X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedrabundfloatvector.cpp;h=71c868b158ab41c2b8d72e7dac301998e2c39537;hp=bda49bf3dcd50b7171eb2d3aaa9f1668692f1fd8;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01

diff --git a/sharedrabundfloatvector.cpp b/sharedrabundfloatvector.cpp
index bda49bf..71c868b 100644
--- a/sharedrabundfloatvector.cpp
+++ b/sharedrabundfloatvector.cpp
@@ -48,7 +48,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
 		//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"
@@ -67,20 +67,40 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
 					if (m->control_pressed) { break; }
 					string temp;
 					iStringStream >> temp;  m->gobble(iStringStream);
-					
+                    
 					m->binLabelsInFile.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->binLabelsInFile.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->binLabelsInFile.push_back(binLabel);
+                }
+            }
+		}else { 
+            label = m->saveNextLabel; 
+            
+            //read in first row since you know there is at least 1 group.
+            f >> groupN >> num;
+        }
 		
 		//reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
-		m->currentBinLabels = m-> binLabelsInFile;
+		m->currentBinLabels = m->binLabelsInFile;
 		
-		//read in first row since you know there is at least 1 group.
-		f >> groupN >> num;
-
 		holdLabel = label;
 		
 		//add new vector to lookup
@@ -108,6 +128,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
 		//read the rest of the groups info in
 		while ((nextLabel == holdLabel) && (f.eof() != true)) {
 			f >> groupN >> num;
+            
 			count++;
 			
 			allGroups.push_back(groupN);
@@ -131,7 +152,6 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
 		
 		m->saveNextLabel = nextLabel;
 		m->setAllGroups(allGroups);
-	
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SharedRAbundFloatVector", "SharedRAbundFloatVector");
@@ -171,6 +191,16 @@ float SharedRAbundFloatVector::getAbundance(int index){
 	return data[index].abundance;	
 }
 /***********************************************************************/
+//returns vector of abundances
+vector<float> SharedRAbundFloatVector::getAbundances(){
+    vector<float> abunds;
+    for (int i = 0; i < data.size(); i++) {
+        abunds.push_back(data[i].abundance);
+    }
+    
+	return abunds;
+}
+/***********************************************************************/
 individualFloat SharedRAbundFloatVector::get(int index){
 	return data[index];	
 }
@@ -252,12 +282,19 @@ int SharedRAbundFloatVector::size(){
 /***********************************************************************/
 void SharedRAbundFloatVector::printHeaders(ostream& output){
 	try {
+		string snumBins = toString(numBins);
 		output << "label\tGroup\tnumOtus\t";
 		if (m->sharedHeaderMode == "tax") {
 			for (int i = 0; i < numBins; i++) {  
 				
 				//if there is a bin label use it otherwise make one
-				string binLabel = "PhyloType" + toString(i+1);
+				string binLabel = "PhyloType";
+				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;
 				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
 				
 				output << binLabel << '\t'; 
@@ -266,7 +303,13 @@ void SharedRAbundFloatVector::printHeaders(ostream& output){
 		}else {
 			for (int i = 0; i < numBins; i++) {  
 				//if there is a bin label use it otherwise make one
-				string binLabel = "Otu" + toString(i+1);
+				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;
 				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
 				
 				output << binLabel << '\t'; 
@@ -335,7 +378,7 @@ SharedRAbundVector SharedRAbundFloatVector::getSharedRAbundVector(){
 		exit(1);
 	}		
 }
-/***********************************************************************/
+***********************************************************************/
 vector<SharedRAbundFloatVector*> SharedRAbundFloatVector::getSharedRAbundFloatVectors(){
 	try {
 		SharedUtil* util;
@@ -406,7 +449,7 @@ SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){
 		exit(1);
 	}
 }
-/***********************************************************************/
+***********************************************************************/
 
 SAbundVector SharedRAbundFloatVector::getSAbundVector() {
 	try {
@@ -448,7 +491,7 @@ SharedOrderVector SharedRAbundFloatVector::getSharedOrderVector() {
 		exit(1);
 	}
 }
-/***********************************************************************/
+***********************************************************************/
 //this is not functional, not sure how to handle it yet, but I need the stub because it is a pure function
 OrderVector SharedRAbundFloatVector::getOrderVector(map<string,int>* nameMap = NULL) {
 	try {
@@ -484,6 +527,7 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
 		
 		//for each bin
 		vector<string> newBinLabels;
+		string snumBins = toString(thislookup[0]->getNumBins());
 		for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
 			if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 			
@@ -499,7 +543,13 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
 					newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
 				}
 				//if there is a bin label use it otherwise make one
-				string binLabel = "Otu" + toString(i+1);
+				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; 
 				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
 				
 				newBinLabels.push_back(binLabel);