--- /dev/null
+ GNU GENERAL PUBLIC LICENSE
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+
+ <signature of Ty Coon>, 1 April 1989
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+
+This General Public License does not permit incorporating your program into
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+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General
+Public License instead of this License.
--- /dev/null
+Mussa: Multi-species sequence analysis
+
+You might think of it as an acronym, but its pretty much become a proper name in my mind. So no going around writing MUSSA or even M.U.S.S.A - this isn't a secret gov't military program or 70s era mainframe (which is what all those caps put me in the mind of).
+
+There isn't much to this README yet. Basic info on compiling and using mussa is available on the website at http://mussa.caltech.edu
+
+I will get around to a more informative README eventually.
+
+
+The main problem you will likely encounter trying to compile Mussa is with the fltk libraries. If you try to compile mussa and you get errors like the following, either you do not have the fltk libraries installed or they are located someplace gcc is not looking. If you know fltk libraries are on the system, you need to try messing with the various LDFLAGS examples in the Makefile.
+
+"""
+g++ -ftemplate-depth-25 -c mussa_gui_seq.cc
+In file included from mussa_gui_annot_window.hh:1,
+ from mussa_gui_load_window.hh:1,
+ from mussa_gui_seq_view.hh:1,
+ from mussa_gui_seq.hh:1,
+ from mussa_gui_seq.cc:1:
+mussa_gui_motif_window.hh:3:19: error: FL/Fl.H: No such file or directory
+mussa_gui_motif_window.hh:4:26: error: FL/Fl_Window.H: No such file or directory
+mussa_gui_motif_window.hh:5:26: error: FL/Fl_Button.H: No such file or directory
+mussa_gui_motif_window.hh:7:25: error: FL/Fl_Input.H: No such file or directory
+mussa_gui_motif_window.hh:8:26: error: FL/Fl_Output.H: No such file or directory
+mussa_gui_motif_window.hh:9:24: error: FL/Fl_Pack.H: No such file or directory
+"""
+
+If you have other issues, or find bugs, email me: tristan@caltech.edu - preferably indicating its about Mussa in the subject :)
+
+There are some known bugs/incomplete features documented in the tutorial info on the website.
+
+If you want to compile this under OSX for use on the command line, just use the appropriate set of marked LDFLAGS in the Makefile. However, there are a number of oddities, of which I will just cover a few. Use from the command line will work just like a unix/linux system, but gui windows will not come into the forground. If you try to put the Mussa executable into a .app folder like the pre-compiled version offered at mussa.caltech.edu, the system sends odd command line args which confuse my poor program. There are things which need to be commented out in the code. Some of these are marked, others not. Why not just use the precompiled version and drink a beer later with the time you saved?
+
+
+Tristan De Buysscher
\ No newline at end of file
--- /dev/null
+- Analysis
+ - finish entropy nway integration
+
+- program control
+ - trap crash conditions in various gui load stats
+ - add annot separate species/seq naming
+ -
+
+- data
+ - switch to saving to dir
+ - save seqcomps to dir
+
+
+
+- functionality
+ - add mini/re analysis option
+ - finish adding PMWs
+ - load motifs, give names
+ - add variable thresholding
\ No newline at end of file
+++ /dev/null
-#include "sequence.hh"
-
-int main(int argc, char **argv)
-{
- Sequence seqA;
- char * seqA_file, * seqA_annot;
- cout << "fee fie foe fum" << endl;
-
-
- seqA_file = * ++argv;
- seqA_annot = * ++argv;
-
- seqA.load_fasta(seqA_file, 1);
- seqA.load_annot(seqA_annot);
- //seqA_len = seqA.len();
-}
-
-/*
- cout << "fee\n";
- cout << "fie\n";
- cout << "foe ";
- cout << "fum\n";
-*/
--- /dev/null
+build 015
+ - added GPL notification to all modules
+ - added LICENSE.txt (the GPL) and beginnings of a README.txt
+ - bug fixes
+ - fixed motif searching not working on sub-analyses
+ (length of sub-analysis sequence not set...)
+ - ...that other bug...
