X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=0f2e48e8ac7bbdc18b10f15f1b764aed7ee58890;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=5ad4b2d7e70d2620c037b498a66b4d16cef62371;hpb=116bbb1533575666a682910a10ae1fa2fc5b605c;p=mothur.git

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index 5ad4b2d..0f2e48e 100644
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -55,7 +55,7 @@ SharedRAbundVector::SharedRAbundVector(string id, vector<individual> rav) : Data
 }
 
 
-/***********************************************************************/
+***********************************************************************/
 //reads a shared file
 SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
 	try {
@@ -72,7 +72,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 		//are we at the beginning of the file??
 		if (m->saveNextLabel == "") {  
 			f >> label; 
-	
+            
 			//is this a shared file that has headers
 			if (label == "label") { 
 				//gets "group"
@@ -86,24 +86,46 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 				
 				//parse labels to save
 				istringstream iStringStream(label);
-				m->binLabelsInFile.clear();
+				m->sharedBinLabelsInFile.clear();
 				while(!iStringStream.eof()){
 					if (m->control_pressed) { break; }
 					string temp;
 					iStringStream >> temp;  m->gobble(iStringStream);
 		
-					m->binLabelsInFile.push_back(temp);
+					m->sharedBinLabelsInFile.push_back(temp);
 				}
 				
-				f >> label;
-			}
-		}else { label = m->saveNextLabel; }
+				f >> label >> groupN >> num;
+			}else {
+                //read in first row since you know there is at least 1 group.
+                f >> groupN >> num;
+                
+                //make binlabels because we don't have any
+                string snumBins = toString(num);
+                m->sharedBinLabelsInFile.clear();
+                for (int i = 0; i < num; i++) {  
+                    //if there is a bin label use it otherwise make one
+                    string binLabel = "Otu";
+                    string sbinNumber = toString(i+1);
+                    if (sbinNumber.length() < snumBins.length()) { 
+                        int diff = snumBins.length() - sbinNumber.length();
+                        for (int h = 0; h < diff; h++) { binLabel += "0"; }
+                    }
+                    binLabel += sbinNumber;
+                    m->sharedBinLabelsInFile.push_back(binLabel);
+                }
+            }
+		}else { 
+            label = m->saveNextLabel; 
+            
+            //read in first row since you know there is at least 1 group.
+            f >> groupN >> num;
+            
+            if (m->debug) { m->mothurOut("[DEBUG]: "+ groupN + '\t' + toString(num)); }
+        }
 		
 		//reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
-		m->currentBinLabels = m->binLabelsInFile;
-		
-		//read in first row since you know there is at least 1 group.
-		f >> groupN >> num;
+		m->currentSharedBinLabels = m->sharedBinLabelsInFile;
 		
 		holdLabel = label;
 		
@@ -118,6 +140,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 		//fill vector.  data = first sharedrabund in file
 		for(int i=0;i<num;i++){
 			f >> inputData;
+            if (m->debug) { m->mothurOut("[DEBUG]: OTU" + toString(i+1)+ '\t' +toString(inputData)); }
 			
 			lookup[0]->push_back(inputData, groupN); //abundance, bin, group
 			push_back(inputData, groupN);
@@ -132,6 +155,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 		//read the rest of the groups info in
 		while ((nextLabel == holdLabel) && (f.eof() != true)) {
 			f >> groupN >> num;
+            if (m->debug) { m->mothurOut("[DEBUG]: "+ groupN + '\t' + toString(num)); }
 			count++;
 			
 			allGroups.push_back(groupN);
@@ -145,6 +169,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 			//fill vector.  
 			for(int i=0;i<num;i++){
 				f >> inputData;
+                if (m->debug) { m->mothurOut("[DEBUG]: OTU" + toString(i+1)+ '\t' +toString(inputData)); }
 				
 				lookup[count]->push_back(inputData, groupN); //abundance, bin, group
 			}
@@ -191,6 +216,18 @@ int SharedRAbundVector::getAbundance(int index){
 	return data[index].abundance;
 	
 }
+/***********************************************************************/
+//returns vector of abundances 
+vector<int> SharedRAbundVector::getAbundances(){
+    vector<int> abunds;
+    for (int i = 0; i < data.size(); i++) {
+        abunds.push_back(data[i].abundance);
+    }
+    
+	return abunds;
+}
+
+
 /***********************************************************************/
 
 int SharedRAbundVector::numNZ(){
@@ -348,7 +385,7 @@ void SharedRAbundVector::printHeaders(ostream& output){
 					for (int h = 0; h < diff; h++) { binLabel += "0"; }
 				}
 				binLabel += sbinNumber;
-				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+				if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
 				
 				output << binLabel << '\t'; 
 			}
@@ -363,14 +400,14 @@ void SharedRAbundVector::printHeaders(ostream& output){
 					for (int h = 0; h < diff; h++) { binLabel += "0"; }
 				}
 				binLabel += sbinNumber;
-				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+				if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
 				
 				output << binLabel << '\t'; 
 			}
 			
 			output << endl;
 		}
-		m->printedHeaders = true;
+		m->printedSharedHeaders = true;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SharedRAbundVector", "printHeaders");
@@ -496,7 +533,7 @@ int SharedRAbundVector::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislooku
 						for (int h = 0; h < diff; h++) { binLabel += "0"; }
 					}
 					binLabel += sbinNumber; 
-					if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+					if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
 					
 					newBinLabels.push_back(binLabel);
 				}
@@ -505,7 +542,7 @@ int SharedRAbundVector::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislooku
 			for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 			
 			thislookup = newLookup;
-			m->currentBinLabels = newBinLabels;
+			m->currentSharedBinLabels = newBinLabels;
 			
 			return 0;