, mems::SMLHeader_s
seq : mems::gnAlignedSequences, mems::PairwiseMatchAdapter, mems::MatchProjectionAdapter
seq_coords : mems::FileSML
seq_count : mems::MatchFinder, mems::Aligner
seq_filename : mems::GenericMatchList< MatchPtrType >, mems::GenericIntervalList< MatchType >
seq_ids : mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >, mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >
seq_mask : mems::MaskedMemHash
seq_pos : mems::seqbuf_s
seq_table : mems::GenericMatchList< MatchPtrType >, mems::MatchFinder, mems::GenericIntervalList< MatchType >
seqI : mems::HssCols, mems::Island
seqI_count : mems::EvenFasterSumOfPairsBreakpointScorer
seqI_first : mems::EvenFasterSumOfPairsBreakpointScorer
seqI_last : mems::EvenFasterSumOfPairsBreakpointScorer
seqJ : mems::HssCols, mems::Island
seqJ_count : mems::EvenFasterSumOfPairsBreakpointScorer
seqJ_first : mems::EvenFasterSumOfPairsBreakpointScorer
seqJ_last : mems::EvenFasterSumOfPairsBreakpointScorer
sequence : mems::SortedMerList, mems::AlignmentTreeNode
sequences : mems::gnAlignedSequences
size : PhyloTree< T >, genome::gnRAWSequence, mems::working_set_s, mems::_aIORec
sml_filename : mems::GenericMatchList< MatchPtrType >
sml_table : mems::GenericMatchList< MatchPtrType >
sol_list : mems::ProgressiveAligner
sort_state : mems::sort_buf_s
ssc : mems::LabelSort< PairType >, mems::IvTrackerComp, mems::LCBLeftEndComp
starts : mems::HybridAbstractMatch< FIXED_SEQ_COUNT, int64Alloc, uintAlloc >
state : mems::sort_buf_s, mems::iodevice_s
subst_scoring : mems::ProgressiveAligner

- t -

table_size : mems::MemHash
tail_free : mems::SlotAllocator< T >
tm : mems::PairwiseMatchAdapter
tm_lcb_id_array : mems::EvenFasterSumOfPairsBreakpointScorer
tm_score_array : mems::EvenFasterSumOfPairsBreakpointScorer
tmp_paths : mems::FileSML
tmpfile : mems::SeedOccurrenceList
to_be_deleted : mems::LCB, mems::TrackingLCB< MatchType >
toclose : mems::_aFILE
total_len : mems::AlnProgressTracker
total_mers : mems::MatchFinder
total_weight : mems::GreedyRemovalScorer, mems::SimpleBreakpointScorer
totalrecs : mems::buffer_s
tracking_matches : mems::EvenFasterSumOfPairsBreakpointScorer
translation_table : mems::SMLHeader, mems::SMLHeader_s

- u -

unique_mers : mems::SMLHeader, mems::SMLHeader_s
use_seed_families : mems::ProgressiveAligner
use_weight_scaling : mems::ProgressiveAligner
using_cache_db : mems::ProgressiveAligner
using_lsd : mems::EvenFasterSumOfPairsBreakpointScorer

- v -

version : mems::SMLHeader, mems::SMLHeader_s

- w -

weight : PhyloTree< T >, mems::LCB, mems::TrackingLCB< MatchType >
word_size : mems::SMLHeader, mems::SMLHeader_s

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