+ - added code for compile under OS X so analyses dir created in
+same directory as the .mupa file when using "Do Analysis" option
+
+build 014
+ - added Annotations window
+ - displays all unique annots
+ (Only uses the first column of annot ids after start & end indices)
+ - allows selecting display colors each annot listed
+ - available under View menu
+ - added Sequence Copy window
+ - enter seq #, start and end indices to display sequence
+ - sequence buffer can selected and copied from
+ - available under View menu
+ - bug fixes
+ - Analysis->Do/Load/Setup/Sub no longer crashes if cancelled/window closed
+ - fixed file path issues with loading .mupa or analysis saves
+ - mainly problem with OS X, which "runs" from harddrive root directory
+ (note, still saves analyses at the root dir...)
+ - problem on linux in some cases when switched build 013 save method
+ (tho I didn't realize since I could run from any directory)
+
+build 013/build 012
+ - finished seqcomp pairwise saving/loading code
+ - can now set a higher threshold than initial analysis hard threshold
+ - changed save format so all file go in a directory of analysis name
+
+
+build 011
+ - added Sub Analysis window
+ - can choose sub regions of the sequences
+ - can set new window and threshold settings
+ - available under Analysis menu
+ - new menu - 'View'
+ - moved bar/line toggle here as radio buttons
+ - add simple motif search entry as well (can still middle click for it)
+ - made sequence view resizable and scale correctly
+
+
+build 010
+ - added Analysis setup window to interactively create analysis without needing to make a .mupa configuration file
+ - added Analysis setup window under file menu
+ - Mussa windows now include the name of the analysis in title bar
+ - Sequence window clears previous scroll offset when new alignment choosen
+
+
+build 009 and earlier
+ - occurred before writing was invented...
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
// ----------------------------------------
// ---------- flp.cc -----------
// ----------------------------------------
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
// ----------------------------------------
// ---------- flp.hh -----------
// ----------------------------------------
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
// ----------------------------------------
// ---------- flp_seqcomp.cc -----------
// ----------------------------------------
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_conn_window.hh"
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
// ----------------------------------------
// ---------- mussa_class.cc -----------
// ----------------------------------------
Mussa::load_mupa_file(string para_file_path)
{
ifstream para_file;
- string file_data_line, file_path_base;
+ string file_data_line;
string param, value, annot_file;
int split_index, fasta_index;
int sub_seq_start, sub_seq_end;
void
Mussa::save()
{
- string save_path_base, save_path, create_dir_cmd, flp_filepath;
+ string save_name, save_path, create_dir_cmd, flp_filepath;
fstream save_file;
ostringstream append_info;
int i, i2, dir_create_status;
{
append_info.str("");
append_info << "_w" << window;
- save_path_base += append_info.str();
+ save_name += append_info.str();
}
if (thres_append)
{
append_info.str("");
append_info << "_t" << threshold;
- save_path_base += append_info.str();
+ save_name += append_info.str();
}
//#include <stdlib.h>
- create_dir_cmd = "mkdir " + save_path_base;
+ // ******* use appropriate for os ------- 1 of 4
+ // the additions for osX make it more sane where it saves the analysis
+ // will come up with a cleaner sol'n later...
+ create_dir_cmd = "mkdir " + save_name; //linux
+ //create_dir_cmd = "mkdir " + file_path_base + save_name; //osX
+
dir_create_status = system( (const char*) create_dir_cmd.c_str());
cout << "action: " << dir_create_status << endl;
// save sequence and annots to a special mussa file
- save_path = save_path_base + "/" + save_path_base + ".museq";
+
+ // ******** use appropriate for OS ---------- 2 of 4
+ save_path = save_name + "/" + save_name + ".museq"; //linux
+ //save_path = file_path_base + save_name + "/" + save_name + ".museq"; //osX
+
save_file.open(save_path.c_str(), ios::out);
save_file << "<Mussa_Sequence>" << endl;
//save_file.close();
save_file.close();
// save nway paths to its mussa save file
- save_path = save_path_base + "/" + save_path_base + ".muway";
+
+ // ******** use appropriate for OS -------- 3 of 4
+ save_path = save_name + "/" + save_name + ".muway"; //linux
+ //save_path = file_path_base + save_name + "/" + save_name + ".muway"; //os X
the_paths.save(save_path);
for(i = 0; i < seq_num; i++)
{
append_info.str("");
append_info << "_sp_" << i << "v" << i2;
- save_path = save_path_base + "/" + save_path_base + append_info.str() + ".flp";
+ // ******** use appropriate for OS --------- 4 of 4
+ //linux
+ save_path = save_name + "/" + save_name + append_info.str() + ".flp";
+ //osX
