#include <boost/filesystem/fstream.hpp>
namespace fs = boost::filesystem;
-#include <boost/spirit/core.hpp>
-#include <boost/spirit/actor/push_back_actor.hpp>
-#include <boost/spirit/iterator/file_iterator.hpp>
-#include <boost/spirit/utility/chset.hpp>
-namespace spirit = boost::spirit;
+#include <boost/algorithm/string.hpp>
#include <iostream>
#include <sstream>
#include "mussa_exceptions.hpp"
-#include "alg/mussa.hpp"
-#include "alg/flp.hpp"
+
+#include "flp.hpp"
+#include "io.hpp"
+#include "mussa.hpp"
+#include "motif_parser.hpp"
using namespace std;
: color_mapper(new AnnotationColors)
{
clear();
- connect(&the_paths, SIGNAL(progress(const std::string&, int, int)),
- this, SIGNAL(progress(const std::string&, int, int)));
+ connect(&the_paths, SIGNAL(progress(const QString&, int, int)),
+ this, SIGNAL(progress(const QString&, int, int)));
}
Mussa::Mussa(const Mussa& m)
analysis_path(m.analysis_path),
dirty(m.dirty)
{
- connect(&the_paths, SIGNAL(progress(const std::string&, int, int)),
- this, SIGNAL(progress(const std::string&, int, int)));
+ connect(&the_paths, SIGNAL(progress(const QString&, int, int)),
+ this, SIGNAL(progress(const QString&, int, int)));
+}
+
+MussaRef Mussa::init()
+{
+ boost::shared_ptr<Mussa> m(new Mussa());
+ return m;
}
boost::filesystem::path Mussa::get_analysis_path() const
the_seqs.clear();
the_paths.clear();
analysis_path = fs::path();
- dirty = false;
+ set_dirty(false);
+}
+
+void Mussa::set_append_window(bool v)
+{
+ win_append = v;
+}
+
+bool Mussa::get_append_window()
+{
+ return win_append;
+}
+
+void Mussa::set_append_threshold(bool v)
+{
+ thres_append = v;
+}
+
+bool Mussa::get_append_threshold()
+{
+ return thres_append;
+}
+
+void Mussa::set_dirty(bool new_state)
+{
+ if (dirty != new_state) {
+ dirty = new_state;
+ emit isModified(dirty);
+ }
}
bool Mussa::is_dirty() const
Mussa::set_name(string a_name)
{
analysis_name = a_name;
- dirty = true;
+ set_dirty(true);
}
string Mussa::get_name() const
Mussa::set_window(int a_window)
{
window = a_window;
- dirty = true;
+ set_dirty(true);
}
int Mussa::get_window() const
Mussa::set_threshold(int a_threshold)
{
threshold = a_threshold;
- dirty = true;
+ set_dirty(true);
if (a_threshold > soft_thres) {
soft_thres = a_threshold;
}
return soft_thres;
}
+
void
Mussa::set_analysis_mode(enum analysis_modes new_ana_mode)
{
ana_mode = new_ana_mode;
- dirty = true;
+ set_dirty(true);
}
enum Mussa::analysis_modes Mussa::get_analysis_mode() const
{
boost::shared_ptr<Sequence> seq_copy(new Sequence(a_seq));
the_seqs.push_back(seq_copy);
- dirty = true;
+ set_dirty(true);
}
void Mussa::append_sequence(boost::shared_ptr<Sequence> a_seq)
{
the_seqs.push_back(a_seq);
- dirty = true;
+ set_dirty(true);
}
-const vector<boost::shared_ptr<Sequence> >&
+const vector<SequenceRef>&
Mussa::sequences() const
{
return the_seqs;
aseq->set_species(*name);
}
the_seqs.push_back(aseq);
- dirty = true;
+ set_dirty(true);
+}
+
+void Mussa::load_mupa_file(std::string para_file_path) {
+ load_mupa_file(boost::filesystem::path(para_file_path));
}
void
Mussa::load_mupa_file(fs::path para_file_path)
{
- fs::ifstream para_file;
- string file_data_line;
- string param, value;
- fs::path annot_file;
- int split_index, fasta_index;
- int sub_seq_start, sub_seq_end;
- bool seq_params, did_seq;
- string err_msg;
- bool parsing_path;
- string::size_type new_index, dir_index;
-
- // initialize values
- clear();
-
- // if file was opened, read the parameter values
if (not fs::exists(para_file_path))
{
throw mussa_load_error("Config File: " + para_file_path.string() + " not found");
} else if (fs::is_empty(para_file_path)) {
throw mussa_load_error("Config File: " + para_file_path.string() + " is empty");
} else {
+ // what directory is the mupa file in?
