Skip to content

Commit

Permalink
fix typo initialise -> initialize
Browse files Browse the repository at this point in the history
  • Loading branch information
@hmehlan
hmehlan committed Nov 7, 2018
1 parent c85fdb5 commit 4afcc6a
Show file tree
Hide file tree
Showing 42 changed files with 62 additions and 62 deletions.
2 changes: 1 addition & 1 deletion augustus-training/grails-app/views/help.gsp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -799,7 +799,7 @@ HS04636 anchor intronpart 7631 7633 0 + 0 source=M
# Setting 1group1gene for E.
# Sources of extrinsic information: M E
# Have extrinsic information about 1 sequences (in the specified range).
# Initialising the parameters ...
# Initializing the parameters ...
# human version. Use default transition matrix.
# Looks like /var/tmp/augustus/AUG-1855139717/input.fa is in fasta format.
# We have hints for 1 sequence and for 1 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion augustus-training/grails-app/views/predictiontutorial.gsp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1065,7 +1065,7 @@ HS04636 anchor intronpart 7631 7633 0 + 0 source=M
# Setting 1group1gene for E.
# Sources of extrinsic information: M E
# Have extrinsic information about 1 sequences (in the specified range).
# Initialising the parameters ...
# Initializing the parameters ...
# human version. Use default transition matrix.
# Looks like /var/tmp/augustus/AUG-1855139717/input.fa is in fasta format.
# We have hints for 1 sequence and for 1 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion augustus-training/plugins/plugins-list-default.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -31822,7 +31822,7 @@ It integrates nicely with the resources plugin.
<title>Git Plugin</title>
<author>Peter Ledbrook</author>
<authorEmail>[email protected]</authorEmail>
<description>Integrates git, the distributed version control system, into Grails projects. It can initialise a local git repository for your project, add a .gitignore file and commit the first version of your source code.
<description>Integrates git, the distributed version control system, into Grails projects. It can initialize a local git repository for your project, add a .gitignore file and commit the first version of your source code.
</description>
<file>http://plugins.grails.org/grails-git/tags/RELEASE_1_0-SNAPSHOT/grails-git-1.0-SNAPSHOT.zip</file>
</release>
Expand Down
2 changes: 1 addition & 1 deletion auxprogs/bam2wig/bam2wig.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -91,7 +91,7 @@ int main(int argc, char *argv[])
}


// Initialising auxiliary data structures
// Initializing auxiliary data structures
data = calloc(1, sizeof(void*)); // data[0] is array for just one BAM file
// set the default region. left-shift "end" by appending 30 zeros (i.e. end=1073741824)
beg = 0; end = 1<<30; tid = -1;
Expand Down
2 changes: 1 addition & 1 deletion auxprogs/filterBam/src/filterBam.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -149,7 +149,7 @@ int main(int argc, char *argv[])
optionalCounters.outPaired = outPaired;
optionalCounters.outUniq = outUniq;
optionalCounters.outBest = outBest;
// Initialising options
// Initializing options
struct globalOptions_t globalOptions;
globalOptions = initOptions(argc, argv);
bool best = globalOptions.best;
Expand Down
4 changes: 2 additions & 2 deletions auxprogs/filterBam/src/functions/MatePairs.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -55,15 +55,15 @@ MatePairs::MatePairs(const MatePairs &copyin) // Copy constructor to handle pa
this->score = copyin.score;
}

// Initialisation method
// Initialization method
MatePairs::MatePairs(int it, int jit, float score)
{
this->alIt = it;
this->alJit = jit;
this->score = score;
}

// Initialisation method
// Initialization method
void MatePairs::setValues(int it, int jit, float score)
{
this->alIt = it;
Expand Down
4 changes: 2 additions & 2 deletions auxprogs/filterBam/src/functions/PairednessCoverage.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ PairednessCoverage::PairednessCoverage(const PairednessCoverage &copyin) // Co
this->chr = copyin.chr;
}

// Initialisation method
// Initialization method
PairednessCoverage::PairednessCoverage(int coord, int label, string chr)
{
this->coord = coord;
Expand All @@ -60,7 +60,7 @@ PairednessCoverage::PairednessCoverage(int coord, int label, string chr)
}