+ //save_path = file_path_base + save_name + "/" + save_name + append_info.str() + ".flp";
all_comps[i][i2].file_save(save_path);
}
}
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
// ----------------------------------------
// ---------- mussa_class.hh -----------
// ----------------------------------------
private:
// Private variables
// parameters needed for a mussa analysis
- string ana_name;
+ string ana_name, file_path_base;
int seq_num, window, threshold, soft_thres;
char ana_mode;
double ent_thres;
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_annot_window.hh"
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_motif_window.hh"
#include <FL/Fl.H>
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_conn_view.hh"
// draw sequence representation lines
fl_font(FL_COURIER, 14);
//fl_color(FL_BLACK);
- fl_color(80,80,80);
- fl_line_style(FL_SOLID, 7, NULL);
+ fl_color(100,100,100);
+ // normally size 7, adjust for various screenshotage
+ fl_line_style(FL_SOLID, 11, NULL);
y_loc = y()+y_pad;
y_offset = 5;
for(i2 = 0; i2 < seq_num; i2++)
// loop thru all annotation entries
for(annot_i = (*S)[i2].annots.begin(); annot_i != (*S)[i2].annots.end(); ++annot_i)
{
- fl_line_style(FL_SOLID, 3, NULL);
+ fl_line_style(FL_SOLID, 7, NULL);
mv_offset = 0;
// loop thru annotation types to determine color
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_subana.hh"
#include <sstream>
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_conn_window.hh"
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_conn_view.hh"
#include <FL/fl_ask.H>
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_load_window.hh"
bool
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_annot_window.hh"
#include <FL/Fl_File_Chooser.H>
#include <FL/Fl_Scroll.H>
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_motif_window.hh"
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_class.hh"
#include <FL/Fl.H>
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_seq.hh"
#include <sstream>
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_seq_view.hh"
#include <FL/Fl_Menu_Bar.H>
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_seq_text.hh"
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_seq.hh"
#include <FL/Fl_Text_Buffer.H>
#include <FL/Fl_Text_Display.H>
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_seq.hh"
#include <sstream>
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_load_window.hh"
#include <math.h>
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_subana.hh"
the_Seqs = some_Seqs;
all_done = false;
+ // initialize parameters
+ ana_name = "";
+ window = -1;
+ threshold = -1;
+
begin();
name_input = new Fl_Input(135, 10, w-140, 30, "SubAnalysis Name ");
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_gui_seq_text.hh"
#include <FL/Fl_File_Chooser.H>
#include <FL/Fl_Scroll.H>
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
// ----------------------------------------
// ---------- mussa_nway.cc -----------
// ----------------------------------------
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
// ----------------------------------------
// ---------- mussa_nway.hh -----------
// ----------------------------------------
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
/*
#include <list>
#include <vector>
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "mussa_nway.hh"
void
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
PathList
ExtendPathWindows(PathList raw_list)
{
+++ /dev/null
-// ----------------------------------------
-// ---------- mussa_overlord.cc -----------
-// ----------------------------------------
-
-
-#include "mussa_overlord.hh"
-
-
-
-char
-MussaOverlord::parse_args(int argc, char **argv)
-{
- an_analysis.parse_args(argc, argv);
-}
-
-
-void
-MussaOverlord::do_analysis()
-{
- an_analysis.analyze(para_file_path, window, threshold);
-}
-
-void
-MussaOverlord::get_analysis()
-{
- an_analysis.load(ana_name);
-}
-
-
-void
-MussaOverlord::spawnConnView(int x_max, int y_max)
-{
- ConnWindow *a_conn_win = new ConnWindow(x_max, y_max, "Mussa Connections",
- &an_analysis);
- Fl::run();
-}
+++ /dev/null
-// ----------------------------------------
-// ---------- mussa_overlord.hh -----------
-// ----------------------------------------
-
-
-#include "mussa_gui_conn_window.hh"
-
-
-
-
-class MussaOverlord
-{
- private:
- Mussa an_analysis;
- string para_file_path, ana_name;
- int window, threshold;
-
-
- public:
- char parse_args(int argc, char **argv);
- void do_analysis();
- void get_analysis();
- void spawnConnView(int x_max, int y_max);
-};
+++ /dev/null
-#include "mussa_class.hh"
-#include "time.h"
-
-int main(int argc, char **argv)
-{
- Mussa overlord;
- char * para_file, * ana_file;
- string an_arg;
- time_t t1, t2, begin, end;
- double setuptime, seqloadtime, seqcomptime, nwaytime, savetime, totaltime;
- string run_mode;
- int seq_num;
-
-
- begin = time(NULL);
-
- // need more sophisticated arg reading structure
- // support -w and -t override options...other stuff??
