change version to v0.2-beta

hybridLambda · Feb 23, 2016 · 1bef83b · 1bef83b
1 parent 74d2f55
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diff --git a/README.md b/README.md
@@ -19,9 +19,8 @@ Development Version | dev     | [![Build Status](https://api.travis-ci.org/hybri
 ##DOCUMENTATION
 [Download](https://github.com/hybridLambda/hybrid-coal/raw/doc/doc/manual.pdf)
 
-##INSTALLATION
+##BEFORE INSTALLATION
 
-### For developers
 To install _hybrid-coal_, first install the following packages and libraries
 
 on Debian/Ubuntu based systems:
@@ -33,6 +32,8 @@ on Mac OS:
 port install git cppunit automake autoconf autoconf-archive graphviz
 ```
 
+## DOWNLOAD AND COMPILE
+
 then type the following commands:
 ```bash
 ./bootstrap
@@ -64,7 +65,6 @@ Options              | Useage |
 ```bash
 hybrid-coal -sp '((((B:1,C:1)s1:1)h1#.5:1,A:3)s2:1,(h1#.5:1,D:3)s3:1)r;'
 hybrid-coal -sp trees/4_tax_sp_nt1_para -gt '(((A,D),C),B);'
-hybrid-coal -sp trees/4_tax_sp_nt1_para -gt trees/4_tax_gt4.tre -latex
 hybrid-coal -sp trees/4_tax_sp_nt1_para -plot
 hybrid-coal -sp trees/4_tax_sp_nt1_para -plot -branch
 hybrid-coal -sp trees/4_tax_sp_nt1_para -plot -label

diff --git a/src/hybridcoal.cpp b/src/hybridcoal.cpp
@@ -1,10 +1,10 @@
-/* 
+/*
  * hybrid-coal is used to compute gene tree probabilities given species network under coalescent process.
- * 
+ *
  * Copyright (C) 2010 -- 2015 Sha (Joe) Zhu
- * 
+ *
  * This file is part of hybrid-coal
- * 
+ *
  * hybrid-coal is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
  * the Free Software Foundation, either version 3 of the License, or
@@ -14,7 +14,7 @@
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
@@ -25,12 +25,12 @@
 #include "tree_topo/all_gene_topo.hpp"
 
 void HybridCoal::init(){
-    this->prefix    = "OUT";    
+    this->prefix    = "OUT";
     this->argc_i = 1;
     this->helpBool = false;
     //this->symb_bool = false;
     this->print_tree_bool = false;
-    this->print_gene_topo_bool = false; 
+    this->print_gene_topo_bool = false;
     this->plot_bool       = false;
     //this->latex_bool = false;
     //this->maple_bool = false;
@@ -50,7 +50,7 @@ void HybridCoal::read_input_lines(const char inchar[], vector <string> & out_vec
     string out_str;
     if ( in_file.good() ){
         getline ( in_file, out_str );
-        while ( out_str.size() > 0 ){   
+        while ( out_str.size() > 0 ){
             out_vec.push_back( out_str );
             getline ( in_file, out_str );
         }
@@ -70,14 +70,14 @@ void HybridCoal::read_input_lines(const char inchar[], vector <string> & out_vec
 void HybridCoal::check_gt_str_and_sign( string &gt_str ){
     if ( gt_str.find('&') != string::npos ){
         throw std::invalid_argument ( "Error: gene tree " + gt_str + " can not be a gene tree string" );
-    }    
+    }
 }
 
 
 void HybridCoal::parse(){
     if ( argc_ == 1 )
         helpBool = true;
-    while (argc_i < argc_){    
+    while (argc_i < argc_){
         std::string argv_i(argv_[argc_i]);
         if      ( argv_i == "-h" || argv_i == "-help" ){ helpBool = true; }
         else if ( argv_i == "-gt"    ){ readNextStringto( this->gt_file_name , this->argc_i, this->argc_,  this->argv_ ); this->enumerate_gt_bool = false; }
@@ -87,7 +87,7 @@ void HybridCoal::parse(){
         //else if ( argv_i == "-maple" ){ this->maple_bool=true; }
         //else if ( argv_i == "-symb"  ){ this->symb_bool=true; }
         else if ( argv_i == "-plot"  || argv_i == "-dot" ){ this->plot_bool = true; }
-        else if ( argv_i == "-label" || argv_i == "-branch" ){ argc_i++; continue; }        
+        else if ( argv_i == "-label" || argv_i == "-branch" ){ argc_i++; continue; }
         else if ( argv_i == "-print" ){ this->print_tree_bool = true; }
         else if ( argv_i == "-gtopo" ){ this->print_gene_topo_bool = true; }
         //else if (argv_i=="-sub"){ list_sub_network_bool=true;}
@@ -102,7 +102,7 @@ void HybridCoal::parse(){
             //maple_F_name=Fname_ext(argv[argc_i+1],".mw");
         //}
         //else { cout <<"  need to change this !!!" << argv_i<<endl; argc_i++;continue; } // need to change this !!!
-        argc_i++;    
+        argc_i++;
     }
     this->finalize();
 }
@@ -111,13 +111,13 @@ void HybridCoal::parse(){
 string HybridCoal::read_input_line(const char *inchar){
     string out_str;
     ifstream in_file( inchar );
-    if (in_file.good())    getline ( in_file, out_str); 
+    if (in_file.good())    getline ( in_file, out_str);
     else{
         string dummy_str(inchar);
         if (dummy_str.find('(')!=string::npos && dummy_str.find(')')!=string::npos) out_str=dummy_str;
