Changeset 573

Timestamp:

04/28/10 17:45:28 (4 months ago)

Author:

reed

Message:

framework for aa models

Location:

current/src

Files:

• include/dawg/details/subst_aa.h (modified) (1 diff)
• include/dawg/subst.h (modified) (2 diffs)
• lib/output.cpp (modified) (1 diff)

current/src/include/dawg/details/subst_aa.h

@@ -167 +167 @@
     return create_aagtr("wagstar", &s[0], &s[190], &p[0], &p[20]);
 }
- 
+
+template<typename It1, typename It2>
+bool subst_model::create_lg(const char *, It1 first1, It1 last1, It2 first2, It2 last2) {
+    static double s[190];
+    static double p[20];
+    if(first2 != last2) { //+F model
+        return create_aagtr("lg+f", &s[0], &s[190], first2, last2);
+    }
+    return create_aagtr("lg", &s[0], &s[190], &p[0], &p[20]);
+}
+
+template<typename It1, typename It2>
+bool subst_model::create_jtt(const char *, It1 first1, It1 last1, It2 first2, It2 last2) {
+    static double s[190];
+    static double p[20];
+    if(first2 != last2) { //+F model
+        return create_aagtr("jtt+f", &s[0], &s[190], first2, last2);
+    }
+    return create_aagtr("jtt", &s[0], &s[190], &p[0], &p[20]);
+}
+
+template<typename It1, typename It2>
+bool subst_model::create_dayhoff(const char *, It1 first1, It1 last1, It2 first2, It2 last2) {
+    static double s[190];
+    static double p[20];
+    if(first2 != last2) { //+F model
+        return create_aagtr("dayhoff+f", &s[0], &s[190], first2, last2);
+    }
+    return create_aagtr("dayhoff", &s[0], &s[190], &p[0], &p[20]);
+}
+
+template<typename It1, typename It2>
+bool subst_model::create_molphy(const char *, It1 first1, It1 last1, It2 first2, It2 last2) {
+    static double s[190];
+    static double p[20];
+    if(first2 != last2) { //+F model
+        return create_aagtr("molphy+f", &s[0], &s[190], first2, last2);
+    }
+    return create_aagtr("molphy", &s[0], &s[190], &p[0], &p[20]);
+}
+
 } // namespace dawg
  

current/src/include/dawg/subst.h

@@ -94 +94 @@
 
     template<typename It1, typename It2>
+    bool create_lg(const char *mod_name, It1 first1, It1 last1, It2 first2, It2 last2);
+
+    template<typename It1, typename It2>
     bool create_wag(const char *mod_name, It1 first1, It1 last1, It2 first2, It2 last2);
 
     template<typename It1, typename It2>
     bool create_wagstar(const char *mod_name, It1 first1, It1 last1, It2 first2, It2 last2);
+    
+    template<typename It1, typename It2>
+    bool create_jtt(const char *mod_name, It1 first1, It1 last1, It2 first2, It2 last2);
+
+    template<typename It1, typename It2>
+    bool create_dayhoff(const char *mod_name, It1 first1, It1 last1, It2 first2, It2 last2);
+
+    template<typename It1, typename It2>
+    bool create_molphy(const char *mod_name, It1 first1, It1 last1, It2 first2, It2 last2);
 };
 
 template<typename It1, typename It2>
 bool subst_model::create(const char *mod_name, It1 first1, It1 last1, It2 first2, It2 last2) {
-    static const char name_keys[][10] = {
+    static const char name_keys[][16] = {
         "jc",  "gtr", "k2p", "hky", "f84", "f81", "tn", "tn-f04",
-        "aagtr", "wag", "wagstar"
+        "aagtr", "lg", "wag", "wagstar", "jtt-dcmut", "dayhoff-dcmut", "molphy"
     };
     
@@ -111 +123 @@
         &subst_model::create_hky, &subst_model::create_f84, &subst_model::create_f81,
         &subst_model::create_tn, &subst_model::create_tn_f04,
-        &subst_model::create_aagtr, &subst_model::create_wag, &subst_model::create_wagstar,
+        &subst_model::create_aagtr, &subst_model::create_lg, &subst_model::create_wag,
+        &subst_model::create_wagstar, &subst_model::create_jtt, &subst_model::create_dayhoff,
+        &subst_model::create_molphy
     };
     std::size_t pos = key_switch(mod_name, name_keys);

current/src/lib/output.cpp

@@ -108 +108 @@
 
     string::iterator it = split_file_name.begin()+split_id_offset;
-    generate(it, right_align(split_width,lit('0'))[uint_], rep);
+    generate(it, right_align(split_width, "0")[uint_], rep);
     
     if(!open_file(split_file_name.c_str()))