Death to stupid mussa pointers

[mussa.git] / qui / MussaAlignedWindow.cpp

diff --git a/qui/MussaAlignedWindow.cpp b/qui/MussaAlignedWindow.cpp
index f418b02e8e7626e088030e4ff513153a90a0b8f4..65e3d7bf27df26328a92692ab7efbb2ecc1055e8 100644 (file)
--- a/qui/MussaAlignedWindow.cpp
+++ b/qui/MussaAlignedWindow.cpp
@@ -12,8 +12,8 @@
 #include <iostream>
 using namespace std;
 
-MussaAlignedWindow::MussaAlignedWindow(Mussa& m, 
-                                       const set<int>& sel_paths, 
+MussaAlignedWindow::MussaAlignedWindow(MussaRef m, 
+                                       const set<int>& sel_paths,
                                        QWidget *parent)
   : QMainWindow(parent),
     analysis(m),
@@ -23,8 +23,8 @@ MussaAlignedWindow::MussaAlignedWindow(Mussa& m,
     alignTB(0)
 {
   setupActions();
-  browser.setSequences(analysis.sequences(), analysis.colorMapper());
-  setSelectedPaths(m, sel_paths);
+  browser.setSequences(analysis->sequences(), analysis->colorMapper());
+  setSelectedPaths(analysis, sel_paths);
   setAlignment(0);
   double zoom_level = browser.zoomToSequence();
 
@@ -107,13 +107,13 @@ void MussaAlignedWindow::setupAlignmentMenus()
 }
 
 
-void MussaAlignedWindow::setSelectedPaths(Mussa &m, const set<int>& sel_paths)
+void MussaAlignedWindow::setSelectedPaths(MussaRef m, const set<int>& sel_paths)
 {
   // sets are sorted
   set<int>::iterator sel_i = sel_paths.begin();
-  list<ConservedPath>::const_iterator path_i = m.paths().refined_pathz.begin();
-  list<ConservedPath>::const_iterator path_end = m.paths().refined_pathz.end();
-  size_t path_size = m.paths().refined_pathz.size();
+  list<ConservedPath>::const_iterator path_i = m->paths().refined_pathz.begin();
+  list<ConservedPath>::const_iterator path_end = m->paths().refined_pathz.end();
+  size_t path_size = m->paths().refined_pathz.size();
   size_t pathid=0;
 
   selected_paths.reserve(sel_paths.size());
@@ -175,10 +175,10 @@ void MussaAlignedWindow::computeMatchLines()
     if (view_paths[count]) 
       filtered_paths.push_back(*path_i);
   }
-  analysis.createLocalAlignment(filtered_paths.begin(), 
-                                filtered_paths.end(),
-                                result, 
-                                reversed);
+  analysis->createLocalAlignment(filtered_paths.begin(), 
+                                 filtered_paths.end(),
+                                 result, 
+                                 reversed);
 
   list<ConservedPath::path_type>::const_iterator result_i = result.begin();
   list<vector<bool> >::const_iterator reversed_i = reversed.begin();