+ fs::path file_path_base( para_file_path.branch_path()) ;
+
+ fs::ifstream para_file;
para_file.open(para_file_path, ios::in);
+
+ load_mupa_stream(para_file, file_path_base);
+ para_file.close();
+ }
+}
- // what directory is the mupa file in?
- fs::path file_path_base = para_file_path.branch_path();
+void
+Mussa::load_mupa_stream(std::istream& para_file, fs::path& file_path_base)
+{
+ std::string line;
+ std::vector< std::string > tokens;
+ int line_count = 0;
+
+ enum parsing_state_enum { START, INSEQUENCE };
+ parsing_state_enum parsing_state = START;
+
+ // sequence file parameters
+ fs::path seq_file;
+ fs::path annot_file;
+ int split_index, fasta_index;
+ int sub_seq_start, sub_seq_end;
+ bool seq_params, did_seq;
+ std::string err_msg;
+
+ // initialize values
+ clear();
+
+ while (para_file.good())
+ {
+ ++line_count;
// setup loop by getting file's first line
- getline(para_file,file_data_line);
- split_index = file_data_line.find(" ");
- param = file_data_line.substr(0,split_index);
- value = file_data_line.substr(split_index+1);
-
- while (para_file)
- {
- did_seq = false;
- if (param == "ANA_NAME")
- analysis_name = value;
- else if (param == "APPEND_WIN")
- win_append = true;
- else if (param == "APPEND_THRES")
- thres_append = true;
- else if (param == "SEQUENCE_NUM")
- ; // ignore sequence_num now
- else if (param == "WINDOW")
- window = atoi(value.c_str());
- else if (param == "THRESHOLD")
- threshold = atoi(value.c_str());
- else if (param == "SEQUENCE")
- {
- fs::path seq_file = file_path_base / value;
- //cout << "seq_file_name " << seq_files.back() << endl;
- fasta_index = 1;
- annot_file = "";
- sub_seq_start = 0;
- sub_seq_end = 0;
- seq_params = true;
-
- while (para_file && seq_params)
- {
- getline(para_file,file_data_line);
- split_index = file_data_line.find(" ");
- param = file_data_line.substr(0,split_index);
- value = file_data_line.substr(split_index+1);
-
- if (param == "FASTA_INDEX")
- fasta_index = atoi(value.c_str());
- else if (param == "ANNOTATION")
- annot_file = file_path_base / value;
- else if (param == "SEQ_START")
- sub_seq_start = atoi(value.c_str());
- else if (param == "SEQ_END")
- {
- sub_seq_end = atoi(value.c_str());
- }
- //ignore empty lines or that start with '#'
- else if ((param == "") || (param == "#")) {}
- else seq_params = false;
- }
+ multiplatform_getline(para_file, line);
+ // strip leading/trailing whitespace
+ boost::trim(line);
+ // ignore commented out or blank lines
+ if ( line.size() == 0 or line[0] == '#' ) {
+ continue;
+ }
+
+ // split the line on white spance
+ boost::split(tokens, line, boost::is_space());
+ // do we have a name/value pair?
