trimAlManager Member List

This is the complete list of members for trimAlManager, including all inherited members.

access_by	trimAlManager	friend
alternative_matrix	trimAlManager
appearErrors	trimAlManager
argumentLength	trimAlManager
argumentReport enum name	trimAlManager
automated1	trimAlManager
automated1_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
automatedMethodCount	trimAlManager
back_trans_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
backtransFile	trimAlManager
backtranslationAlig	trimAlManager
block_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
blockSize	trimAlManager
c	trimAlManager
Catch::SectionInfo	trimAlManager	friend
check_absolute_gap_theshold()	trimAlManager	inlineprivate
check_and_prepare_coding_sequence()	trimAlManager	private
check_arguments_incompatibilities()	trimAlManager	private
check_arguments_needs(char *argv[])	trimAlManager	private
check_automated_manual_incompatibilities()	trimAlManager	private
check_automated_methods_incompatibilities()	trimAlManager	private
check_backtranslation_infile_names_correspondence()	trimAlManager	private
check_backtranslations()	trimAlManager	private
check_block_size()	trimAlManager	private
check_clusters_incompatibilities()	trimAlManager	private
check_coding_sequences_type()	trimAlManager	private
check_codon_behaviour_incompatibility()	trimAlManager	private
check_col_numbering()	trimAlManager	private
check_combinations_among_thresholds_incompatibility()	trimAlManager	private
check_compareset_window_argument()	trimAlManager	private
check_file_aligned()	trimAlManager	private
check_force_selection()	trimAlManager	private
check_inFile_incompatibilities()	trimAlManager	private
check_input_file_with_coding_sequences_argument()	trimAlManager	private
check_max_identity_incompatibilities()	trimAlManager	private
check_output_file_with_statistics()	trimAlManager	private
check_output_format()	trimAlManager	private
check_output_relevance()	trimAlManager	private
check_outputs_coincidence()	trimAlManager	private
check_residue_and_sequence_overlap()	trimAlManager	private
check_select_cols_and_seqs_incompatibilities()	trimAlManager	private
check_similarity_matrix()	trimAlManager	private
check_stats_incompatibilities()	trimAlManager	private
check_thresholds_dependencies()	trimAlManager	private
check_thresholds_incompatibilities()	trimAlManager	private
check_vcf_incompatibility()	trimAlManager	private
check_windows_incompatibilities()	trimAlManager	private
clean_alignment()	trimAlManager	private
CleanResiduesAuto()	trimAlManager	private
CleanResiduesNonAuto()	trimAlManager	private
CleanSequences()	trimAlManager	private
clusters	trimAlManager
clusters_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
col_numbering_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
columnNumbering	trimAlManager
compare	trimAlManager
compareAlignmentsArray	trimAlManager
compareset	trimAlManager
compareset_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
complementary_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
conservation_threshold_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
conservationThreshold	trimAlManager
consistency_threshold_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
consistency_window_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
consistencyThreshold	trimAlManager
consistencyWindow	trimAlManager
create_or_use_similarity_matrix()	trimAlManager	private
CS	trimAlManager
delColumns	trimAlManager
delete_variables()	trimAlManager
delSequences	trimAlManager
Errored enum value	trimAlManager
examples()	trimAlManager	private
filesToCompare	trimAlManager
Final enum value	trimAlManager
force_select_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
forceFile	trimAlManager
formatManager	trimAlManager	private
gap_threshold_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
gap_window_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
gapAbsoluteThreshold	trimAlManager
gappy_out_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
gappyout	trimAlManager
gapThreshold	trimAlManager
gapWindow	trimAlManager
getComplementary	trimAlManager
getComplementarySeq	trimAlManager
getFormatManager()	trimAlManager
help_arguments(const int *argc, char **argv, int *currentArg)	trimAlManager	private
html_out_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
htmlOutFile	trimAlManager
i	trimAlManager
ignore_filter_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
ignore_stop_codon_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
ignoreFilter	trimAlManager
ignoreStopCodon	trimAlManager
in_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
infile	trimAlManager
innerPerform()	trimAlManager	private
keep_header_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
keep_seqs_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
keepSeqs	trimAlManager
line	trimAlManager
matrix_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
matrixFile	trimAlManager
max_identity_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
maxIdentity	trimAlManager
menu()	trimAlManager	private
min_coverage_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
min_quality_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
minCoverage	trimAlManager
minQuality	trimAlManager
no_all_gaps_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
no_gaps_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
noallgaps	trimAlManager
nogaps	trimAlManager
NotRecognized enum value	trimAlManager
oformats	trimAlManager
origAlig	trimAlManager
out_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
out_format_arguments(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
outfile	trimAlManager
output_reports()	trimAlManager	private
parseArguments(int argc, char **argv)	trimAlManager
perform()	trimAlManager
performCompareset()	trimAlManager	private
postprocess_alignment()	trimAlManager	private
print_statistics()	trimAlManager	private
processArguments(char *argv[])	trimAlManager
Recognized enum value	trimAlManager
remove_duplicates_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
removeDuplicates	trimAlManager
residue_overlap_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
residuesOverlap	trimAlManager
save_alignment()	trimAlManager	private
select_cols_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
selectCols	trimAlManager
selectSeqs	trimAlManager
seqs_select_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
sequence_overlap_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
sequenceOverlap	trimAlManager
sequencesLengths	trimAlManager
sequencesNames	trimAlManager
set_window_size()	trimAlManager	private
sfc	trimAlManager
sft	trimAlManager
sgc	trimAlManager
sgt	trimAlManager
sident	trimAlManager
similarity_threshold_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
similarity_window_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
similarityThreshold	trimAlManager
similarityWindow	trimAlManager
similMatrix	trimAlManager
singleAlig	trimAlManager
soverlap	trimAlManager
split_by_stop_codon_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
splitByStopCodon	trimAlManager
ssc	trimAlManager
sst	trimAlManager
stats	trimAlManager
stats_arguments(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
strict	trimAlManager
strict_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
strict_plus_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
strictplus	trimAlManager
svg_out_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
svg_stats_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
svg_stats_out()	trimAlManager	private
svgOutFile	trimAlManager
svgStatsOutFile	trimAlManager
tempAlig	trimAlManager
terminal_only_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
terminalOnly	trimAlManager
timetracker_out_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
trimAlManager()	trimAlManager
vcf_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
vcfs	trimAlManager
verbosity_argument(const int *argc, char *argv[])	trimAlManager	private
window_argument(const int *argc, char *argv[], int *currentArg)	trimAlManager	private
windowSize	trimAlManager
~trimAlManager()	trimAlManager