X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=alg%2Fmussa.hpp;h=6a0ca4eeca4743df44d7af040233d788c40ed147;hb=2534e631c7aca3a93823ea3dc868808bba6cd824;hp=64f46499b2ccd0eb450d051e219335eb59256c2e;hpb=81354ba90b6b670d361263bb3ff70bef67f83d9f;p=mussa.git

diff --git a/alg/mussa.hpp b/alg/mussa.hpp
index 64f4649..6a0ca4e 100644
--- a/alg/mussa.hpp
+++ b/alg/mussa.hpp
@@ -13,7 +13,8 @@
 //                        ----------------------------------------
 //                          ---------- mussa_class.hh -----------
 //                        ----------------------------------------
-#include <QObject> 
+#include <QObject>
+#include <QString> 
 
 #include <boost/filesystem/path.hpp>
 #include <boost/shared_ptr.hpp>
@@ -31,13 +32,19 @@
 
 std::string int_to_str(int an_int);
 
+class Mussa;
+//! provide a simple name to point to our Mussa shared_ptr
+typedef boost::shared_ptr<Mussa> MussaRef;
+
 class Mussa : public QObject
 {
     Q_OBJECT 
 
 signals:
     //! call whatever signaling system we want
-    void progress(const std::string& description, int cur, int max);
+    void progress(const QString& description, int cur, int max);
+    //! triggered when our state changes between unsaved(true) and saved(false)
+    void isModified(bool);
 
 public:
     typedef std::set<Sequence> motif_set;
@@ -47,12 +54,23 @@ public:
     Mussa();
     Mussa(const Mussa &);
 
+    //! dynamically construct a new Mussa object and return a reference to it
+    static MussaRef init();
+    
     //! save all of mussa
     void save(boost::filesystem::path save_path="");
+    //! save all of mussa
+    void save(const std::string& save_path) {
+      save(boost::filesystem::path(save_path));
+    }
     //! save the nway comparison
     void save_muway(boost::filesystem::path save_path);
     //! load a saved analysis directory
     void load(boost::filesystem::path ana_path);
+    //! load a saved analysis 
+    void load(const std::string& ana_path) { 
+       load(boost::filesystem::path(ana_path)); 
+    }
     // ! return path to the where the analysis is stored
     boost::filesystem::path get_analysis_path() const;
     //! set analysis path
@@ -62,8 +80,16 @@ public:
     void clear();
 
     //! set parameters from a file - 'mupa' ~ mussa parameters
-    void load_mupa_file(std::string para_file_path) { load_mupa_file(boost::filesystem::path(para_file_path));}
+    void load_mupa_file(const std::string& para_file_path) {
+      load_mupa_file(boost::filesystem::path(para_file_path));
+    }
     void load_mupa_file(boost::filesystem::path para_file_path);
+    //! load mussa parameters from a stream, specifing output location
+    void load_mupa_stream(
+           std::istream & para_file, 
+           boost::filesystem::path& file_path_base
+         );
+    
 
     // set parameters individually (eg from user input into gui classes)
     //! set analysis name
@@ -95,11 +121,23 @@ public:
     //! must be in range [threshold..window size]
     void set_soft_threshold(int sft_thres);
     int get_soft_threshold() const;
+
+    //! should we append the window size to the analysis name
+    void set_append_window(bool v);
+    //! should we append the window size to the analysis name
+    bool get_append_window();
+
+    //! should we append the threshold to the analysis name
+    void set_append_threshold(bool v);
+    //! should we append the threshold to the analysis name
+    bool get_append_threshold();
  
     void set_analysis_mode(enum analysis_modes new_ana_mode);
     enum analysis_modes get_analysis_mode() const;
     //! return a string name for an analysis mode
     std::string get_analysis_mode_name() const;
+    //! set our current dirty state
+    void set_dirty(bool);
     //! return if we have unsaved changes
     bool is_dirty() const;
     //! is there anything loaded into this analysis?
@@ -122,7 +160,7 @@ public:
      */
     void analyze();
     /*! Run the nway filtering algorithm, 
-     *  this might be used when changing the soft threshhold?
+     *  automatically called when the soft threshhold has changed?
      */
     void nway();
 
@@ -181,6 +219,10 @@ public:
     /*! \sa Mussa::load_motifs(boost::filesystem::path)
      */
     void load_motifs(std::istream &);
+    //! save motif list to the specified filename
+    void save_motifs(boost::filesystem::path filename);
+    //! save motif list to an ostream
+    void save_motifs(std::ostream &);
     //! return our motifs;
     const motif_set& motifs() const;
 
@@ -230,6 +272,4 @@ public:
     void seqcomp();
 
 };
-//! provide a simple name to point to our Mussa shared_ptr
-typedef boost::shared_ptr<Mussa> MussaRef;
 #endif