added read.shared, broke up globaldata a bit

[mothur.git] / sharedordervector.cpp

diff --git a/sharedordervector.cpp b/sharedordervector.cpp
index 575ae18ea050e90c416efa480181773799a25af5..6aeb4ce5ab19a655c832343cb601c715777c2534 100644 (file)
--- a/sharedordervector.cpp
+++ b/sharedordervector.cpp
@@ -26,25 +26,74 @@ SharedOrderVector::SharedOrderVector(string id, vector<individual>  ov) :
                updateStats();
 }
 
-/***********************************************************************
-
-//does not work since we don't have a shared order file format yet.
+/***********************************************************************/
+//This function is used to read a .shared file for the collect.shared, rarefaction.shared and summary.shared commands
+//if you don't use a list and groupfile.  
 
 SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
        try {
-               int hold;
-       
-               f >> label;
-               f >> hold;
-       
-               data.assign(hold, -1);
-       
-               int inputData;
-       
-               for(int i=0;i<hold;i++){
+               globaldata = GlobalData::getInstance();
+               
+               if (globaldata->gGroupmap == NULL) {  groupmap = new GroupMap(); }
+               
+               int num, inputData, pos, count;
+               count = 0;  numSeqs = 0;
+               string holdLabel, nextLabel, groupN;
+               individual newguy;
+               
+               //read in first row since you know there is at least 1 group.
+               f >> label >> groupN >> num;
+               holdLabel = label;
+               
+               if (globaldata->gGroupmap == NULL) { 
+                       //save group in groupmap
+                       groupmap->namesOfGroups.push_back(groupN);
+                       groupmap->groupIndex[groupN] = 0;
+               }
+               
+               for(int i=0;i<num;i++){
                        f >> inputData;
-                       set(i, inputData, inputData, group);
+                       for (int j = 0; j < inputData; j++) {
+                               push_back(i+1, i+1, groupN);
+                               numSeqs++;
+                       }
                }
+               
+               //save position in file in case next line is a new label.
+               pos = f.tellg();
+               
+               if (f.eof() != true) { f >> nextLabel; }
+               
+               //read the rest of the groups info in
+               while ((nextLabel == holdLabel) && (f.eof() != true)) {
+                       f >> groupN >> num;
+                       count++;
+                       
+                       if (globaldata->gGroupmap == NULL) { 
+                               //save group in groupmap
+                               groupmap->namesOfGroups.push_back(groupN);
+                               groupmap->groupIndex[groupN] = count;
+                       }
+                       
+                       for(int i=0;i<num;i++){
+                               f >> inputData;
+                               for (int j = 0; j < inputData; j++) {
+                                       push_back(i+1, i+1, groupN);
+                                       numSeqs++;
+                               }
+                       }
+                       
+                       //save position in file in case next line is a new label.
+                       pos = f.tellg();
+       
+                       if (f.eof() != true) { f >> nextLabel; }
+
+               }
+               
+               //put file pointer back since you are now at a new distance label
+               f.seekg(pos, ios::beg);
+       
+               if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; }
        
                updateStats();
        }
@@ -57,10 +106,8 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
                exit(1);
        }
 }
-
 /***********************************************************************/
 
-
 int SharedOrderVector::getNumBins(){
        if(needToUpdate == 1){  updateStats();  }
        return numBins;