From: Diane Trout Date: Tue, 23 May 2006 05:44:08 +0000 (+0000) Subject: rename ExtendedConservedPath for the old fltk code X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=commitdiff_plain;h=31bd9c9aec765da210f442d07b048af30221098b rename ExtendedConservedPath for the old fltk code --- diff --git a/gui/ConnView.cpp b/gui/ConnView.cpp index b6ba946..4c089ed 100644 --- a/gui/ConnView.cpp +++ b/gui/ConnView.cpp @@ -125,8 +125,8 @@ ConnView::setup(string name, int sq_num, int win_len, void ConnView::scale_paths() { - ExtendedConservedPath a_path; - list::iterator pathz_i; + ConservedPath a_path; + list::iterator pathz_i; int i2; @@ -246,7 +246,7 @@ ConnView::draw() void ConnView::draw_paths() { - list::iterator i; + list::iterator i; int i2, i3, y_loc, x_loc, x_start, x_end; list::iterator highlight_i; int window_size; @@ -257,7 +257,7 @@ ConnView::draw_paths() highlight.clear(); for(i = scaled_pathz.begin(); i != scaled_pathz.end(); ++i) { - ExtendedConservedPath& a_path = *i; + ConservedPath& a_path = *i; // determine if path falls within the selected region and mark it for // highlighted color path_start = abs(a_path[ref_seq_num]); @@ -276,7 +276,7 @@ ConnView::draw_paths() highlight_i = highlight.begin(); for(i = scaled_pathz.begin(); i != scaled_pathz.end(); ++i) { - ExtendedConservedPath& a_path = *i; + ConservedPath& a_path = *i; y_loc = y()+y_pad; window_size = a_path.window_size; @@ -311,7 +311,7 @@ ConnView::draw_paths() highlight_i = highlight.begin(); for(i = scaled_pathz.begin(); i != scaled_pathz.end(); ++i) { - ExtendedConservedPath& a_path = *i; + ConservedPath& a_path = *i; y_loc = y()+y_pad; // get window size to determine line width @@ -606,8 +606,8 @@ ConnView::check_new_motifs() void ConnView::spawnSeq() { - list selected_paths; - list::iterator pathz_i; + list selected_paths; + list::iterator pathz_i; int i2, i3, y_loc, x_loc, x_start, x_end; list::iterator highlight_i; int y_max; diff --git a/gui/ConnView.hpp b/gui/ConnView.hpp index 6d52a5f..ed0066a 100644 --- a/gui/ConnView.hpp +++ b/gui/ConnView.hpp @@ -65,7 +65,7 @@ class ConnView : public Fl_Box std::list highlight; //path data scaled for current view size - std::list scaled_pathz; + std::list scaled_pathz; std::vector seq_lens; std::vector seq_scales; int bar_interval, line_interval; diff --git a/gui/SeqView.cpp b/gui/SeqView.cpp index 419d21e..66a6714 100644 --- a/gui/SeqView.cpp +++ b/gui/SeqView.cpp @@ -20,7 +20,7 @@ using namespace std; void SeqView::setup(string name, int sq_num, vector *some_seqs, - list some_paths, vector some_lens, + list some_paths, vector some_lens, vector *some_motifs) { int seq_i; @@ -45,7 +45,7 @@ SeqView::setup(string name, int sq_num, for(seq_i = 0; seq_i < seq_num; ++seq_i) raw_sequence.push_back( (*S)[seq_i].get_seq() ); - for(list::iterator pathz_i = P.begin(); + for(list::iterator pathz_i = P.begin(); pathz_i != P.end(); ++pathz_i) { @@ -233,13 +233,13 @@ SeqView::draw_match_lines(double ch_width) align_counter = 0; - for(list::iterator pathz_i = P.begin(); + for(list::iterator pathz_i = P.begin(); pathz_i != P.end(); ++pathz_i) { if (show_aligns[align_counter]) { - ExtendedConservedPath& a_path = *pathz_i; + ConservedPath& a_path = *pathz_i; window_length = a_path.window_size; // determine which parts of the path are RC relative to first species rc_list = a_path.reverseComplimented(); @@ -393,7 +393,7 @@ SeqView::toggle_align(int align_num) void SeqView::align_offsets(int align_num) { - list::iterator pathz_i; + list::iterator pathz_i; int i; int window_length; diff --git a/gui/SeqView.hpp b/gui/SeqView.hpp index aab023f..354acd9 100644 --- a/gui/SeqView.hpp +++ b/gui/SeqView.hpp @@ -33,7 +33,7 @@ class SeqView : public Fl_Box } void setup(std::string name, int sq_num, std::vector *some_seqs, - std::list some_paths, + std::list some_paths, std::vector some_lens, std::vector *some_motifs); void align_offsets(int align_num); void toggle_align(int align_num); @@ -48,7 +48,7 @@ class SeqView : public Fl_Box //this data is passed as pointers to the instantiated classes std::vector *S; //list of paths in selection box - std::list P; + std::list P; std::vector seq_lens; //pointer to passed fltk_motif data std::vector *the_motifs; diff --git a/gui/SeqWindow.cpp b/gui/SeqWindow.cpp index 8578f49..5a3351c 100644 --- a/gui/SeqWindow.cpp +++ b/gui/SeqWindow.cpp @@ -88,7 +88,7 @@ SeqWindow::real_toggle_motifs_cb() SeqWindow::SeqWindow(int w, int h, const char* title, int sq_num, vector *some_seqs, - list some_paths, + list some_paths, vector some_lens, vector *some_motifs): Fl_Double_Window(w,h,title) @@ -98,7 +98,7 @@ SeqWindow::SeqWindow(int w, int h, const char* title, int sq_num, int i; ostringstream align_id_ostr; string align_id_string; - list::iterator align_iter; + list::iterator align_iter; // most of this stuff is here just to pass to SeqView object // some is needed to setup the window menus diff --git a/gui/SeqWindow.hpp b/gui/SeqWindow.hpp index c6b8cc8..920d496 100644 --- a/gui/SeqWindow.hpp +++ b/gui/SeqWindow.hpp @@ -30,7 +30,7 @@ class SeqWindow : public Fl_Double_Window //this data is passed as pointers to the instantiated classes std::vector *S; // list of paths in selection box - std::list P; + std::list P; std::vector seq_lens; //pointer to passed fltk_motif data std::vector *the_motifs; @@ -46,7 +46,7 @@ class SeqWindow : public Fl_Double_Window SeqWindow(int w, int h, const char* title, int sq_num, std::vector *some_seqs, - std::list some_paths, + std::list some_paths, std::vector some_lens, std::vector *some_motifs); virtual ~SeqWindow(){ std::cout << "dying\n"; }