modified trim.seqs command

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 16bc8d32b6bc75c2b4cbabfdb4ef6dfb78890d4c..89089ad8686a20a5ee855a1405d4800729ee325a 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -4,8 +4,9 @@
 #include "mothur.h"
 #include "groupmap.h"
 #include "treemap.h"
-
-using namespace std;
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
+#include "listvector.hpp"
 
 class ListVector;
 class SharedListVector;
@@ -17,6 +18,8 @@ class InputData;
 class GroupMap;
 class TreeMap;
 class SAbundVector;
+class RAbundVector;
+class SequenceDB;
 
 class GlobalData {
 public:
@@ -29,14 +32,17 @@ 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();
@@ -62,27 +68,63 @@ public:
        string getGroups();
        string getStep();
        string getForm();
-
+       string getSorted();
+       string getCountEnds();
+       string getProcessors();
+       string getSize();
+       string getCandidateFile();
+       string getSearch();
+       string getKSize();
+       string getAlign();
+       string getMatch();
+       string getMismatch();
+       string getGapopen();
+       string getGapextend();
+       string getVertical();
+       string getTrump();
+       string getSoft();
+       string getHard();
+       string getScale();
+       string getStartPos();
+       string getEndPos();
+       string getMaxAmbig();
+       string getMaxHomoPolymer();
+       string getMinLength();
+       string getMaxLength();
+       string getFlip();
+       string getOligosFile();
+       
        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 setCountEnds(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, treefile, sharedfile, line, label, randomtree, groups, cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, hard, scale, countends, processors, candidatefile, search, ksize, align, match, size, mismatch, gapopen, gapextend, minLength, maxLength, startPos, endPos, maxAmbig, maxHomoPolymer, flip, oligoFile;
+
 
        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&);