changed all shared commands so that they read the shared file generated by the read...

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 2c02ca9ad560f73ecea8277420fb569b04844d82..494b664fb841389aff6dca6305963d68a1a5a8cf 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -42,6 +42,9 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        cutoff = "1.0";
                }
                
+               //set default value for cutoff
+               if (commandName == "distance") {        cutoff = "1.0";         }
+
                string key, value;              
                //reads in parameters and values
                if((optionText != "") && (commandName != "help")){
@@ -54,7 +57,9 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
                                if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
                                if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       } 
-                               if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         } 
+                               if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
+                               if (key == "nexus" )    { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";         } 
+                               if (key == "clustal" )  { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
                                if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
                                if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
                                if (key == "name" )             { namefile = value;             }
@@ -73,7 +78,15 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "step")                      { step = value;                 }
                                if (key == "form")                      { form = value;                 }
                                if (key == "sorted")            { sorted = value;               }
-                               if (key == "scaler")            { scaler = value;               }
+                               if (key == "vertical")          { vertical = value;             }
+                               if (key == "trump")                 { trump = value;            }
+                               if (key == "filter")            { filter = value;               }
+                               if (key == "soft")                  { soft = value;                 }
+                               if (key == "scale")                     { scale = value;                }
+                               if (key == "ends" )                     { ends = value;                 }
+                               if (key == "processors" )       { processors = value;   }
+                               
+
                                
 
                                
@@ -111,6 +124,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
                        if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
                        if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
+                       if (key == "nexus" )    { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";         }
+                       if (key == "clustal" )  { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; } 
                        if (key == "tree" )             { treefile = value; inputFileName = value; fileroot = value; format = "tree";           } 
                        if (key == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   } 
                        if (key == "name" )             { namefile = value;             }
@@ -129,8 +144,14 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "step")                      { step = value;                 }
                        if (key == "form")                      { form = value;                 }
                        if (key == "sorted")            { sorted = value;               }
-                       if (key == "scaler")            { scaler = value;               }
-                       
+                       if (key == "vertical")          { vertical = value;             }
+                       if (key == "trump")                 { trump = value;            }
+                       if (key == "filter")            { filter = value;               }
+                       if (key == "soft")                  { soft = value;                 }
+                       if (key == "scale")                     { scale = value;                }
+                       if (key == "ends" )                     { ends = value;                 }
+                       if (key == "processors" )       { processors = value;   }
+
 
