X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedrabundvector.cpp;h=3901650cef965dc7a3c0126ecb54a8fb425e434d;hp=56b7d094b1444a2afada95807a36b52e235c70e8;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index 56b7d09..3901650 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"
@@ -95,16 +95,36 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 					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;
 		
-		//read in first row since you know there is at least 1 group.
-		f >> groupN >> num;
-
 		holdLabel = label;
 		
 		//add new vector to lookup
@@ -155,7 +175,6 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
 		}
 		m->saveNextLabel = nextLabel;
 		m->setAllGroups(allGroups);
-		
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector");
@@ -336,13 +355,19 @@ int SharedRAbundVector::size(){
 /***********************************************************************/
 void SharedRAbundVector::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'; 
@@ -351,10 +376,16 @@ void SharedRAbundVector::printHeaders(ostream& output){
 		}else {
 			for (int i = 0; i < numBins; i++) {  
 				//if there is a bin label use it otherwise make one
-				string mybinLabel = "Otu" + toString(i+1);
-				if (i < m->currentBinLabels.size()) {  mybinLabel = m->currentBinLabels[i]; }
+				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 << mybinLabel << '\t'; 
+				output << binLabel << '\t'; 
 			}
 			
 			output << endl;
@@ -395,7 +426,7 @@ int SharedRAbundVector::getGroupIndex()  { return index; }
 void SharedRAbundVector::setGroupIndex(int vIndex)	{ index = vIndex; }
 /***********************************************************************/
 int SharedRAbundVector::getNumBins(){
-	return numBins;
+		return numBins;
 }
 
 /***********************************************************************/
@@ -423,6 +454,7 @@ vector<SharedRAbundVector*> SharedRAbundVector::getSharedRAbundVectors(){
 		vector<string> Groups = m->getGroups();
 		vector<string> allGroups = m->getAllGroups();
 		util->setGroups(Groups, allGroups);
+		m->setGroups(Groups);
 		
 		bool remove = false;
 		for (int i = 0; i < lookup.size(); i++) {
@@ -460,6 +492,7 @@ int SharedRAbundVector::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislooku
 			
 			//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; }
 				
@@ -476,7 +509,13 @@ int SharedRAbundVector::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislooku
 					}
 					
 					//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);