MESSAGE
| DATE | 2016-11-26 |
| FROM | Ruben Safir
|
| SUBJECT | Subject: [Hangout-NYLXS] Fitch etc
|
I finally fixed the type problem with my fitch program. Not that I've finished
the program, but I finally understand the problem. I got lost in the data flow
of the program. I am trying to print out the vector of states, which have objects
of pairs. That requires an overload of operator<<() of the states object AND a range
operation of the vector itself.
http://www.nylxs.com/docs/thesis/src/fitch/nodes.h.html
1 /*
2 * =====================================================================================
3 *
4 * Filename: nodes.h
5 *
6 * Description: description of phylogentic nodes as per
7 * Fitch and Sannkoff as describd by Felenstein
8 *
9 * Version: 1.0
10 * Created: Nov 4 21:15:49 EDT 2016
11 * Revision: none
12 * Compiler: gcc
13 *
14 * Author: Ruben Safir,
15 * Company: LIU Thesis
16 *
17 * =====================================================================================
18 */
19 #ifndef NODES_H
20 #define NODES_H
21 #include
22 #include
23 #include
24 namespace tree {
25
26
27 /* ==============================================================================
28 * Class NODE -
29 * Description - This is a node in the tree that must undergo parsimony evaluation
30 * ================================================================================
31 */
32 template
33 class NODE{
34 public:
35 ¦ //=========================LIFECYCLE=========================================
36 ¦ /* Constructor */
37 NODE( std::string xt, const unk &x , NODE *xcl= 0, NODE *xcr = 0, NODE *xp = 0 ):_trait{xt},_states{x}, _cl{xcl}, _cr{xcr}, _p{xp} {//child left, child right etc
38 std::cout << trait() << " node " << "has the following states => " << states() << std::endl;
39 };
40
41 NODE(const NODE &other); //copy constructor
42 ¦ ~NODE();
43 ¦
44 ¦ /* ==================== ACCESSORS ======================================= */
45 //no need for inline when you are defineing functions within the class definition
46 std::string trait()const{
47 return _trait;
48 }
49 unk states()const{
50 ¦ ¦ return _states;
51 ¦ };
52 NODE * cl()const{
53 ¦ ¦ return _cl;
54 ¦ };
55 NODE * cr()const{
56 ¦ ¦ return _cr;
57 ¦ };
58 NODE * p()const{
59 ¦ ¦ return _p;
60 ¦ };
61 void states(const unk &x){
62 ¦ ¦ _states = x;
63 ¦ }
64 void trait(std::string xt){
65 ¦_trait = xt; //With genetics this is a A C G T although it is just a label
66 ¦}
67 void cl(NODE *xcl){ //This is the left child node in the tree
68 ¦ ¦ _cl = xcl;
69 ¦ }
70 void cr(NODE *xcr){//This is the right node child node in the tree
71 ¦ ¦ _cr = xcr;
72 ¦ }
73 void p(NODE *xp){//This is the parent node in the tree
74 ¦ ¦ _p = xp;
75 ¦ }
76 ¦ /* ==================== MUTATORS ======================================= */
77 ¦
78 ¦ /* ==================== OPERATORS ======================================= */
79 //void display();
80 template
81 friend std::ostream& operator<<(std::ostream& os, const T&);
82
83 template
84 friend std::ostream& operator<<(std::ostream& os, const NODE &);
85
86 protected:
87 ¦ /* ==================== DATA MEMBERS ======================================= */
88 ¦
89 ¦
90 private:
91 ¦ /* ==================== DATA MEMBERS ======================================= */
92 ¦std::string _trait;
93 ¦unk _states;
94 ¦NODE * _cl, * _cr, * _p;
95
96
97 }; /* ----- end of template class NODE ----- */
98
99 template
100 std::ostream& operator<<(std::ostream& os, const NODE& vec){
101
102 for( auto& y : vec.state() )
103 os << y << std::endl;
104 return os;
105 }
106
107
108
109 template
110 tree::NODE::~NODE(){
111 }
112
113 /*
114 * =====================================================================================
115 * Class: State
116 * Description: This describes a possible individual state or charactoristic
117 * =====================================================================================
118 */
119 template
120 class state
121 {
122 public:
123 /* ==================== LIFECYCLE ======================================= */
124 ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦/* constructor */
125 //r is the minimum cost of a single state when compared to the child nodes
126 explicit state(std::string const xa, cost xr)
127 :_nam{xa}, _r{xr}
128 {
129 std::cout << "Building a state pair" << std::endl;
130 std::cout << "nam => " << nam() << "\tcost=> " << r() << std::endl;
131 };
132
133
134 /* ==================== ACCESSORS ======================================= */
135 std::string nam()const {return _nam;};
136 cost r() const {return _r;};
137 void r(cost b ){_r = b;};
138 /* ==================== MUTATORS ======================================= */
139
140 /* ==================== OPERATORS ======================================= */
141 friend std::ostream & operator << ( std::ostream & os, const state & obj )
142 {
143 os << obj.nam() << ": " << obj.r() ;
144 return os;
145 } /* ----- end of function operator << ----- */
146
147 /* ==================== DATA MEMBERS ======================================= */
148 protected:
149
150 private:
151 std::string _nam;
152 cost _r;
153
154 }; /* ----- end of class State ----- */
155
156 /*
157 * =====================================================================================
158 * Class: Pstates
159 * Description: vector of all possible states
160 * =====================================================================================
161 */
162 template
163 class Pstates
164 {
165 public:
166
167 /* ==================== LIFECYCLE ======================================= */
168 /* constructor */
169 Pstates (std::vector< state > x)
170 : _vstate{x}
171 {
172 for( auto& y : _vstate)
173 std::cout << y << std::endl;
174 };
175
176 ~Pstates (){}; /* destructor */
177
178 /* ==================== ACCESSORS ======================================= */
179 const std::vector< state >& vstate() const{
180 return _vstate;
181 }
182 void vstate(std::vector< state > in ){
183 _vstate = in;
184 }
185
186 /* ==================== MUTATORS ======================================= */
187
188 /* ==================== OPERATORS ======================================= */
189
190 const Pstates& operator = ( const Pstates &other ); /* assignment operator */
191 ¦
192 friend std::ostream & operator << ( std::ostream & os, const Pstates & obj )
193 {
194 for(auto state_pair : obj.vstate() )
195 std::cout << state_pair;
196 return os;
197 } /* ----- end of function operator << ----- */
198
199 /* ==================== DATA MEMBERS ======================================= */
200 protected:
201
202 private:
203 std::vector< state > _vstate;
204
205 }; /* ----- end of class Pstates ----- */
--
So many immigrant groups have swept through our town
that Brooklyn, like Atlantis, reaches mythological
proportions in the mind of the world - RI Safir 1998
http://www.mrbrklyn.com
DRM is THEFT - We are the STAKEHOLDERS - RI Safir 2002
http://www.nylxs.com - Leadership Development in Free Software
http://www2.mrbrklyn.com/resources - Unpublished Archive
http://www.coinhangout.com - coins!
http://www.brooklyn-living.com
Being so tracked is for FARM ANIMALS and and extermination camps,
but incompatible with living as a free human being. -RI Safir 2013
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