+ if (tokens.size() != 2) {
+ std::stringstream errmsg;
+ errmsg << "Error parsing MUPA file line: "
+ << line_count << std::endl
+ << line;
+ throw mussa_load_error(errmsg.str());
+ }
+
+ boost::to_upper(tokens[0]);
+ // Parameters only useful after a sequence block
+ if (parsing_state == INSEQUENCE) {
+ // in the following if blocks, if we do
+ // successfully match a token we should continue
+ // on to the next token
+ // but if we don't match a token we want to
+ // fall through to the top level parsing
+
+ if (tokens[0] == "FASTA_INDEX") {
+ fasta_index = atoi(tokens[1].c_str());
+ continue;
+ } else if (tokens[0] == "ANNOTATION") {
+ annot_file = file_path_base / tokens[1];
+ continue;
+ } else if (tokens[0] == "SEQ_START") {
+ sub_seq_start = atoi(tokens[1].c_str());
+ continue;
+ } else if (tokens[0] == "SEQ_END") {
+ sub_seq_end = atoi(tokens[1].c_str());
+ continue;
+ } else {
+ // any other token means we're done with this
+ // sequence so we should load it
+ // (and let the "unknown" token fall through into the
+ // top level token parser)
load_sequence(seq_file, annot_file, fasta_index, sub_seq_start,
sub_seq_end);
- did_seq = true;
+ parsing_state = START;
}
- //ignore empty lines or that start with '#'
- else if ((param == "") || (param == "#")) {}
- else
- {
- clog << "Illegal/misplaced mussa parameter in file\n";
- clog << param << "\n";
- }
-
- if (!did_seq)
- {
- getline(para_file,file_data_line);
- split_index = file_data_line.find(" ");
- param = file_data_line.substr(0,split_index);
- value = file_data_line.substr(split_index+1);
- did_seq = false;
+ }
+ // if we didn't consume a token from the previous if block
+ // try
+ // top level token parsing
+ if (tokens[0] == "ANA_NAME") {
+ analysis_name = tokens[1];
+ } else if (tokens[0] == "APPEND_WIN") {
+ win_append = true;
+ } else if (tokens[0] == "APPEND_THRES") {
+ thres_append = true;
+ } else if (tokens[0] == "SEQUENCE_NUM") {
+ ; // ignore sequence_num now
+ } else if (tokens[0] == "WINDOW") {
+ window = atoi(tokens[1].c_str());
+ } else if (tokens[0] == "THRESHOLD") {
+ threshold = atoi(tokens[1].c_str());
+ } else if (tokens[0] == "SEQUENCE") {
+ if (parsing_state == INSEQUENCE) {
+ cout << "seq_file_name call2" << seq_file << endl;
+ load_sequence(seq_file, annot_file, fasta_index, sub_seq_start,
+ sub_seq_end);
+ parsing_state = START;
}
+ // reset sequence parameters
+ seq_file = file_path_base / tokens[1];
+ fasta_index = 1;
+ annot_file = "";
+ sub_seq_start = 0;
+ sub_seq_end = 0;
+ seq_params = true;
+ parsing_state = INSEQUENCE;
+ } else {
+ clog << "Illegal/misplaced mussa parameter in file\n";
+ clog << tokens[0] << "\n";
+ std::stringstream errmsg;
+ errmsg << "Invalid mussa paaramater '"
+ << tokens[0]
+ << "' on line: "
+ << line_count << std::endl
+ << line;
+ throw mussa_load_error(errmsg.str());
+ throw mussa_load_error("Error parsing MUPA file");
}
+ }
- para_file.close();
-
- soft_thres = threshold;
- //cout << "nway mupa: analysis_name = " << analysis_name
- // << " window = " << window
- // << " threshold = " << threshold << endl;
+ // if we hit the end of the file and there's a sequence
+ // pending, go ahead and load it
+ if (parsing_state == INSEQUENCE) {
+ load_sequence(seq_file, annot_file, fasta_index, sub_seq_start,
+ sub_seq_end);
}
- // no file was loaded, signal error
- dirty = true;
+
+ soft_thres = threshold;
+ set_dirty(true);
}
void
Mussa::save(fs::path save_path)
{
- fs::path flp_filepath;
fs::fstream save_file;
ostringstream append_info;
int dir_create_status;
if (not fs::exists(save_path)) {
fs::create_directory(save_path);
}
+
+ std::string basename = save_path.leaf();
+ fs::path museq(basename + ".museq", fs::native);
+
// save sequence and annots to a special mussa file
- save_file.open(save_path / (save_path.leaf()+".museq"), ios::out);
+ save_file.open(save_path / museq, ios::out);
save_file << "<Mussa_Sequence>" << endl;
for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
// if we have any motifs, save them.
