#include "mussa_class.hh"
+// doesn't do neg ints...
+string
+int_to_str(int an_int)
+{
+ string converted_int;
+ int remainder;
+
+ converted_int = "";
+
+ if (an_int == 0)
+ converted_int = "0";
+
+ while (an_int != 0)
+ {
+ remainder = an_int % 10;
+
+ if (remainder == 0)
+ converted_int = "0" + converted_int;
+ else if (remainder == 1)
+ converted_int = "1" + converted_int;
+ else if (remainder == 2)
+ converted_int = "2" + converted_int;
+ else if (remainder == 3)
+ converted_int = "3" + converted_int;
+ else if (remainder == 4)
+ converted_int = "4" + converted_int;
+ else if (remainder == 5)
+ converted_int = "5" + converted_int;
+ else if (remainder == 6)
+ converted_int = "6" + converted_int;
+ else if (remainder == 7)
+ converted_int = "7" + converted_int;
+ else if (remainder == 8)
+ converted_int = "8" + converted_int;
+ else if (remainder == 9)
+ converted_int = "9" + converted_int;
+
+ an_int = an_int / 10;
+ }
+
+ return converted_int;
+}
+
Mussa::Mussa()
{
}
+char
+Mussa::parse_args(int argc, char **argv)
+{
+ int i;
+ string an_arg;
+ char run_mode;
+
+ win_override = false;
+ thres_override = false;
+ // minimal arg reading structure, not very robust to errors
+
+
+ i = 1;
+ while (i < argc)
+ {
+ an_arg = * ++argv;
+ i++;
+
+ if (an_arg == "-v")
+ {
+ ana_name = * ++argv;
+ i++;
+ run_mode = 'v';
+ }
+ else if (an_arg == "-n")
+ {
+ para_file_path = * ++argv;
+ i++;
+ run_mode = 'n';
+ }
+ else if (an_arg == "-w")
+ {
+ window = atoi(* ++argv);
+ i++;
+ win_override = true;
+ }
+ else if (an_arg == "-t")
+ {
+ threshold = atoi(* ++argv);
+ i++;
+ thres_override = true;
+ cout << thres_override << endl;
+ }
+ else
+ {
+ para_file_path = an_arg;
+ run_mode = 'f';
+ }
+ }
+ return run_mode;
+}
+
+
void
-Mussa::setup(char * para_file_path)
+Mussa::setup()
{
ifstream para_file;
string file_data_line;
string param, value, annot_file;
int split_index, fasta_index;
+ int sub_seq_start, sub_seq_end;
bool seq_params, did_seq;
int bogo;
win_append = false;
thres_append = false;
+ seq_files.clear();
+ fasta_indices.clear();
+ annot_files.clear();
+ sub_seq_starts.clear();
+ sub_seq_ends.clear();
- para_file.open(para_file_path, ios::in);
+ para_file.open(para_file_path.c_str(), ios::in);
getline(para_file,file_data_line);
split_index = file_data_line.find(" ");
else if (param == "SEQUENCE_NUM")
seq_num = atoi(value.c_str());
else if (param == "WINDOW")
- window = atoi(value.c_str());
+ {
+ if (!win_override)
+ window = atoi(value.c_str());
+ }
else if (param == "THRESHOLD")
- threshold = atoi(value.c_str());
+ {
+ if (!thres_override)
+ threshold = atoi(value.c_str());
+ }
else if (param == "SEQUENCE")
{
seq_files.push_back(value);
fasta_index = 1;
annot_file = "";
+ sub_seq_start = 0;
+ sub_seq_end = 0;
seq_params = true;
while ((!para_file.eof()) && seq_params)
fasta_index = atoi(value.c_str());
else if (param == "ANNOTATION")
annot_file = value;
+ else if (param == "SEQ_START")
+ sub_seq_start = atoi(value.c_str());
+ else if (param == "SEQ_END")
+ {
+ cout << "hey! " << atoi(value.c_str()) << endl;
+ sub_seq_end = atoi(value.c_str());
+ }
//ignore empty lines or that start with '#'
else if ((param == "") || (param == "#")) {}
else seq_params = false;
fasta_indices.push_back(fasta_index);
annot_files.push_back(annot_file);
+ sub_seq_starts.push_back(sub_seq_start);
+ sub_seq_ends.push_back(sub_seq_end);
did_seq = true;
}
cout << "window = " << window << " threshold = " << threshold << "\n";
}
+// if (!((param == "") || (param == "#")))
+// cout << value << " = " << param << endl;
void
Mussa::get_Seqs()
{
list<string>::iterator seq_files_i, annot_files_i;
- list<int>::iterator fasta_indices_i;
+ list<int>::iterator fasta_indices_i, seq_starts_i, seq_ends_i;
Sequence aSeq;
seq_files_i = seq_files.begin();
fasta_indices_i = fasta_indices.begin();
annot_files_i = annot_files.begin();
+ seq_starts_i = sub_seq_starts.begin();
+ seq_ends_i = sub_seq_ends.begin();
- while ( (seq_files_i != seq_files.end()) &&
+
+ while (seq_files_i != seq_files.end())