- an_arg = * ++argv;
-
- if (an_arg == "-v")
- {
- ana_file = * ++argv;
- run_mode = "v";
- }
- else
- {
- para_file = (char*) an_arg.c_str();
- run_mode = "f";
- }
-
- if (run_mode == "v")
- {
- cout << "load file = " << ana_file << endl;
- overlord.load(ana_file);
- //overlord.FuckingPieceOfShit(1000,500);
- }
- else if (run_mode == "f")
- {
- t1 = time(NULL);
- overlord.setup(para_file);
- t2 = time(NULL);
- setuptime = difftime(t2, t1);
-
-
- cout << "fee\n";
- t1 = time(NULL);
- overlord.get_Seqs();
- t2 = time(NULL);
- seqloadtime = difftime(t2, t1);
-
-
- cout << "fie\n";
- t1 = time(NULL);
- overlord.seqcomp();
- t2 = time(NULL);
- seqcomptime = difftime(t2, t1);
-
-
- cout << "foe\n";
- t1 = time(NULL);
- overlord.nway();
- t2 = time(NULL);
- nwaytime = difftime(t2, t1);
-
-
- cout << "fum\n";
- t1 = time(NULL);
- overlord.save_old();
- t2 = time(NULL);
- savetime = difftime(t2, t1);
-
- end = time(NULL);
- totaltime = difftime(end, begin);
-
- cout << "setup\tseqload\tseqcomp\tnway\tsave\ttotal\n";
- cout << setuptime << "\t";
- cout << seqloadtime << "\t";
- cout << seqcomptime << "\t";
- cout << nwaytime << "\t";
- cout << savetime << "\t";
- cout << totaltime << "\n";
- }
-}
-
-
-
-
-/*
- cout << "fee\n";
- cout << "fie\n";
- cout << "foe\n";
- cout << "fum\n";
-*/
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
#include "flp.hh"
#include <time.h>
#include <iomanip>
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
// ----------------------------------------
// ---------- sequence.cc -----------
// ----------------------------------------
Sequence::set_seq(string a_seq)
{
sequence = a_seq;
+ length = sequence.length();
}
cout << "motif is: " << a_motif << endl;
a_motif = motif_validate(a_motif);
- cout << "motif is: " << a_motif << endl;
+ //cout << "motif is: " << a_motif << endl;
- motif_scan(a_motif, &motif_match_starts);
- a_motif_rc = rc_motif(a_motif);
- // make sure not to do search again if it is a palindrome
- if (a_motif_rc != a_motif)
- motif_scan(a_motif_rc, &motif_match_starts);
+ if (a_motif != "")
+ {
+ cout << "Sequence: none blank motif\n";
+ motif_scan(a_motif, &motif_match_starts);
+ a_motif_rc = rc_motif(a_motif);
+ // make sure not to do search again if it is a palindrome
+ if (a_motif_rc != a_motif)
+ motif_scan(a_motif_rc, &motif_match_starts);
+ }
return motif_match_starts;
}
// faster to loop thru the sequence as a old c string (ie char array)
seq_c = (char*)sequence.c_str();
+ //cout << "Sequence: motif, seq len = " << sequence.length() << endl;
motif_len = a_motif.length();
//cout << "motif_length: " << motif_len << endl;
motif_i = 0;
- cout << "motif: " << a_motif << endl;
+ //cout << "motif: " << a_motif << endl;
- //cout << "length: " << length << endl;
+ //cout << "Sequence: motif, length= " << length << endl;
seq_i = 0;
while (seq_i < length)
{
+ cout << seq_c[seq_i];
//if ((seq_i > 10885) && (seq_i < 10917))
//cout << seq_c[seq_i] << "?" << a_motif[motif_i] << ":" << motif_i << " ";
// this is pretty much a straight translation of Nora's python code
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
// ----------------------------------------
// ---------- sequence.hh -----------
// ----------------------------------------
projects / mussa.git / commitdiff