Method List

Classes Methods Files

Search:

#+ SequenceLogo::Alignment
#== IUPAC
#add_image SequenceLogo::VerticalGluingCanvas
#add_image SequenceLogo::GluingCanvas
#add_image SequenceLogo::HorizontalGluingCanvas
#add_letter SequenceLogo::LogoCanvas
#add_position_ordered SequenceLogo::LogoCanvas
#allele_variants SequenceLogo::SequenceWithSNP
#arglist_augmented_with_stdin Top Level Namespace
#average Array
#background SequenceLogo::GluingCanvas
#background_fill SequenceLogo::CanvasFactory
basename_wo_extname File
#best_hit Ytilib::PM
#best_score Ytilib::PPM
#best_score Ytilib::PM
#best_word Ytilib::PM
calc_probs Ytilib::Randoom
calc_probs_m Ytilib::Randoom
#canvas_factory SequenceLogo::LogoCanvas
#checkerr Top Level Namespace
#col_sum Ytilib::PM
col_sum Ytilib::PM
#collect_hits Ytilib::PM
#compl String
#compl IUPAC
#compl! String
#compl! IUPAC
complement SequenceLogo::Sequence
#consensus Ytilib::PM
#consensus_string Ytilib::PM
#cut_to Float
#deep_dup Object
#direct_image SequenceLogo::PredefinedLogo
#direct_output_filename Top Level Namespace
#draw_threshold_line SequenceLogo::LogoCanvas
#dup Ytilib::PM
#dup IUPAC
#each_position Ytilib::PM
#each_position_index Ytilib::PM
#enable_threshold_lines SequenceLogo::PPMLogo
#eql? Ytilib::PM
equalize! Ytilib::Randoom
ext_wo_name File
#fast_score_sigma Ytilib::PM
#fast_score_sigma_precise Ytilib::PM
#fill Magick::SolidFill
#find_hit Ytilib::PM
#find_hits Ytilib::PM
#fixwc Ytilib::PM
#flexeql? Ytilib::PM
from_IUPAC Ytilib::PPM
from_bismark Ytilib::PM
from_string SequenceLogo::SequenceWithSNP
#getXML Ytilib::Bismark
#get_consensus Ytilib
#get_line PPM
#get_logo PPM
#get_logo_discrete PPM
#get_logo_weblogo PPM
#get_pcm Ytilib::PPM
#get_pm Ytilib::Bismark
#get_ppm Ytilib::PM
#get_ppm PPM
#get_ppm_from_file Top Level Namespace
#get_pwm Ytilib::PPM
#get_pwm Ytilib::PM
#get_pwm0pc Ytilib::PPM
#i_logo SequenceLogo::GluingCanvas
#icd Ytilib::PPM
#icd2of4 Ytilib::PM
#icd3of4 Ytilib::PM
#icd4of4 Ytilib::PM
#icdThc Ytilib::PM
#icdTlc Ytilib::PM
#icd_mode SequenceLogo::PPMLogo
#image SequenceLogo::GluingCanvas
#in_necessary_orientations Top Level Namespace
#include? IUPAC
#infocod Ytilib::PM
#infocod Ytilib::PPM
#initialize Magick::SolidFill
#initialize Ytilib::PPM
#initialize SequenceLogo::CanvasFactory
#initialize SequenceLogo::LogoCanvas
#initialize Ytilib::PM
#initialize SequenceLogo::Sequence
#initialize SequenceLogo::PredefinedLogo
#initialize SequenceLogo::Alignment
#initialize SequenceLogo::Alignment::Item
#initialize SequenceLogo::CLI
#initialize IUPAC
#initialize REXML::Formatters::Transitive
#initialize SequenceLogo::SequenceWithSNP
#initialize SequenceLogo::GluingCanvas
#initialize SequenceLogo::PPMLogo
#initialize Ytilib::Bismark
#iupacomp! Ytilib::PM
#iupacomp! Ytilib::PPM
#left SequenceLogo::SequenceWithSNP
#length SequenceLogo::PPMLogo
#length SequenceLogo::SequenceWithSNP
#length SequenceLogo::Sequence
#length SequenceLogo::Alignment::Item
#length SequenceLogo::PredefinedLogo
#letter_image SequenceLogo::CanvasFactory
#letter_images SequenceLogo::CanvasFactory