if (motif_sequences.size()) {
- save_motifs(save_path/(save_path.leaf()+".mtl"));
+ fs::path mtl(basename + ".mtl", fs::native);
+ save_motifs(save_path / mtl);
}
// save nway paths to its mussa save file
- the_paths.save(save_path / (save_path.leaf()+ ".muway"));
+ fs::path muway(basename + ".muway", fs::native);
+ the_paths.save(save_path / muway);
for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++) {
for(vector<Sequence>::size_type i2 = i+1; i2 < the_seqs.size(); i2++)
{
append_info.str("");
append_info << "_sp_" << i << "v" << i2;
- all_comps[i][i2].save(save_path/(save_path.leaf()+append_info.str()+".flp"));
+ fs::path flp(basename+append_info.str()+".flp", fs::native);
+ all_comps[i][i2].save(save_path / flp);
}
}
- dirty = false;
+ set_dirty(false);
analysis_path = save_path;
}
vector<FLPs> empty_FLP_vector;
FLPs dummy_comp;
+
+ //--------------------------------------------------------
+ // Load Muway
+ //--------------------------------------------------------
analysis_path = ana_file;
analysis_name = ana_path.leaf();
- file_path_base = ana_path.branch_path() / analysis_name;
- a_file_path = file_path_base / (analysis_name + ".muway");
+ fs::path muway(analysis_name+".muway", fs::native);
+ a_file_path = analysis_path / muway;
the_paths.load(a_file_path);
// perhaps this could be more elegent, but at least this'll let
// us know what our threshold and window sizes were when we load a muway
window = the_paths.get_window();
threshold = the_paths.get_threshold();
- soft_thres = threshold;
+ soft_thres = the_paths.get_soft_threshold();
- int seq_num = the_paths.sequence_count();
- a_file_path = file_path_base / (analysis_name + ".museq");
+ //--------------------------------------------------------
+ // Load Sequence
+ //--------------------------------------------------------
+ //int seq_num = the_paths.sequence_count();
+
+ fs::path museq(analysis_name + ".museq", fs::native);
+ a_file_path = analysis_path / museq;
// this is a bit of a hack due to C++ not acting like it should with files
- for (i = 1; i <= seq_num; i++)
+ /*for (i = 1; i <= seq_num; i++)
{
boost::shared_ptr<Sequence> tmp_seq(new Sequence);
tmp_seq->load_museq(a_file_path, i);
the_seqs.push_back(tmp_seq);
+ }*/
+
+ i = 1;
+ //int seq_num = 0;
+ boost::filesystem::fstream load_museq_fs;
+ load_museq_fs.open(a_file_path, std::ios::in);
+ boost::shared_ptr<Sequence> tmp_seq;
+ while (1)
+ {
+ tmp_seq = Sequence::load_museq(load_museq_fs);
+
+ if (tmp_seq)
+ {
+ the_seqs.push_back(tmp_seq);
+ }
+ else
+ {
+ break;
+ }
+
+
+ //safe guard in case of an infinate loop.
+ //FIXME: If mussa can handle a comparison of 10000 sequences
+ // in the future, then this code should be fixed.
+ if (i == 10000)
+ {
+ throw mussa_load_error(" Run away sequence load!");
+ }
+ i++;
}
+ load_museq_fs.close();
- fs::path motif_file = file_path_base / (analysis_name + ".mtl");
+ //--------------------------------------------------------
+ // Load Motifs
+ //--------------------------------------------------------
+ fs::path mtl(analysis_name + ".mtl", fs::native);
+ fs::path motif_file = analysis_path / mtl;
if (fs::exists(motif_file)) {
load_motifs(motif_file);
}
+
+ vector<Sequence>::size_type seq_num = the_seqs.size();
empty_FLP_vector.clear();
for(i = 0; i < seq_num; i++)
{
all_comps[i].push_back(dummy_comp);
}
+
for(i = 0; i < seq_num; i++)
{
for(i2 = i+1; i2 < seq_num; i2++)
append_info.str("");
append_info << analysis_name << "_sp_" << i << "v" << i2 << ".flp";
//clog << append_info.str() << endl;
- a_file_path = file_path_base / append_info.str();
- //clog << "path " << a_file_path.string() << endl;
+ fs::path flp(append_info.str(), fs::native);
+ a_file_path = analysis_path / flp;
all_comps[i][i2].load(a_file_path);
- //clog << "real size = " << all_comps[i][i2].size() << endl;
}
}
}
-
void
Mussa::save_old()
{
{
motif_sequences.insert(motif);
color_mapper->appendInstanceColor("motif", motif.get_sequence(), color);
- dirty = true;
+ set_dirty(true);
}
void Mussa::set_motifs(const vector<Sequence>& motifs,
update_sequences_motifs();
}
-// Helper functor to append created motifs to our Mussa analysis
-struct push_back_motif {
- Mussa::motif_set& motifs;
- boost::shared_ptr<AnnotationColors> color_mapper;
- std::string& seq_string;
- std::string& name;
- float& red;
- float& green;
- float& blue;
- float& alpha;
- int& parsed;
-
- push_back_motif(Mussa::motif_set& motifs_,
- boost::shared_ptr<AnnotationColors> color_mapper_,
- std::string& seq_,
- std::string& name_,
- float &red_, float &green_, float &blue_, float &alpha_,
- int &parsed_)
- : motifs(motifs_),
- color_mapper(color_mapper_),
- seq_string(seq_),
- name(name_),
- red(red_),
- green(green_),
- blue(blue_),
- alpha(alpha_),
- parsed(parsed_)
- {
- }
-
- void operator()(std::string::const_iterator,
- std::string::const_iterator) const
- {
- Sequence seq(seq_string, Sequence::nucleic_alphabet);
- // shouldn't we have a better field than "fasta header" and speices?