// Initialisation method
// Initialization method
void PairednessCoverage::setValues(int coord, int label, string chr)
{
this->coord = coord;
Expand Down
2 changes: 1 addition & 1 deletion auxprogs/filterBam/src/functions/SingleAlignment.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ SingleAlignment::SingleAlignment(BamAlignment *al, float coverage, float percId,
}


// Initialisation method
// Initialization method
void SingleAlignment::setValues(BamAlignment *al, float coverage, float percId, const RefVector *refData)
{
this->al = al;
Expand Down
2 changes: 1 addition & 1 deletion auxprogs/filterBam/src/functions/initOptions.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,7 @@ void displayUsage(int argc, char *argv[])
}


// Options initialisation
// Options initialization
globalOptions_t initOptions(int argc, char *argv[])
{
int opt = 0, longIndex;
Expand Down
2 changes: 1 addition & 1 deletion auxprogs/filterBam/src/headers/filterBam.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ uint32_t sumMandIOperations(vector<CigarOp> cigar, string printFlag);
uint32_t sumDandIOperations(vector<CigarOp> cigar, string printFlag);
int printElapsedTime(int tEnd, int tStart);

// For option initialisation
// For option initialization
struct globalOptions_t {
bool best;
bool help;
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial-cgp/results/aug_rnaseq/bosTau8.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Sources of extrinsic information: M RM
# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# human version. Using default transition matrix.
# Looks like ../genomes/bosTau8.fa is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial-cgp/results/aug_rnaseq/canFam3.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Sources of extrinsic information: M RM
# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# human version. Using default transition matrix.
# Looks like ../genomes/canFam3.fa is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial-cgp/results/aug_rnaseq/galGal4.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
# Setting UTRpart local malus: 0.985
# reading in the file ../hints/galGal4.hints.gff ...
# Have extrinsic information about 1 sequences (in the specified range).
# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# human version. Using species specific transition matrix: /home/mario/augustus/git/Augustus/config/species/human/human_trans_shadow_partial_utr.pbl
# Looks like ../genomes/galGal4.fa is in fasta format.
# We have hints for 1 sequence and for 1 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial-cgp/results/aug_rnaseq/hg38.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
# Setting UTRpart local malus: 0.985
# reading in the file ../hints/hg38.hints.gff ...
# Have extrinsic information about 1 sequences (in the specified range).
# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# human version. Using species specific transition matrix: /home/mario/augustus/git/Augustus/config/species/human/human_trans_shadow_partial_utr.pbl
# Looks like ../genomes/hg38.fa is in fasta format.
# We have hints for 1 sequence and for 1 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial-cgp/results/aug_rnaseq/mm10.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
# Setting UTRpart local malus: 0.985
# reading in the file ../hints/mm10.hints.gff ...
# Have extrinsic information about 1 sequences (in the specified range).
# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# human version. Using species specific transition matrix: /home/mario/augustus/git/Augustus/config/species/human/human_trans_shadow_partial_utr.pbl
# Looks like ../genomes/mm10.fa is in fasta format.
# We have hints for 1 sequence and for 1 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial-cgp/results/aug_rnaseq/monDom5.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Sources of extrinsic information: M RM
# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# human version. Using default transition matrix.
# Looks like ../genomes/monDom5.fa is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial-cgp/results/aug_rnaseq/rheMac3.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
# Setting UTRpart local malus: 0.985
# reading in the file ../hints/rheMac3.hints.gff ...
# Have extrinsic information about 1 sequences (in the specified range).
# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# human version. Using species specific transition matrix: /home/mario/augustus/git/Augustus/config/species/human/human_trans_shadow_partial_utr.pbl
# Looks like ../genomes/rheMac3.fa is in fasta format.
# We have hints for 1 sequence and for 1 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial-cgp/results/aug_rnaseq/rn6.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Sources of extrinsic information: M RM
# Initialising the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# human version. Using default transition matrix.
# Looks like ../genomes/rn6.fa is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial/results/augustus-ppx.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters ...
# Initializing the parameters ...
# Using protein profile unknown
# --[8..1336]--> unknown_A (9) <--[16..88]--> unknown_B (7) <--[19..46]--> unknown_D (8) <--[0..1]--> unknown_E (10) <--[2..42]--> unknown_F (10) <--[9..128]--> unknown_G (11) <--[16..74]--> unknown_H (16) <--[10..54]--> unknown_I (8) <--[8..29]--> unknown_J (13) <--[8..42]--> unknown_K (15) <--[1..3]--> unknown_L (12) <--[6..15]--> unknown_M (13) <----
# human version. Use default transition matrix.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial/results/augustus.abinitio.