line and label no longer persist between commands. Added phylip formated output...

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 02b9013887308ef118212b2d7fb06d14b0fd6012..6138e2cc1b8f4fc70b8febc1105fcecca0448306 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -26,6 +26,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) { 
                        clear();
                        gGroupmap = NULL;
+                       gListVector = NULL;
+                       gSparseMatrix = NULL;
                        gTree.clear();
                        Treenames.clear();
                        labels.clear(); lines.clear(); Groups.clear();
@@ -58,8 +60,6 @@ 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;             }
@@ -94,22 +94,29 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "mismatch")          { mismatch = value;         }
                                if (key == "gapopen")           { gapopen = value;              }
                                if (key == "gapextend" )        { gapextend = value;    }
+                               if (key == "start" )            { startPos = value;     }
+                               if (key == "end" )                      { endPos = value;       }
+                               if (key == "maxambig" )         { maxAmbig = value;     }
+                               if (key == "maxhomop" )         { maxHomoPolymer = value;       }
+                               if (key == "minlength" )        { minLength = value;    }
+                               if (key == "maxlength" )        { maxLength = value;    }
                                
-                               if (key == "line") {//stores lines to be used in a set
+                               if (key == "line") {//stores lines to be used in a vector
                                        lines.clear();
                                        labels.clear();
                                        line = value;
                                        label = "";
-                                       splitAtDash(value, lines);
-                                       allLines = 0;
+                                       if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
+                                       else { allLines = 1;  }
                                }
-                               if (key == "label") {//stores labels to be used in a set
+                       
+                               if (key == "label") {//stores lines to be used in a vector
                                        labels.clear();
                                        lines.clear();
                                        label = value;
                                        line = "";
-                                       splitAtDash(value, labels);
-                                       allLines = 0;
+                                       if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
+                                       else { allLines = 1;  }
                                }
 
                                if (key == "groups") {//stores groups to be used in a vector
@@ -129,10 +136,8 @@ 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 == "shared" )   { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";   }
                        if (key == "name" )             { namefile = value;             }
                        if (key == "order" )    { orderfile = value;    }
                        if (key == "group" )    { groupfile = value;    }
@@ -165,6 +170,13 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "mismatch")          { mismatch = value;         }
                        if (key == "gapopen")           { gapopen = value;              }
                        if (key == "gapextend" )        { gapextend = value;    }
+                       if (key == "start" )            { startPos = value;     }
+                       if (key == "end" )                      { endPos = value;       }
+                       if (key == "maxambig" )         { maxAmbig = value;     }
+                       if (key == "maxhomop" )         { maxHomoPolymer = value;       }
+                       if (key == "minlength" )        { minLength = value;    }
+                       if (key == "maxlength" )        { maxLength = value;    }
+
 
                        if (key == "line") {//stores lines to be used in a vector
                                lines.clear();
@@ -208,7 +220,6 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        splitAtDash(calc, Estimators); 
                }
                if (commandName == "collect.shared") {
-
                        if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
                        Estimators.clear();
                        splitAtDash(calc, Estimators); 
@@ -288,8 +299,6 @@ 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;       }
@@ -320,6 +329,12 @@ string GlobalData::getMatch()                      {       return match;           }
 string GlobalData::getMismatch()               {       return mismatch;        }
 string GlobalData::getGapopen()                        {       return gapopen;         }
 string GlobalData::getGapextend()              {       return gapextend;       }
+string GlobalData::getStartPos()               {       return startPos;        }
+string GlobalData::getEndPos()                 {       return endPos;          }
+string GlobalData::getMaxAmbig()               {       return maxAmbig;        }
+string GlobalData::getMaxHomoPolymer() {       return maxHomoPolymer;  }
+string GlobalData::getMinLength()              {       return minLength;       }
+string GlobalData::getMaxLength()              {       return maxLength;       }
 
 
 void GlobalData::setListFile(string file)              {       listfile = file;        inputFileName = file;                                   }
@@ -345,8 +360,8 @@ GlobalData::GlobalData() {
        //option definitions should go here...
        helpRequest = "";
        clear();
-       gListVector == NULL;            
-       gSparseMatrix == NULL;  
+       gListVector = NULL;             
+       gSparseMatrix = NULL;   
 }
 /*******************************************************/
 
@@ -362,8 +377,6 @@ void GlobalData::clear() {
        groupfile               =       ""; 
        orderfile               =       "";
        fastafile               =   "";
-       nexusfile               =   "";
-       clustalfile             =   "";
        treefile                =       "";
        sharedfile              =       "";
        candidatefile   =       "";
@@ -383,7 +396,7 @@ void GlobalData::clear() {
        step                    =       "0.01";
        form                    =       "integral";
        sorted                  =       "T";  //F means don't sort, T means sort.
-       vertical        =   "";         
+       vertical        =   "F";                
        trump           =       "";             
        hard                    =   "";         
        soft            =   ""; 
@@ -392,18 +405,27 @@ void GlobalData::clear() {
        processors              =       "1";
        size            =   "0";
        search                  =       "kmer";
-       ksize                   =       "7";
+       ksize                   =       "8";
        align                   =       "needleman";
        match                   =       "1.0";
        mismatch                =       "-1.0";
        gapopen                 =       "-1.0";
        gapextend               =       "-2.0";
+       startPos                =       "-1";
+       endPos                  =       "-1";
+       maxAmbig                =       "-1";
+       maxHomoPolymer  =       "-1";
+       minLength               =       "-1";
+       maxLength               =       "-1";
+       
 }
 
 //*******************************************************/
 
 /******************************************************/
 void GlobalData::reset() {
+       label                   =       "";
+       line                    =   "";
        cutoff                  =       "10.00";
        precision               =       "100";
        iters                   =       "1000"; 
@@ -421,7 +443,7 @@ void GlobalData::reset() {
        processors              =       "1";
        size            =   "0";
        search                  =       "kmer";
-       ksize                   =       "7";
+       ksize                   =       "8";
        align                   =       "needleman";
        match                   =       "1.0";
        mismatch                =       "-1.0";
@@ -431,7 +453,13 @@ void GlobalData::reset() {
        trump           =   "";         
        hard                    =   "";         
        soft            =   ""; 
-
+       startPos                =       "-1";
+       endPos                  =       "-1";
+       maxAmbig                =       "-1";
+       maxHomoPolymer  =       "-1";
+       minLength               =       "-1";
+       maxLength               =       "-1";
+       
 }
 /*******************************************************/
 
@@ -446,6 +474,8 @@ GlobalData::~GlobalData() {
 
 /*******************************************************/
 void GlobalData::parseTreeFile() {
+       //Why is THIS in GlobalData??? - PDS
+       
        //only takes names from the first tree and assumes that all trees use the same names.
        try {
                string filename = treefile;