rename motif class used in fltk code to fltk_motif

I forgot to build the fltk code and so my patch that added the motif derived
from the annot class, conflicted with the motif in the fltk code.

So I renamed it. darcs replace is really neat, it made dealing with that
sooo much easier.

diff --git a/gui/ConnView.cpp b/gui/ConnView.cpp
index 178a8eacbb57d6c3940e190a68acfbc0d514b0f6..a25d6324f729c06253ddf391ffd5c5c50613e490 100644 (file)
--- a/gui/ConnView.cpp
+++ b/gui/ConnView.cpp
@@ -25,7 +25,7 @@ ConnView::setup(string name, int sq_num, int win_len,
 {
   int i, i2, seq_length;
   Sequence a_seq;
-  motif blank_motif;
+  fltk_motif blank_motif;
   annot_color new_annot;
 
 
@@ -435,7 +435,7 @@ ConnView::draw_sequence_stuff()
 
 
   // draw motifs found
-  vector<motif>::iterator motif_i;
+  vector<fltk_motif>::iterator motif_i;
   vector<int> some_motif_locs;
   vector<int>::iterator i_locs;
   int scale_len, motif_len;
@@ -567,7 +567,7 @@ ConnView::handle(int e)
 void
 ConnView::check_new_motifs()
 {
-  vector<motif>::iterator i;
+  vector<fltk_motif>::iterator i;
   int i2;
   vector<int> some_motif_locs;
   vector<int>::iterator i_locs;

diff --git a/gui/ConnView.hpp b/gui/ConnView.hpp
index f5a95c416d963a634335eb04f3ef2abcdea17fb5..6d52a5fe6f4970806bd26bc40b86cae1bb6af6fd 100644 (file)
--- a/gui/ConnView.hpp
+++ b/gui/ConnView.hpp
@@ -72,10 +72,10 @@ class ConnView : public Fl_Box
     bool show_bars, show_lines;
 
   //keeps track of all the motifs the user has inputed
-    std::vector<motif> some_motifs;
+    std::vector<fltk_motif> some_motifs;
     MotifWindow *motif_find_window;
 
-  //keeps track of the colors assigned to each motif type
+  //keeps track of the colors assigned to each fltk_motif type
     std::vector<annot_color> some_annots;
     AnnotWindow *annot_color_window;
 

diff --git a/gui/MotifWindow.cpp b/gui/MotifWindow.cpp
index 7a7708b9029183e4784aad07e0dda75b8c6b6ca2..ef93260bdf3145541f4241e2947679ef3276a8ed 100644 (file)
--- a/gui/MotifWindow.cpp
+++ b/gui/MotifWindow.cpp
@@ -16,12 +16,12 @@
 
 using namespace std;
 
-motif
+fltk_motif
 new_blank_motif()
 {
-  motif *a_motif;
+  fltk_motif *a_motif;
 
-  a_motif = new motif;
+  a_motif = new fltk_motif;
   a_motif->name = "";
   a_motif->seq = "";
   a_motif->color = (Fl_Color) 5;
@@ -53,7 +53,7 @@ cb_motif_color(Fl_Button* o, void* v)
 
 
 MotifWindow::MotifWindow(int w, int h, const char* title, 
-                         vector<motif> * some_motifs):Fl_Window(w,h,title)
+                         vector<fltk_motif> * some_motifs):Fl_Window(w,h,title)
 {
   int i;
 
@@ -66,15 +66,15 @@ MotifWindow::MotifWindow(int w, int h, const char* title,
   motif_input_pack = new Fl_Pack(0, 0, w, h);
   motif_input_pack->spacing(4);
 
-  // button to add new motif inputs
+  // button to add new fltk_motif inputs
   add_motif = new Fl_Button(0,0,100,24,"Add Motif Slot");
   add_motif->callback((Fl_Callback*)add_motif_cb, this);
   motif_input_pack->add(add_motif);
-  // test button to make sure motif data is being stored
+  // test button to make sure fltk_motif data is being stored
   test = new Fl_Button(0,0,100,24,"show motifs");
   test->callback((Fl_Callback*)print_cb, this);
   motif_input_pack->add(test);
-  // creat an initial set of motif input widgets and attach to motif vector
+  // creat an initial set of fltk_motif input widgets and attach to fltk_motif vector
   for (i = 0; i < 5; i++)
   {
     add_motif_input(i);
@@ -121,7 +121,7 @@ MotifWindow::add_motif_input(int index)
   motif_hor_pack->add(new_color_button);
 
 
-  // setup the motif inputs
+  // setup the fltk_motif inputs
   new_input = new Fl_Input(0, 0, 200, 24, "");
   new_input->value( ((*the_motifs)[index].seq).c_str() );
   new_input->callback((Fl_Callback*)cb_motif_in, (void*) something);
@@ -164,7 +164,7 @@ void MotifWindow::add_motif_cb(Fl_Button* o, void* v)
 
 void MotifWindow::add_motif_cb_real(Fl_Button* , void*)
 {
-  motif blank_motif;
+  fltk_motif blank_motif;
 
   //blank_motif.name = "";
   //blank_motif.seq = "";

diff --git a/gui/MotifWindow.hpp b/gui/MotifWindow.hpp
index 84f5de21b2dea84aca096143682ccdc604b8dd1b..efbeffffba7aeba764f5fbba2453141628ccb158 100644 (file)
--- a/gui/MotifWindow.hpp
+++ b/gui/MotifWindow.hpp
@@ -21,7 +21,7 @@
 