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters ...
# Initializing the parameters ...
# fly version. Use default transition matrix.
# Looks like chr2R.fa is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial/results/augustus.hints.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
# Setting UTRpart local malus: 0.96
# Sources of extrinsic information: M E W
# Have extrinsic information about 1 sequences (in the specified range).
# Initialising the parameters ...
# Initializing the parameters ...
# fly version. Use default transition matrix.
# Looks like chr2R.fa is in fasta format.
# We have hints for 1 sequence and for 1 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial/results/output-abinitio.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters ...
# Initializing the parameters ...
# human version. Use default transition matrix.
# Looks like chr4.103M.fa is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial/results/output.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters ...
# Initializing the parameters ...
# Using protein profile unknown
# --[8..1336]--> unknown_A (9) <--[16..88]--> unknown_B (7) <--[19..46]--> unknown_D (8) <--[0..1]--> unknown_E (10) <--[2..42]--> unknown_F (10) <--[9..128]--> unknown_G (11) <--[16..74]--> unknown_H (16) <--[9..54]--> unknown_I (8) <--[8..29]--> unknown_J (13) <--[8..42]--> unknown_K (15) <--[1..3]--> unknown_L (12) <--[6..15]--> unknown_M (13) <----
# human version. Use default transition matrix.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial2015/results/aug.nasonia.1-1M.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Sources of extrinsic information: M RM
# Initialising the parameters using config directory /home/mario/augustus/trunks/config/ ...
# Initializing the parameters using config directory /home/mario/augustus/trunks/config/ ...
# nasonia version. Using default transition matrix.
# Looks like chr2L.sm.fa is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial2015/results/aug.nasonia.hints.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
# Setting UTRpart local malus: 0.985
# reading in the file hints.gff ...
# Have extrinsic information about 1 sequences (in the specified range).
# Initialising the parameters using config directory /home/mario/augustus/trunks/config/ ...
# Initializing the parameters using config directory /home/mario/augustus/trunks/config/ ...
# nasonia version. Using default transition matrix.
# start gene g1
chr2L AUGUSTUS gene 6774 9276 0.44 + . g1
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial2015/results/aug.tomato.1-1M.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Sources of extrinsic information: M RM
# Initialising the parameters using config directory /home/mario/augustus/trunks/config/ ...
# Initializing the parameters using config directory /home/mario/augustus/trunks/config/ ...
# tomato version. Using default transition matrix.
# Looks like chr2L.sm.fa is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial2015/results/aug.zebrafish.1-1M.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Sources of extrinsic information: M RM
# Initialising the parameters using config directory /home/mario/augustus/trunks/config/ ...
# Initializing the parameters using config directory /home/mario/augustus/trunks/config/ ...
# zebrafish version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(0.999), CTG(0.000667), TTG(0)
# Looks like chr2L.sm.fa is in fasta format.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial2015/results/firsttest.out
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters using config directory /home/mario/augustus/trunks/config/ ...
# Initializing the parameters using config directory /home/mario/augustus/trunks/config/ ...
# bug version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like genes.gb.test is in genbank format. Augustus uses the annotation for evaluation of accuracy.
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial2018/data/augustus_ab_initio.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters ...
# Initializing the parameters ...
# o.tauri version. Using default transition matrix.
# Looks like masking/genome.fa.softmasked is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
Expand Down
2 changes: 1 addition & 1 deletion examples/profile/chr1.161M.gff
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters ...
# Initializing the parameters ...
# Using protein profile HSP70
# --[0..159]--> PF00012.13_A (30) <--[0..3]--> PF00012.13_B (33) <--[0..7]--> PF00012.13_C (13) <--[13..24]--> PF00012.13_D (75) <--[1..13]--> PF00012.13_E (21) <--[10..20]--> PF00012.13_F (12) <--[0..18]--> PF00012.13_G (11) <--[3..4]--> PF00012.13_H (27) <--[0..2]--> PF00012.13_I (13) <--[1..8]--> PF00012.13_J (34) <--[5..20]--> PF00012.13_K (26) <--[0..1]--> PF00012.13_L (26) <--[0..8]--> PF00012.13_M (39) <--[0..1]--> PF00012.13_N (35) <--[0..11]--> PF00012.13_O (33) <--[0..1]--> PF00012.13_P (15) <--[0..1]--> PF00012.13_Q (46) <--[34,...]--
# human version. Use default transition matrix.
Expand Down
2 changes: 1 addition & 1 deletion include/extrinsicinfo.hh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -258,7 +258,7 @@ private:
*/
struct FeatureTypeInfo {
FeatureTypeInfo(int numSources=1, double b=-1.0, double m=1.0, double lm=1.0) :
bonus(b), // -1 means not initialised
bonus(b), // -1 means not initialized
malus(m), // don't change anything unless we have at least searched
localMalus(lm),
gradeclassbounds(numSources, vector<double>()),
Expand Down
2 changes: 1 addition & 1 deletion include/pp_profile.hh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -612,7 +612,7 @@ namespace PP {

