Mussa::Mussa()
+ : color_mapper(new AnnotationColors)
{
clear();
connect(&the_paths, SIGNAL(progress(const std::string&, int, int)),
win_append = false;
thres_append = false;
motif_sequences.clear();
- color_mapper.clear();
+ if(color_mapper) color_mapper->clear();
the_paths.clear();
}
std::list<ConservedPath::path_type>& result,
std::list<std::vector<bool> >& reversed)
{
- const vector<Sequence>& raw_seq = the_seqs;
+ const vector_sequence_type& raw_seq = the_seqs;
ConservedPath::path_type aligned_path;
size_t i2, i3;
int x_start, x_end;
x_start = (abs(a_path[i2]-rc_1+win_i));
x_end = (abs(a_path[i2+1]-rc_2+win_i));
+ boost::shared_ptr<Sequence> cur(raw_seq[i2]) ;
+ boost::shared_ptr<Sequence> next(raw_seq[i2+1]);
// RC case handling
// ugh, and xor...only want rc coloring if just one of the nodes is rc
// if both nodes are rc, then they are 'normal' relative to each other
if((rc_list[i2] || rc_list[i2+1] )&&!(rc_list[i2] && rc_list[i2+1]))
{ //the hideous rc matching logic - not complex, but annoying
- if(!(( (raw_seq[i2][x_start]=='A')&&(raw_seq[i2+1][x_end]=='T')) ||
- ((raw_seq[i2][x_start]=='T')&&(raw_seq[i2+1][x_end]=='A')) ||
- ((raw_seq[i2][x_start]=='G')&&(raw_seq[i2+1][x_end]=='C')) ||
- ((raw_seq[i2][x_start]=='C')&&(raw_seq[i2+1][x_end]=='G'))) )
+ if(!(( ((*cur)[x_start]=='A')&&((*next)[x_end]=='T')) ||
+ (((*cur)[x_start]=='T')&&((*next)[x_end]=='A')) ||
+ (((*cur)[x_start]=='G')&&((*next)[x_end]=='C')) ||
+ (((*cur)[x_start]=='C')&&((*next)[x_end]=='G'))) )
{
full_match = false;
} else {
}
else
{ // forward match
- if (!( (raw_seq[i2][x_start] == raw_seq[i2+1][x_end]) &&
- (raw_seq[i2][x_start] != 'N') &&
- (raw_seq[i2+1][x_end] != 'N') ) ) {
+ if (!( ((*cur)[x_start] == (*next)[x_end]) &&
+ ((*cur)[x_start] != 'N') && ((*next)[x_end] != 'N') ) ) {
full_match = false;
} else {
aligned_path.push_back(x_start);
}
-void Mussa::append_sequence(Sequence a_seq)
+void Mussa::append_sequence(const Sequence& a_seq)
+{
+ boost::shared_ptr<Sequence> seq_copy(new Sequence(a_seq));
+ the_seqs.push_back(seq_copy);
+}
+
+void Mussa::append_sequence(boost::shared_ptr<Sequence> a_seq)
{
the_seqs.push_back(a_seq);
}
-const vector<Sequence>&
+
+const vector<boost::shared_ptr<Sequence> >&
Mussa::sequences() const
{
return the_seqs;
void Mussa::load_sequence(fs::path seq_file, fs::path annot_file,
int fasta_index, int sub_seq_start, int sub_seq_end)
{
- Sequence aseq;
- aseq.load_fasta(seq_file, fasta_index, sub_seq_start, sub_seq_end);
+ boost::shared_ptr<Sequence> aseq(new Sequence);
+ aseq->load_fasta(seq_file, fasta_index, sub_seq_start, sub_seq_end);
if ( not annot_file.empty() ) {
- aseq.load_annot(annot_file, sub_seq_start, sub_seq_end);
+ aseq->load_annot(annot_file, sub_seq_start, sub_seq_end);
}
the_seqs.push_back(aseq);
}
all_comps[i].push_back(dummy_comp);
}
for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++) {
- seq_lens.push_back(the_seqs[i].size());
+ seq_lens.push_back(the_seqs[i]->size());
}
int seqcomps_done = 0;
int seqcomps_todo = (the_seqs.size() * (the_seqs.size()-1)) / 2;
{
//cout << "seqcomping: " << i << " v. " << i2 << endl;
all_comps[i][i2].setup(window, threshold);