- seq.set_fasta_header(name);
- // we need to clear the name in case the next motif doesn't have one.
- name.clear();
- // be nice if glsequence was a subclass of sequence so we could
- // just attach colors directly to the motif.
- Color c(red, green, blue, alpha);
- color_mapper->appendInstanceColor("motif", seq.c_str(), c);
- alpha = 1.0;
- motifs.insert(seq);
- ++parsed;
- };
-};
-
void Mussa::load_motifs(fs::path filename)
{
fs::ifstream f;
f.open(filename, ifstream::in);
load_motifs(f);
}
-
-// I mostly split the ifstream out so I can use a stringstream to test it.
+
void Mussa::load_motifs(std::istream &in)
{
std::string data;
- const char *alphabet = Alphabet::nucleic_alphabet.c_str();
- string seq;
- string name;
- float red = 1.0;
- float green = 0.0;
- float blue = 0.0;
- float alpha = 1.0;
- int parsed = 1;
+ const char *alphabet = Alphabet::dna_cstr;
+ motif_parser::ParsedMotifs parsed_motifs(motif_sequences, color_mapper);
// slurp our data into a string
std::streamsize bytes_read = 1;
bytes_read = in.readsome(buf, bufsiz);
data.append(buf, buf+bytes_read);
}
- // parse our string
- bool ok = spirit::parse(data.begin(), data.end(),
- *(
- (
- (
- (+spirit::chset<>(alphabet))[spirit::assign_a(seq)] >>
- +spirit::space_p
- ) >>
- !(
- (
- // names can either be letter followed by non-space characters
- (spirit::alpha_p >> *spirit::graph_p)[spirit::assign_a(name)]
- |
- // or a quoted string
- (
- spirit::ch_p('"') >>
- (+(~spirit::ch_p('"')))[spirit::assign_a(name)] >>
- spirit::ch_p('"')
- )
- ) >> +spirit::space_p
- ) >>
- spirit::real_p[spirit::assign_a(red)] >> +spirit::space_p >>
- spirit::real_p[spirit::assign_a(green)] >> +spirit::space_p >>
- spirit::real_p[spirit::assign_a(blue)] >> +spirit::space_p >>
- !(spirit::real_p[spirit::assign_a(alpha)] >> +spirit::space_p)
- )[push_back_motif(motif_sequences, color_mapper, seq, name, red, green, blue, alpha, parsed)]
- )).full;
- if (not ok) {
- stringstream msg;
- msg << "Error parsing motif #" << parsed;
- // erase our potentially broken motif list
- motif_sequences.clear();
- throw motif_load_error(msg.str());
- }
+ parsed_motifs.parse(data);
update_sequences_motifs();
}
{
// once we've loaded all the motifs from the file,
// lets attach them to the sequences
- for(vector<boost::shared_ptr<Sequence> >::iterator seq_i = the_seqs.begin();
+ for(vector<SequenceRef >::iterator seq_i = the_seqs.begin();
seq_i != the_seqs.end();
++seq_i)
{
projects / mussa.git / blobdiff