letter_images SequenceLogo::CanvasFactory
#letter_index SequenceLogo::CanvasFactory
load Ytilib::PM
#load_alignment_infos Top Level Namespace
#log_fact Float
#log_fact Integer
#logo_canvas SequenceLogo::CanvasFactory
#logo_for_ordered_letters SequenceLogo::CanvasFactory
#logo_matrix SequenceLogo::PPMLogo
#logo_shift SequenceLogo::CanvasFactory
#logo_with_name SequenceLogo::CanvasFactory
#m3sd Ytilib::PM
#make_logo_alignment Top Level Namespace
make_probs! Ytilib::Randoom
make_probs_m! Ytilib::Randoom
#matrix Ytilib::PM
#merge IUPAC
mfa2array Ytilib
#name SequenceLogo::PPMLogo
#name PPM
#name SequenceLogo::Sequence
#name SequenceLogo::SequenceWithSNP
#name SequenceLogo::Alignment::Item
#name SequenceLogo::PredefinedLogo
name_wo_ext File
new_mysql_conn Ytilib
new_pcm Ytilib::PM
new_pwm Ytilib::PM
#object SequenceLogo::Alignment::Item
#options SequenceLogo::CLI
#p_value Ytilib::PM
#parse_options! SequenceLogo::CLI
#parser SequenceLogo::CLI
#positiv! Ytilib::PM
#ppm SequenceLogo::PPMLogo
#prev String
#prev! String
probs2IUPAC! Ytilib::PPM
#put_image_at Magick::ImageList
rand_seq Ytilib::Randoom
read_mfa2array Ytilib
read_mfa2hash Ytilib
read_plain2array Ytilib
read_seqs2array Ytilib
#readlines_from_file_or_stdin Top Level Namespace
#render SequenceLogo::SequenceWithSNP
#render SequenceLogo::PPMLogo
#render SequenceLogo::Sequence
#render SequenceLogo::Alignment::Item
#render SequenceLogo::PredefinedLogo
#render SequenceLogo::Alignment
#render_threshold_line SequenceLogo::LogoCanvas
#report Top Level Namespace
#revcomp String
#revcomp SequenceLogo::PredefinedLogo
revcomp SequenceLogo::Sequence
#revcomp SequenceLogo::Sequence
#revcomp SequenceLogo::PPMLogo
#revcomp PPM
#revcomp SequenceLogo::SequenceWithSNP
#revcomp SequenceLogo::Alignment
#revcomp! String
#revcomp! Ytilib::PM
#reverse IUPAC
#reverse_image SequenceLogo::PredefinedLogo
#reverse_output_filename Top Level Namespace
#reverse_string IUPAC
#right SequenceLogo::SequenceWithSNP
#round_to Float
#save Ytilib::PM
#score Ytilib::PPM
#score Ytilib::PM
#score_mean Ytilib::PM
#score_sigma Ytilib::PM
#score_variance Ytilib::PM
#sequence SequenceLogo::Sequence
#set_minimal_size Magick::ImageList
#shift SequenceLogo::Alignment::Item
#shifted_logo SequenceLogo::CanvasFactory
#shuffle Array
#shuffle! Array
#size SequenceLogo::GluingCanvas
#size Ytilib::PM
#start Top Level Namespace
#strict_consensus Ytilib::PM
#sum Array
#text_image SequenceLogo::CanvasFactory
#text_size SequenceLogo::CanvasFactory
time Ytilib
#to_bismark Ytilib::PPM
#to_bismark Ytilib::PM
#to_id String
#to_pwm! Ytilib::PPM
#to_pwm! Ytilib::PM
twostrand! Ytilib::Randoom
valid_sequence? SequenceLogo::Sequence
#variance Array
#words_count SequenceLogo::PPMLogo
#words_count Ytilib::PM
#worst_score Ytilib::PPM
#worst_score Ytilib::PM
#write REXML::Document
write_mfa Ytilib
#x_size SequenceLogo::HorizontalGluingCanvas
#x_size SequenceLogo::VerticalGluingCanvas
#x_unit SequenceLogo::CanvasFactory
#y_size SequenceLogo::HorizontalGluingCanvas
#y_size SequenceLogo::VerticalGluingCanvas
#y_unit SequenceLogo::CanvasFactory