 #include "alg/mussa.hpp"
 
-struct motif
+struct fltk_motif
 {
   std::string name, seq;
   Fl_Color color;
@@ -29,13 +29,13 @@ struct motif
   bool dirty;
 };
 
-//typedef motif_ptr *motif;
+//typedef motif_ptr *fltk_motif;
  
 
 class MotifWindow : public Fl_Window
 { 
   public:
-    MotifWindow(int w, int h, const char* title, std::vector<motif> * some_motifs);
+    MotifWindow(int w, int h, const char* title, std::vector<fltk_motif> * some_motifs);
     ~MotifWindow();
     Fl_Pack * motif_input_pack;
     std::list<Fl_Input*> motif_ins;
@@ -48,7 +48,7 @@ class MotifWindow : public Fl_Window
     void cb_motif_color_i(Fl_Button* o, int i);
 
   private:
-    std::vector<motif> * the_motifs;
+    std::vector<fltk_motif> * the_motifs;
     int motif_count;
 
     void add_motif_input(int index);
@@ -68,5 +68,5 @@ struct motif_instance
   int index;
 };
 
-motif new_blank_motif();
+fltk_motif new_blank_motif();
 #endif

diff --git a/gui/SeqView.cpp b/gui/SeqView.cpp
index 30c1dd3393687d6006a2b34075a5c19c9be7863e..24f7819cbbca0cdef288f6fd1bdc103d1d50fbc4 100644 (file)
--- a/gui/SeqView.cpp
+++ b/gui/SeqView.cpp
@@ -21,7 +21,7 @@ void
 SeqView::setup(string name, int sq_num, 
                vector<Sequence> *some_seqs,
                list<ExtendedConservedPath > some_paths, vector<int> some_lens,
-               vector<motif> *some_motifs)
+               vector<fltk_motif> *some_motifs)
 {
   int seq_i;
   list<ExtendedConservedPath >::iterator pathz_i;
@@ -129,7 +129,7 @@ SeqView::draw()
 void
 SeqView::draw_motifs(double ch_width)
 {
-  vector<motif>::iterator motif_i;
+  vector<fltk_motif>::iterator motif_i;
   vector<int> some_motif_locs;
   vector<int>::iterator i_locs;
   int scale_len, motif_len, i2;

diff --git a/gui/SeqView.hpp b/gui/SeqView.hpp
index 40a43dd508ef59ebbf56a3cc5042fe1677ac8022..aab023fbeb5594d7a9365f7798fce7aa31999d89 100644 (file)
--- a/gui/SeqView.hpp
+++ b/gui/SeqView.hpp
@@ -34,7 +34,7 @@ class SeqView : public Fl_Box
              
     void setup(std::string name, int sq_num, std::vector<Sequence> *some_seqs, 
                std::list<ExtendedConservedPath > some_paths, 
-               std::vector<int> some_lens, std::vector<motif> *some_motifs);
+               std::vector<int> some_lens, std::vector<fltk_motif> *some_motifs);
     void align_offsets(int align_num);
     void toggle_align(int align_num);
     void toggle_bars();
@@ -50,8 +50,8 @@ class SeqView : public Fl_Box
   //list of paths in selection box
     std::list<ExtendedConservedPath > P;
     std::vector<int> seq_lens;
-  //pointer to passed motif data
-    std::vector<motif> *the_motifs;
+  //pointer to passed fltk_motif data
+    std::vector<fltk_motif> *the_motifs;
 
     int x_max, y_max, x_min, y_min;
     int y_seq_incre;

diff --git a/gui/SeqWindow.cpp b/gui/SeqWindow.cpp
index 0e011e2b230c5260b77f56be55c0ebcc31b81b9a..46a73b8bfafba932ae5464b34a294ca3af571058 100644 (file)
--- a/gui/SeqWindow.cpp
+++ b/gui/SeqWindow.cpp
@@ -91,7 +91,7 @@ SeqWindow::SeqWindow(int w, int h, const char* title, int sq_num,
                     vector<Sequence> *some_seqs, 
                     list<ExtendedConservedPath > some_paths, 
                     vector<int> some_lens,
-                    vector<motif> *some_motifs):
+                    vector<fltk_motif> *some_motifs):
   Fl_Double_Window(w,h,title)
 {
   menu_align_data_bundle * some_menu_data;

diff --git a/gui/SeqWindow.hpp b/gui/SeqWindow.hpp
index 467445c6941a4e2e6cfc290718608972238b9a62..c6b8cc829002036d4eb7bee483eaaad9a30d474c 100644 (file)
--- a/gui/SeqWindow.hpp
+++ b/gui/SeqWindow.hpp
@@ -32,8 +32,8 @@ class SeqWindow : public Fl_Double_Window
     // list of paths in selection box
     std::list<ExtendedConservedPath > P;
     std::vector<int> seq_lens;
-    //pointer to passed motif data
-    std::vector<motif> *the_motifs;
+    //pointer to passed fltk_motif data
+    std::vector<fltk_motif> *the_motifs;
 
     int x_max, y_max;
     Fl_Menu_Button *choose_align_menu;
@@ -48,7 +48,7 @@ class SeqWindow : public Fl_Double_Window
               std::vector<Sequence> *some_seqs, 
               std::list<ExtendedConservedPath > some_paths, 
               std::vector<int> some_lens,
-              std::vector<motif> *some_motifs);
+              std::vector<fltk_motif> *some_motifs);
     virtual ~SeqWindow(){ std::cout << "dying\n"; }
 
     void make_choose_menu();