                        if (key == "line") {//stores lines to be used in a vector
                                lines.clear();
@@ -163,7 +184,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                
                //input defaults for calculators
                if (commandName == "collect.single") {
-                       if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-qstat-logsd-bergerparker-bstick"; }
+
+                       if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
@@ -173,17 +195,18 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        splitAtDash(calc, Estimators); 
                }
                if (commandName == "collect.shared") {
-                       if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
+
+                       if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
                if (commandName == "summary.single") {
-                       if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-logsd-qstat-bergerparker-bstick"; }
+                       if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
                if (commandName == "summary.shared") {
-                       if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
+                       if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
@@ -192,6 +215,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
+               if (commandName == "distance") {
+                       if ((calc == "default") || (calc == "")) {  calc = "onegap";  }
+                       Estimators.clear();
+                       splitAtDash(calc, Estimators); 
+               }
                if (commandName == "venn") {
                        if ((calc == "default") || (calc == "")) { 
                                if (format == "list") { calc = "sobs"; }
@@ -200,7 +228,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
                }
-               if (commandName == "tree.groups") {
+               if ((commandName == "tree.shared") || (commandName == "bootstrap.shared")) {
                        if (calc != "") { 
                                Estimators.clear();
                                splitAtDash(calc, Estimators);                  
@@ -239,6 +267,8 @@ string GlobalData::getOrderFile()           {       return orderfile;       }
 string GlobalData::getTreeFile()               {       return treefile;        }
 string GlobalData::getSharedFile()             {       return sharedfile;      }
 string GlobalData::getFastaFile()              {       return fastafile;       }
+string GlobalData::getNexusFile()              {       return nexusfile;       }
+string GlobalData::getClustalFile()     {   return clustalfile; }
 string GlobalData::getCutOff()                 {       return cutoff;          }
 string GlobalData::getFormat()                 {       return format;          }
 string GlobalData::getPrecision()              {       return precision;       }
@@ -253,17 +283,28 @@ string GlobalData::getGroups()                    {       return groups;          }
 string GlobalData::getStep()                   {       return step;            }
 string GlobalData::getForm()                   {       return form;            }
 string GlobalData::getSorted()                 {       return sorted;          }
-string GlobalData::getScaler()                 {       return scaler;          }
-void GlobalData::setListFile(string file)      {       listfile = file;        inputFileName = file;}
-void GlobalData::setRabundFile(string file)    {       rabundfile = file;      inputFileName = file;}
-void GlobalData::setSabundFile(string file)    {       sabundfile = file;      inputFileName = file;}
-void GlobalData::setPhylipFile(string file)    {       phylipfile = file;    inputFileName = file;}
-void GlobalData::setColumnFile(string file)    {       columnfile = file;    inputFileName = file;}
+string GlobalData::getTrump()                  {   return trump;       }
+string GlobalData::getSoft()                   {   return soft;                }
+string GlobalData::getFilter()                 {   return filter;              }
+string GlobalData::getScale()                  {       return scale;           }
+string GlobalData::getEnds()                   {   return ends;                }
+string GlobalData::getProcessors()             {       return processors;      }
+
+void GlobalData::setListFile(string file)              {       listfile = file;        inputFileName = file;}
+void GlobalData::setGroupFile(string file)             {       groupfile = file;       }
+void GlobalData::setRabundFile(string file)            {       rabundfile = file;      inputFileName = file;}
+void GlobalData::setSabundFile(string file)            {       sabundfile = file;      inputFileName = file;}
+void GlobalData::setPhylipFile(string file)            {       phylipfile = file;    inputFileName = file;}
+void GlobalData::setColumnFile(string file)            {       columnfile = file;    inputFileName = file;}
+void GlobalData::setSharedFile(string file)            {       sharedfile = file;      inputFileName = file; fileroot = file;}
 void GlobalData::setNameFile(string file)              {       namefile = file;                }
 void GlobalData::setFormat(string Format)              {       format = Format;                }
 void GlobalData::setRandomTree(string Random)  {       randomtree = Random;    }
 void GlobalData::setGroups(string g)                   {       groups = g;                             }
 void GlobalData::setCalc(string Calc)                  {       calc = Calc;                    }
+void GlobalData::setEnds(string e)                             {   ends = e;                           }
+void GlobalData::setProcessors(string p)               {       processors = p;                 }
+
 
 /*******************************************************/
 
@@ -272,6 +313,8 @@ GlobalData::GlobalData() {
        //option definitions should go here...
        helpRequest = "";
        clear();
+       gListVector == NULL;            
+       gSparseMatrix == NULL;  
 }
 /*******************************************************/
 
@@ -287,6 +330,8 @@ void GlobalData::clear() {
        groupfile               =       ""; 
        orderfile               =       "";
        fastafile               =   "";
+       nexusfile               =   "";
+       clustalfile             =   "";
        treefile                =       "";
        sharedfile              =       "";
        cutoff                  =       "10.00";
@@ -304,8 +349,15 @@ void GlobalData::clear() {
        abund           =   "10";
        step                    =       "0.01";
        form                    =       "integral";
-       sorted                  =       "1";  //0 means don't sort, 1 means sort.
-       scaler                  =       "log2";
+       sorted                  =       "T";  //F means don't sort, T means sort.
+       vertical        =   "";         
+       trump           =   "";         
+       filter          =   "";         
+       soft            =   ""; 
+       scale                   =       "log10";
+       ends                    =   "T";  //yes
+       processors              =       "1";
+
 }
 
 //*******************************************************/
@@ -317,7 +369,7 @@ void GlobalData::reset() {
        iters                   =       "1000"; 
        groups                  =       "";
        jumble                  =       "1";    //0 means don't jumble, 1 means jumble.
-       sorted                  =       "1";  //0 means don't sort, 1 means sort.
+       sorted                  =       "T";  //F means don't sort, T means sort.
        randomtree              =       "";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
        freq                    =       "100";
        method                  =       "furthest";
@@ -325,6 +377,8 @@ void GlobalData::reset() {
        abund                   =   "10";
        step                    =       "0.01";
        form                    =       "integral";
+       ends                    =   "T";
+       processors              =       "1";
 }
 /*******************************************************/
 
@@ -392,7 +446,7 @@ void GlobalData::parseTreeFile() {
                        
                        //use nexus translation rather than parsing tree to save time
                        if ((holder == "translate") || (holder == "Translate")) {
-cout << "there is a translate " << endl;
+
                                string number, name, h;
                                h = ""; // so it enters the loop the first time
                                while((h != ";") && (number != ";")) {