- all_comps[i][i2].seqcomp(the_seqs[i], the_seqs[i2], false);
- all_comps[i][i2].seqcomp(the_seqs[i], the_seqs[i2].rev_comp(),true);
+ all_comps[i][i2].seqcomp(*the_seqs[i], *the_seqs[i2], false);
+ all_comps[i][i2].seqcomp(*the_seqs[i], the_seqs[i2]->rev_comp(),true);
++seqcomps_done;
emit progress("seqcomp", seqcomps_done, seqcomps_todo);
}
void
Mussa::nway()
{
- vector<string> some_Seqs;
the_paths.set_soft_threshold(soft_thres);
}
else if (ana_mode == EntropyNway)
{
+ vector<string> some_Seqs;
//unlike other methods, entropy needs to look at the sequence at this stage
some_Seqs.clear();
for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
{
- some_Seqs.push_back(the_seqs[i]);
+ some_Seqs.push_back(*the_seqs[i]);
}
the_paths.setup_ent(ent_thres, some_Seqs); // ent analysis extra setup
for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
{
- the_seqs[i].save(save_file);
+ the_seqs[i]->save(save_file);
}
save_file << "</Mussa_Sequence>" << endl;
fs::path a_file_path;
fs::path ana_path(ana_file);
bool parsing_path;
- Sequence tmp_seq;
string err_msg;
ostringstream append_info;
vector<FLPs> empty_FLP_vector;
// this is a bit of a hack due to C++ not acting like it should with files
for (i = 1; i <= seq_num; i++)
{
- tmp_seq.clear();
+ boost::shared_ptr<Sequence> tmp_seq(new Sequence);
//cout << "mussa_class: loading museq frag... " << a_file_path.string() << endl;
- tmp_seq.load_museq(a_file_path, i);
+ tmp_seq->load_museq(a_file_path, i);
the_seqs.push_back(tmp_seq);
}
save_file.open(analysis_name, ios::out);
for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
- save_file << the_seqs[i] << endl;
+ save_file << *(the_seqs[i]) << endl;
save_file << window << endl;
save_file.close();
for(i = 0; i < seq_num; i++)
{
getline(save_file, file_data_line);
- a_seq = file_data_line;
+ boost::shared_ptr<Sequence> a_seq(new Sequence(file_data_line));
the_seqs.push_back(a_seq);
}
for(size_t i = 0; i != motifs.size(); ++i)
{
motif_sequences.insert(motifs[i]);
- color_mapper.appendInstanceColor("motif", motifs[i], colors[i]);
+ color_mapper->appendInstanceColor("motif", motifs[i], colors[i]);
}
update_sequences_motifs();
}
// sequence wasn't found
motif_sequences.insert(seq);
Color c(red, green, blue);
- color_mapper.appendInstanceColor("motif", seq, c);
+ color_mapper->appendInstanceColor("motif", seq, c);
} else {
clog << "sequence " << seq << " was already defined skipping"
<< endl;
{
// once we've loaded all the motifs from the file,
// lets attach them to the sequences
- for(vector<Sequence>::iterator seq_i = the_seqs.begin();
+ for(vector<boost::shared_ptr<Sequence> >::iterator seq_i = the_seqs.begin();
seq_i != the_seqs.end();
++seq_i)
{
// clear out old motifs
- seq_i->clear_motifs();
+ (*seq_i)->clear_motifs();
// for all the motifs in our set, attach them to the current sequence
for(set<string>::iterator motif_i = motif_sequences.begin();
motif_i != motif_sequences.end();
++motif_i)
{
- seq_i->add_motif(*motif_i);
+ (*seq_i)->add_motif(*motif_i);
}
}
}
return motif_sequences;
}
-AnnotationColors& Mussa::colorMapper()
+boost::shared_ptr<AnnotationColors> Mussa::colorMapper()
{
return color_mapper;
}
projects / mussa.git / blobdiff