fixed blast code path problem

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 16bc8d32b6bc75c2b4cbabfdb4ef6dfb78890d4c..0c2548971555b599ea87eba61623fb2dfcf9a8ac 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -5,6 +5,11 @@
 #include "groupmap.h"
 #include "treemap.h"
 
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
+#include "listvector.hpp"
+
+
 using namespace std;
 
 class ListVector;
@@ -17,6 +22,8 @@ class InputData;
 class GroupMap;
 class TreeMap;
 class SAbundVector;
+class RAbundVector;
+class SequenceDB;
 
 class GlobalData {
 public:
@@ -29,14 +36,17 @@ public:
        vector<Tree*> gTree;
        SharedListVector* gSharedList;
        SAbundVector* sabund;
+       RAbundVector* rabund;
        GroupMap* gGroupmap;
        FullMatrix* gMatrix;
        TreeMap* gTreemap;
-       string inputFileName, helpRequest, commandName;
+       SequenceDB* gSequenceDB;
+       string inputFileName, helpRequest, commandName, vertical, argv;
        bool allLines;
        vector<string>  Estimators, Groups; //holds estimators to be used
        set<int> lines; //hold lines to be used
        set<string> labels; //holds labels to be used
+       vector<string> Treenames;
        
        string getPhylipFile();
        string getColumnFile();
@@ -47,6 +57,8 @@ public:
        string getGroupFile();
        string getOrderFile();
        string getFastaFile();
+       string getNexusFile();
+       string getClustalFile();
        string getTreeFile();
        string getSharedFile();
        string getCutOff();
@@ -62,27 +74,57 @@ public:
        string getGroups();
        string getStep();
        string getForm();
+       string getSorted();
+       string getEnds();
+       string getProcessors();
+       string getSize();
+       string getTemplateFile();
+       string getSearch();
+       string getKSize();
+       string getAlign();
+       string getMatch();
+       string getMismatch();
+       string getGapopen();
+       string getGapextend();
+       string getTrump();
+       string getSoft();
+       string getFilter();
+       string getScale();
+
 
        void setListFile(string);
+       void setGroupFile(string file); 
        void setPhylipFile(string);
        void setColumnFile(string);
        void setNameFile(string);
        void setRabundFile(string);
        void setSabundFile(string);
+       void setSharedFile(string);
        void setFormat(string);
        void setRandomTree(string);
        void setGroups(string);
        void setCalc(string);
+       void setEnds(string);
+       void setProcessors(string);
 
        void clear(); 
        void clearLabels();
        void clearAbund();
        
        void parseGlobalData(string, string);
+       
+       void parseTreeFile();           //parses through tree file to find names of nodes and number of them
+                                                       //this is required in case user has sequences in the names file that are
+                                                       //not included in the tree. 
+                                                       //only takes names from the first tree in the tree file and assumes that all trees use the same names.
+
                
 private:
-       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups;
-       string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form;
+
+       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, line, label, randomtree, groups;
+       string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, filter, scale, ends, processors, templatefile, search, ksize, align, match, size;
+       string mismatch, gapopen, gapextend;
+
 
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor
@@ -90,6 +132,7 @@ private:
        GlobalData();
        ~GlobalData();
        void reset();   //clears all non filename parameters
+       void readTreeString(ifstream&);