public:
// methods of class ProteinProfile
// initialise pattern from file <filename>
// initialize pattern from file <filename>
Profile(string filename);


Expand Down
6 changes: 3 additions & 3 deletions src/augustus.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -115,7 +115,7 @@ int main( int argc, char* argv[] ){
Constant::init();
Gene::init();
GeneticCode::init();
setParameters(); // NOTE: need Constant and GeneticCode to be initialised first
setParameters(); // NOTE: need Constant and GeneticCode to be initialized first
StateModel::init(); // set global parameters of state models

if(Properties::hasProperty("trainFeatureFile"))
Expand Down Expand Up @@ -145,7 +145,7 @@ int main( int argc, char* argv[] ){
cout << PREAMBLE << endl;

/*
* check for extrinsic information and initialise when existent
* check for extrinsic information and initialize when existent
*/
FeatureCollection extrinsicFeatures;
const char *extrinsicfilename;
Expand All @@ -169,7 +169,7 @@ int main( int argc, char* argv[] ){
}

if (verbosity > 1)
cout << "# Initialising the parameters using config directory " << Properties::getProperty(CFGPATH_KEY) << " ..." << endl;
cout << "# Initializing the parameters using config directory " << Properties::getProperty(CFGPATH_KEY) << " ..." << endl;
BaseCount::init();
PP::initConstants();
NAMGene namgene; // creates and initializes the states
Expand Down
2 changes: 1 addition & 1 deletion src/compgenepred.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -593,7 +593,7 @@ void CompGenePred::start(){
GeneMSA::topologies.clear();

if(Properties::hasProperty("referenceFile")){
// initialise training of log reg parameters
// initialize training of log reg parameters
train_OEscore_params(speciesNames.size());
}
}
Expand Down
2 changes: 1 addition & 1 deletion src/consensus.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ consensus::consensus(int starting1,int ending1){
for(i=pattern_size-1;i>=0;i--)
powers.push_back(pow((double)4,(double)i));

//initialises the mean value, significance value, relevant value vectors
//initializes the mean value, significance value, relevant value vectors
for(i=0;i<pow((double)4,(double)pattern_size);i++){
t_values.push_back(0);
f_values.push_back(0);
Expand Down
2 changes: 1 addition & 1 deletion src/espoca.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -114,7 +114,7 @@ int main( int argc, char* argv[] ){
GeneticCode::chooseTranslationTable(Properties::getIntProperty("translation_table"));
}

// setParameters(); // NOTE: need Constant and GeneticCode to be initialised first
// setParameters(); // NOTE: need Constant and GeneticCode to be initialized first
StateModel::init(); // set global parameters of state models

// calculate omega on input codon alignment
Expand Down
Loading

0 comments on commit 4afcc6a

Please sign in to comment.