         else  throw std::invalid_argument("Invalid input file. " + string (inchar) );
     }
-    in_file.close();            
+    in_file.close();
     return     out_str;
 }
 
@@ -128,9 +128,9 @@ void HybridCoal::finalize(){
     if ( this->gt_file_name.size() > 0 ) {
         this->read_input_lines( this->gt_file_name.c_str(), this->gt_tree_str_s);
     }
-    
+
     if ( this->print_tree_bool || this->plot_bool ) return;
-    
+
     if ( this->enumerate_gt_bool ){
         Net net( this->sp_str );
         GeneTopoList topologies( net.tip_name );
@@ -143,20 +143,20 @@ void HybridCoal::HybridCoal_core(){
         this->print_help();
         return;
     }
-    
+
     if ( this->print_tree_bool ) {
         this->print();
         return;
     }
-   
+
     if ( this->plot_bool ){
         Figure figure_para ( this->argc_, this->argv_ );
         figure_para.figure_file_prefix = this->prefix;
         figure_para.finalize();
         figure_para.plot( this->sp_str );
         return;
     }
-        
+
     if ( this->print_gene_topo_bool ){
         string gt_out = this->prefix+".topo";
 
@@ -212,32 +212,33 @@ void HybridCoal::print(){
 
 
 void HybridCoal::print_example(){
-    cout << "Examples:" 
-         << endl 
+    cout << "Examples:"
+         << endl
          << endl;
-    cout << "hybrid-coal -sp '((((B:1,C:1)s1:1)h1#.5:1,A:3)s2:1,(h1#.5:1,D:3)s3:1)r;'"<<endl;    
-    cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -gt '(((A,D),C),B);'"<<endl;    
-    cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -gt trees/4_tax_gt4.tre -maple"<<endl;    
-    cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -gt trees/4_tax_gt4.tre -latex"<<endl;
-    cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -maple -latex"<<endl;    
+    cout << "hybrid-coal -sp '((((B:1,C:1)s1:1)h1#.5:1,A:3)s2:1,(h1#.5:1,D:3)s3:1)r;'"<<endl;
+    cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -gt '(((A,D),C),B);'"<<endl;
+    cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -gt trees/4_tax_gt4.tre"<<endl;
+    //cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -gt trees/4_tax_gt4.tre -maple"<<endl;
+    //cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -gt trees/4_tax_gt4.tre -latex"<<endl;
+    //cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -maple -latex"<<endl;
     cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -plot"<<endl;
     cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -plot -branch"<<endl;
     cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -plot -label"<<endl;
     cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -dot"<<endl;
-    cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -print"<<endl;
+    //cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -print"<<endl;
     cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -gtopo"<<endl;
-    cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -sub"<<endl;
+    //cout << "hybrid-coal -sp trees/4_tax_sp_nt1_para -sub"<<endl;
     //cout << "./hybrid-coal_dbg -sp trees/7_tax_sp_james02.tre -gt trees/7_tax_gt_james"<<endl;
-    cout << endl;    
+    cout << endl;
 }
 
 
 void HybridCoal::print_option(){
-    cout << endl 
-         << "hybrid-coal " << VERSION 
-         << endl 
+    cout << endl
+         << "hybrid-coal " << VERSION
+         << endl
          << endl;
-    cout << "Usage:" 
+    cout << "Usage:"
          << endl;
     cout << setw(20) << "-h or -help"         << "  --  " << "Help. List the following content."<<endl;
     cout << setw(20) << "-gt STR"             << "  --  " << "Input the gene tree string string through command line or a file."<<endl;
@@ -248,7 +249,7 @@ void HybridCoal::print_option(){
     cout << setw(20) << "-gtopo"              << "  --  " << "To generate the gene tree topologies of a given set of taxa."<<endl;
     //cout<<"-sub -- Produce file sub_networks, which contanis all sub trees of a species network"<<endl;
 
-    cout << setw(20) << "-plot/-dot [option]" << "  --  " << "Use LaTEX(-plot) or Dot (-dot) to draw the input (defined by -spcu) network(tree)."<<endl;
+    cout << setw(20) << "-plot/-dot [option]" << "  --  " << "Use LaTEX(-plot) or Dot (-dot) to draw the input (defined by -sp) network(tree)."<<endl;
     cout << setw(20) << "    [-branch]"       << "  --  " << "Branch lengths will be labelled in the figure."<<endl;
     cout << setw(20) << "-o STR "             << "  --  " << "Specify the file name prefix of the output."<<endl;
 }

diff --git a/version b/version
@@ -1 +1 @@
-v0.1-beta
+v0.2-beta