rename ExtendedConservedPath for the old fltk code

diff --git a/gui/ConnView.cpp b/gui/ConnView.cpp
index b6ba9468a1d5263cb31deb4095433d460c633b53..4c089edf1314365ce5f20e7167cd71824f0e887f 100644 (file)
--- 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<ExtendedConservedPath >::iterator pathz_i;
+  ConservedPath a_path;
+  list<ConservedPath >::iterator pathz_i;
   int i2;
 
 
@@ -246,7 +246,7 @@ ConnView::draw()
 void
 ConnView::draw_paths()
 {
-  list<ExtendedConservedPath >::iterator i;
+  list<ConservedPath >::iterator i;
   int i2, i3, y_loc, x_loc, x_start, x_end;
   list<bool>::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<ExtendedConservedPath > selected_paths;
-  list<ExtendedConservedPath >::iterator pathz_i;
+  list<ConservedPath > selected_paths;
+  list<ConservedPath >::iterator pathz_i;
   int i2, i3, y_loc, x_loc, x_start, x_end;
   list<bool>::iterator highlight_i;
   int y_max;

diff --git a/gui/ConnView.hpp b/gui/ConnView.hpp
index 6d52a5fe6f4970806bd26bc40b86cae1bb6af6fd..ed0066ae5f9f8f039918ab148cf5340cb86abff3 100644 (file)
--- a/gui/ConnView.hpp
+++ b/gui/ConnView.hpp
@@ -65,7 +65,7 @@ class ConnView : public Fl_Box
     std::list<bool> highlight;
 
   //path data scaled for current view size
-    std::list<ExtendedConservedPath > scaled_pathz;
+    std::list<ConservedPath > scaled_pathz;
     std::vector<int> seq_lens;
     std::vector<int> seq_scales;
     int bar_interval, line_interval;

diff --git a/gui/SeqView.cpp b/gui/SeqView.cpp
index 419d21e2d887ae70b9709a14a8c2bf56c81de1d2..66a6714d27687eab603d9b2bdff1500e5b3ca7fd 100644 (file)
--- a/gui/SeqView.cpp
+++ b/gui/SeqView.cpp
@@ -20,7 +20,7 @@ using namespace std;
 void
 SeqView::setup(string name, int sq_num, 
                vector<Sequence> *some_seqs,
-               list<ExtendedConservedPath > some_paths, vector<int> some_lens,
+               list<ConservedPath > some_paths, vector<int> some_lens,
                vector<fltk_motif> *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<ExtendedConservedPath >::iterator pathz_i = P.begin(); 
+  for(list<ConservedPath >::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<ExtendedConservedPath >::iterator pathz_i = P.begin(); 
+  for(list<ConservedPath >::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<ExtendedConservedPath >::iterator pathz_i;
+  list<ConservedPath >::iterator pathz_i;
   int i;
   int window_length;
 

diff --git a/gui/SeqView.hpp b/gui/SeqView.hpp
index aab023fbeb5594d7a9365f7798fce7aa31999d89..354acd90641d5c9766b3135ecb21300c879bff8c 100644 (file)
--- 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<Sequence> *some_seqs, 
-               std::list<ExtendedConservedPath > some_paths, 
+               std::list<ConservedPath > some_paths, 
                std::vector<int> some_lens, std::vector<fltk_motif> *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<Sequence> *S;
   //list of paths in selection box
-    std::list<ExtendedConservedPath > P;
+    std::list<ConservedPath > P;
     std::vector<int> seq_lens;
   //pointer to passed fltk_motif data
     std::vector<fltk_motif> *the_motifs;

diff --git a/gui/SeqWindow.cpp b/gui/SeqWindow.cpp
index 8578f4974e1d2c0fa11e01807bc5cd77342e5a46..5a3351cdddb5f42b8a4d86c868e78bc852a2e194 100644 (file)
--- 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<Sequence> *some_seqs, 
-                    list<ExtendedConservedPath > some_paths, 
+                    list<ConservedPath > some_paths, 
                     vector<int> some_lens,
                     vector<fltk_motif> *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<ExtendedConservedPath >::iterator align_iter;
+  list<ConservedPath >::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 c6b8cc829002036d4eb7bee483eaaad9a30d474c..920d49671499e4bbb324ada0fb005e1d61226143 100644 (file)
--- 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<Sequence> *S;
     // list of paths in selection box
-    std::list<ExtendedConservedPath > P;
+    std::list<ConservedPath > P;
     std::vector<int> seq_lens;
     //pointer to passed fltk_motif data
     std::vector<fltk_motif> *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<Sequence> *some_seqs, 
-              std::list<ExtendedConservedPath > some_paths, 
+              std::list<ConservedPath > some_paths, 
               std::vector<int> some_lens,
               std::vector<fltk_motif> *some_motifs);
     virtual ~SeqWindow(){ std::cout << "dying\n"; }