+ /* it should be guarenteed that each of the following exist
+ &&
(fasta_indices_i != fasta_indices.end()) &&
- (annot_files_i != annot_files.end()) )
+ (annot_files_i != annot_files.end()) &&
+ (seq_starts_i != sub_seq_starts.end()) &&
+ (seq_ends_i != sub_seq_ends.end()) )
+ */
{
- aSeq.load_fasta(*seq_files_i, *fasta_indices_i);
+ aSeq.load_fasta(*seq_files_i, *fasta_indices_i,*seq_starts_i,*seq_ends_i);
+ if (*annot_files_i != "")
+ aSeq.load_annot(*annot_files_i);
the_Seqs.push_back(aSeq);
cout << aSeq.hdr() << endl;
+ //cout << aSeq.seq() << endl;
aSeq.clear();
++seq_files_i;
++fasta_indices_i;
++annot_files_i;
+ ++seq_starts_i;
+ ++seq_ends_i;
}
}
all_comps[i][i2].setup("m", window, threshold, seq_lens[i],seq_lens[i2]);
all_comps[i][i2].seqcomp(the_Seqs[i].seq(), the_Seqs[i2].seq(), false);
all_comps[i][i2].seqcomp(the_Seqs[i].seq(),the_Seqs[i2].rev_comp(),true);
- save_file_string = "ana";
- if (i == 0)
- save_file_string += "0";
- else if (i == 1)
- save_file_string += "1";
- if (i2 == 1)
- save_file_string += "1";
- else if (i2 == 2)
- save_file_string += "2";
all_comps[i][i2].file_save(save_file_string);
}
}
+
void
Mussa::nway()
{
- the_paths.setup(seq_num);
+ the_paths.setup(seq_num, window, threshold);
the_paths.find_paths_r(all_comps);
+ the_paths.simple_refine();
}
+void
+Mussa::save()
+{
+ string save_path_base, save_path;
+ fstream save_file;
+ int i;
+
+ // gotta do bit with adding win & thres if to be appended - need itos
+
+ // not sure why, but gotta close file each time since can't pass file streams
+
+ save_path_base = ana_name;
+
+ if (win_append)
+ save_path_base += "_w" + int_to_str(window);
+
+ if (thres_append)
+ save_path_base += "_t" + int_to_str(threshold);
+
+ // save sequence and annots to a special mussa file
+ save_path = save_path_base + ".museq";
+ save_file.open(save_path.c_str(), ios::out);
+ save_file << "<Mussa_Sequence>" << endl;
+ //save_file.close();
+
+ for(i = 0; i < seq_num; i++)
+ the_Seqs[i].save(save_file);
+
+ //save_file.open(save_path.c_str(), ios::app);
+ save_file << "</Mussa_Sequence>" << endl;
+ save_file.close();
+
+ // save nway paths to its mussa save file
+ save_path = save_path_base + ".muway";
+ the_paths.save(save_path);
+}
+
+void
+Mussa::load()
+{
+ int i;
+ string load_file_path;
+ Sequence tmp_seq;
+
+
+ load_file_path = ana_name + ".muway";
+ seq_num = the_paths.load(load_file_path);
+
+ load_file_path = ana_name + ".museq";
+ for (i = 1; i <= seq_num; i++)
+ {
+ tmp_seq.clear();
+ tmp_seq.load_museq(load_file_path, i);
+ the_Seqs.push_back(tmp_seq);
+ }
+}
+
+
+
+// In Memorial to Everything that's gone wrong in the last week
+// and Everything that will go wrong in the next 2 weeks 03/02/2004 - Tristan
+void
+Mussa::FuckingPieceOfShit(int x_max, int y_max)
+{
+ Fl_Window *conn_window = new Fl_Window(x_max, y_max, "Mussa Connections");
+ ConnView *conn_box = new ConnView(0, 0, x_max, y_max);
+ conn_box->setup(ana_name, seq_num, window, &the_Seqs, &the_paths);
+ conn_box->scale_paths();
+ conn_window->end();
+ conn_window->show();
+
+ Fl::run();
+}
+
+/*
+ cout << "fee\n";
+ cout << "fie\n";
+ cout << "foe\n";
+ cout << "fum\n";
+*/
+
+
void
Mussa::save_old()
Sequence a_seq;
seq_num = s_num;
- the_paths.setup(seq_num);
+ the_paths.setup(seq_num, 0, 0);
save_file.open(load_file_path, ios::in);
// currently loads old mussa format
//the_paths.save("tmp.save");
}
-
-
-// In Memorial to Everything that's gone wrong in the last week
-// and Everything that will go wrong in the next 2 weeks 03/02/2004 - Tristan
-void
-Mussa::FuckingPieceOfShit(int x_max, int y_max)
-{
-
- Fl_Window *conn_window = new Fl_Window(x_max, y_max, "Mussa Connections");
- ConnView *conn_box = new ConnView(0, 0, x_max, y_max);
- conn_box->setup(ana_name, seq_num, window, &the_Seqs, &the_paths);
- conn_box->scale_paths();
- conn_box->spawnSeq();
- conn_window->end();
- conn_window->show();
-
- Fl::run();
-}
-
-/*
- cout << "fee\n";
- cout << "fie\n";
- cout << "foe\n";
- cout << "fum\n";
-*/
-
-
projects / mussa.git / blobdiff