From c117a6a41d8e8f04511919f5d3c224480816b685 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Wed, 21 Sep 2005 23:26:49 +0000 Subject: [PATCH] [project @ 13] mussa015 --- LICENSE.txt | 340 ++++++++++++++++++++++++++++++++++++++ README.txt | 34 ++++ TODO.txt | 19 +++ annot_test.cc | 23 --- builds_summary.txt | 54 ++++++ flp.cc | 10 ++ flp.hh | 10 ++ flp_seqcomp.cc | 10 ++ mussa.cc | 10 ++ mussa_class.cc | 42 ++++- mussa_class.hh | 12 +- mussa_gui_annot_window.cc | 10 ++ mussa_gui_annot_window.hh | 10 ++ mussa_gui_conn_view.cc | 17 +- mussa_gui_conn_view.hh | 10 ++ mussa_gui_conn_window.cc | 10 ++ mussa_gui_conn_window.hh | 10 ++ mussa_gui_load_window.cc | 10 ++ mussa_gui_load_window.hh | 10 ++ mussa_gui_motif_window.cc | 10 ++ mussa_gui_motif_window.hh | 10 ++ mussa_gui_seq.cc | 10 ++ mussa_gui_seq.hh | 10 ++ mussa_gui_seq_text.cc | 10 ++ mussa_gui_seq_text.hh | 10 ++ mussa_gui_seq_view.cc | 10 ++ mussa_gui_seq_view.hh | 10 ++ mussa_gui_subana.cc | 15 ++ mussa_gui_subana.hh | 10 ++ mussa_nway.cc | 10 ++ mussa_nway.hh | 10 ++ mussa_nway_entropy.cc | 10 ++ mussa_nway_other.cc | 10 ++ mussa_nway_refine.cc | 10 ++ mussa_overlord.cc | 36 ---- mussa_overlord.hh | 24 --- mussa_test.cc | 94 ----------- seqcomp.cc | 10 ++ sequence.cc | 43 ++++- sequence.hh | 10 ++ 40 files changed, 826 insertions(+), 197 deletions(-) create mode 100644 LICENSE.txt create mode 100644 README.txt create mode 100644 TODO.txt delete mode 100644 annot_test.cc create mode 100644 builds_summary.txt delete mode 100644 mussa_overlord.cc delete mode 100644 mussa_overlord.hh delete mode 100644 mussa_test.cc diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..3912109 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,340 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc. + 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. 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See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program; if not, write to the Free Software + Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + + +Also add information on how to contact you by electronic and paper mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) year name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + , 1 April 1989 + Ty Coon, President of Vice + +This General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may +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. diff --git a/README.txt b/README.txt new file mode 100644 index 0000000..4747b88 --- /dev/null +++ b/README.txt @@ -0,0 +1,34 @@ +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 diff --git a/TODO.txt b/TODO.txt new file mode 100644 index 0000000..0243cbe --- /dev/null +++ b/TODO.txt @@ -0,0 +1,19 @@ +- 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 diff --git a/annot_test.cc b/annot_test.cc deleted file mode 100644 index 1df5a86..0000000 --- a/annot_test.cc +++ /dev/null @@ -1,23 +0,0 @@ -#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"; -*/ diff --git a/builds_summary.txt b/builds_summary.txt new file mode 100644 index 0000000..e085610 --- /dev/null +++ b/builds_summary.txt @@ -0,0 +1,54 @@ +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... diff --git a/flp.cc b/flp.cc index ff7fa6c..801060c 100644 --- a/flp.cc +++ b/flp.cc @@ -1,3 +1,13 @@ +// 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 ----------- // ---------------------------------------- diff --git a/flp.hh b/flp.hh index 7be0229..094cdbe 100644 --- a/flp.hh +++ b/flp.hh @@ -1,3 +1,13 @@ +// 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 ----------- // ---------------------------------------- diff --git a/flp_seqcomp.cc b/flp_seqcomp.cc index 76a173a..e48a3b5 100644 --- a/flp_seqcomp.cc +++ b/flp_seqcomp.cc @@ -1,3 +1,13 @@ +// 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 ----------- // ---------------------------------------- diff --git a/mussa.cc b/mussa.cc index 2eb4f5c..150d92f 100644 --- a/mussa.cc +++ b/mussa.cc @@ -1,3 +1,13 @@ +// 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" diff --git a/mussa_class.cc b/mussa_class.cc index 7b29763..91e279e 100644 --- a/mussa_class.cc +++ b/mussa_class.cc @@ -1,3 +1,13 @@ +// 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 ----------- // ---------------------------------------- @@ -93,7 +103,7 @@ string 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; @@ -435,7 +445,7 @@ Mussa::nway() 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; @@ -450,23 +460,32 @@ Mussa::save() { 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 - 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 << "" << endl; //save_file.close(); @@ -479,7 +498,10 @@ Mussa::save() 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++) @@ -487,7 +509,11 @@ Mussa::save() { 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); } } diff --git a/mussa_class.hh b/mussa_class.hh index a27de82..c6b3ae8 100644 --- a/mussa_class.hh +++ b/mussa_class.hh @@ -1,3 +1,13 @@ +// 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 ----------- // ---------------------------------------- @@ -16,7 +26,7 @@ class Mussa 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; diff --git a/mussa_gui_annot_window.cc b/mussa_gui_annot_window.cc index 45f45ec..26f733d 100644 --- a/mussa_gui_annot_window.cc +++ b/mussa_gui_annot_window.cc @@ -1,3 +1,13 @@ +// 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" diff --git a/mussa_gui_annot_window.hh b/mussa_gui_annot_window.hh index c0d1151..9229713 100644 --- a/mussa_gui_annot_window.hh +++ b/mussa_gui_annot_window.hh @@ -1,3 +1,13 @@ +// 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 diff --git a/mussa_gui_conn_view.cc b/mussa_gui_conn_view.cc index 5f17b32..a77afa8 100644 --- a/mussa_gui_conn_view.cc +++ b/mussa_gui_conn_view.cc @@ -1,3 +1,13 @@ +// 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" @@ -349,8 +359,9 @@ ConnView::draw_sequence_stuff() // 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++) @@ -392,7 +403,7 @@ ConnView::draw_sequence_stuff() // 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 diff --git a/mussa_gui_conn_view.hh b/mussa_gui_conn_view.hh index 80e4846..7f29004 100644 --- a/mussa_gui_conn_view.hh +++ b/mussa_gui_conn_view.hh @@ -1,3 +1,13 @@ +// 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 diff --git a/mussa_gui_conn_window.cc b/mussa_gui_conn_window.cc index 00290ef..0b3e374 100644 --- a/mussa_gui_conn_window.cc +++ b/mussa_gui_conn_window.cc @@ -1,3 +1,13 @@ +// 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" diff --git a/mussa_gui_conn_window.hh b/mussa_gui_conn_window.hh index 9fc0001..24e4248 100644 --- a/mussa_gui_conn_window.hh +++ b/mussa_gui_conn_window.hh @@ -1,3 +1,13 @@ +// 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 diff --git a/mussa_gui_load_window.cc b/mussa_gui_load_window.cc index 28374d6..6706d53 100644 --- a/mussa_gui_load_window.cc +++ b/mussa_gui_load_window.cc @@ -1,3 +1,13 @@ +// 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 diff --git a/mussa_gui_load_window.hh b/mussa_gui_load_window.hh index ce23f49..2c92a9e 100644 --- a/mussa_gui_load_window.hh +++ b/mussa_gui_load_window.hh @@ -1,3 +1,13 @@ +// 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 #include diff --git a/mussa_gui_motif_window.cc b/mussa_gui_motif_window.cc index 54b5328..9923ce5 100644 --- a/mussa_gui_motif_window.cc +++ b/mussa_gui_motif_window.cc @@ -1,3 +1,13 @@ +// 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" diff --git a/mussa_gui_motif_window.hh b/mussa_gui_motif_window.hh index 248e06b..77c44b3 100644 --- a/mussa_gui_motif_window.hh +++ b/mussa_gui_motif_window.hh @@ -1,3 +1,13 @@ +// 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 diff --git a/mussa_gui_seq.cc b/mussa_gui_seq.cc index 075302c..0ab4589 100644 --- a/mussa_gui_seq.cc +++ b/mussa_gui_seq.cc @@ -1,3 +1,13 @@ +// 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 diff --git a/mussa_gui_seq.hh b/mussa_gui_seq.hh index f90052a..0d44c33 100644 --- a/mussa_gui_seq.hh +++ b/mussa_gui_seq.hh @@ -1,3 +1,13 @@ +// 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 diff --git a/mussa_gui_seq_text.cc b/mussa_gui_seq_text.cc index 074ecd2..6cf9a52 100644 --- a/mussa_gui_seq_text.cc +++ b/mussa_gui_seq_text.cc @@ -1,3 +1,13 @@ +// 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" diff --git a/mussa_gui_seq_text.hh b/mussa_gui_seq_text.hh index e4ecf7b..84a460f 100644 --- a/mussa_gui_seq_text.hh +++ b/mussa_gui_seq_text.hh @@ -1,3 +1,13 @@ +// 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 #include diff --git a/mussa_gui_seq_view.cc b/mussa_gui_seq_view.cc index f542ca7..fc1408a 100644 --- a/mussa_gui_seq_view.cc +++ b/mussa_gui_seq_view.cc @@ -1,3 +1,13 @@ +// 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 diff --git a/mussa_gui_seq_view.hh b/mussa_gui_seq_view.hh index 4efcfea..1e2e73c 100644 --- a/mussa_gui_seq_view.hh +++ b/mussa_gui_seq_view.hh @@ -1,3 +1,13 @@ +// 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 diff --git a/mussa_gui_subana.cc b/mussa_gui_subana.cc index bccee4d..b877702 100644 --- a/mussa_gui_subana.cc +++ b/mussa_gui_subana.cc @@ -1,3 +1,13 @@ +// 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" @@ -147,6 +157,11 @@ SubanaWindow::SubanaWindow(int w, int h, const char* title,Mussa *the_analysis, 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 "); diff --git a/mussa_gui_subana.hh b/mussa_gui_subana.hh index d859c6a..1ce5878 100644 --- a/mussa_gui_subana.hh +++ b/mussa_gui_subana.hh @@ -1,3 +1,13 @@ +// 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 #include diff --git a/mussa_nway.cc b/mussa_nway.cc index f68f8da..3e233b0 100644 --- a/mussa_nway.cc +++ b/mussa_nway.cc @@ -1,3 +1,13 @@ +// 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 ----------- // ---------------------------------------- diff --git a/mussa_nway.hh b/mussa_nway.hh index dba2de6..2d64442 100644 --- a/mussa_nway.hh +++ b/mussa_nway.hh @@ -1,3 +1,13 @@ +// 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 ----------- // ---------------------------------------- diff --git a/mussa_nway_entropy.cc b/mussa_nway_entropy.cc index 95aac06..c2d5904 100644 --- a/mussa_nway_entropy.cc +++ b/mussa_nway_entropy.cc @@ -1,3 +1,13 @@ +// 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 #include diff --git a/mussa_nway_other.cc b/mussa_nway_other.cc index 12921a8..1ddbd72 100644 --- a/mussa_nway_other.cc +++ b/mussa_nway_other.cc @@ -1,3 +1,13 @@ +// 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 diff --git a/mussa_nway_refine.cc b/mussa_nway_refine.cc index ea11273..b5d665c 100644 --- a/mussa_nway_refine.cc +++ b/mussa_nway_refine.cc @@ -1,3 +1,13 @@ +// 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) { diff --git a/mussa_overlord.cc b/mussa_overlord.cc deleted file mode 100644 index a8683f1..0000000 --- a/mussa_overlord.cc +++ /dev/null @@ -1,36 +0,0 @@ -// ---------------------------------------- -// ---------- 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(); -} diff --git a/mussa_overlord.hh b/mussa_overlord.hh deleted file mode 100644 index 92e4829..0000000 --- a/mussa_overlord.hh +++ /dev/null @@ -1,24 +0,0 @@ -// ---------------------------------------- -// ---------- 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); -}; diff --git a/mussa_test.cc b/mussa_test.cc deleted file mode 100644 index 13b4021..0000000 --- a/mussa_test.cc +++ /dev/null @@ -1,94 +0,0 @@ -#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"; -*/ diff --git a/seqcomp.cc b/seqcomp.cc index ad541ec..f2bc843 100644 --- a/seqcomp.cc +++ b/seqcomp.cc @@ -1,3 +1,13 @@ +// 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 #include diff --git a/sequence.cc b/sequence.cc index c706f47..4351f89 100644 --- a/sequence.cc +++ b/sequence.cc @@ -1,3 +1,23 @@ +// 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 ----------- // ---------------------------------------- @@ -301,6 +321,7 @@ void Sequence::set_seq(string a_seq) { sequence = a_seq; + length = sequence.length(); } @@ -543,15 +564,19 @@ Sequence::find_motif(string a_motif) 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; } @@ -563,6 +588,7 @@ Sequence::motif_scan(string a_motif, vector * 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; @@ -570,12 +596,13 @@ Sequence::motif_scan(string a_motif, vector * motif_match_starts) 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 diff --git a/sequence.hh b/sequence.hh index ec0e89c..cb59afc 100644 --- a/sequence.hh +++ b/sequence.hh @@ -1,3 +1,13 @@ +// 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 ----------- // ---------------------------------------- -- 2.30.2