fixed summary.shared bug and set jumble default to 1.

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index f09ea358b61c3e30b6880937a9f606969bfca63b..87f1ccae776b9e435c00189ed63317e1595cc374 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -9,6 +9,7 @@ using namespace std;
 
 #include "globaldata.hpp"
 #include "sparsematrix.hpp"
+#include "tree.h"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 #include "listvector.hpp"
@@ -80,7 +81,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                commandName = commandString; //save command name to be used by other classes
                
                //clears out data from previous read
-               if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.list")) { 
+               if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) { 
                        clear();
                }
                
@@ -102,6 +103,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                if (key == "rabundfile" )       { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
                                if (key == "sabundfile" )       { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       } 
                                if (key == "fastafile" )        { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         } 
+                               if (key == "treefile" )         { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
                                if (key == "namefile" )         { namefile = value;             }
                                if (key == "orderfile" )        { orderfile = value;    }
                                if (key == "groupfile" )        { groupfile = value;    }
@@ -165,7 +167,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        if (key == "listfile" )         { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
                        if (key == "rabundfile" )       { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
                        if (key == "sabundfile" )       { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
-                       if (key == "fastafile" )        { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         } 
+                       if (key == "fastafile" )        { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
+                       if (key == "treefile" )         { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }  
                        if (key == "namefile" )         { namefile = value;             }
                        if (key == "orderfile" )        { orderfile = value;    }
                        if (key == "groupfile" )        { groupfile = value;    }
@@ -226,25 +229,32 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                if ((listfile != "") && (groupfile != "")) { format = "shared"; }
                                
                //input defaults
-               if (commandString == "collect.single") {
-                       if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); }    
+               if (commandName == "collect.single") {
+                       if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); }
                }
-               if (commandString == "rarefaction.single") {
+               if (commandName == "rarefaction.single") {
                        if (rareEstimators.size() == 0) { splitAtDash(rarefaction, rareEstimators);  }  
                }
-               if (commandString == "collect.shared") {
+               if (commandName == "collect.shared") {
                        if (sharedEstimators.size() == 0) { splitAtDash(shared, sharedEstimators); }    
                }
-               if (commandString == "summary.single") {
+               if (commandName == "summary.single") {
                        if (summaryEstimators.size() == 0) { splitAtDash(summary, summaryEstimators); }
                }
-               if (commandString == "summary.shared") {
+               if (commandName == "summary.shared") {
                        if (sharedSummaryEstimators.size() == 0) { splitAtDash(sharedsummary, sharedSummaryEstimators); }
                }
-               if (commandString == "rarefaction.shared") {
+               if (commandName == "rarefaction.shared") {
                        if (sharedRareEstimators.size() == 0) { splitAtDash(sharedrarefaction, sharedRareEstimators); }
                }
 
+
+               //if you have done a read.otu with a groupfile but don't want to use it anymore because you want to do single commands
+               if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
+                       if (listfile != "") { format = "list"; }
+                       else if (sabundfile != "") { format = "sabund"; }
+                       else if (rabundfile != "") { format = "rabund"; }
+               }
                                
        }
        catch(exception& e) {
@@ -269,6 +279,7 @@ string GlobalData::getSabundFile()          {       return sabundfile;      }
 string GlobalData::getNameFile()               {       return namefile;        }
 string GlobalData::getGroupFile()              {       return groupfile;       }
 string GlobalData::getOrderFile()              {       return orderfile;       }
+string GlobalData::getTreeFile()               {       return treefile;        }
 string GlobalData::getFastaFile()              {       return fastafile;       }
 string GlobalData::getCutOff()                 {       return cutoff;          }
 string GlobalData::getFormat()                 {       return format;          }
@@ -312,13 +323,14 @@ void GlobalData::clear() {
        groupfile               =       ""; 
        orderfile               =       "";
        fastafile               =   "";
+       treefile                =       "";
        cutoff                  =       "10.00";
        format                  =       "";
        precision               =       "100";
        iters                   =       "1000"; 
        line                    =   "";
        label                   =       "";
-       jumble                  =       "0";
+       jumble                  =       "1";
        freq                    =       "100";
        method                  =       "furthest";
        fileroot                =       "";