X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=listvector.cpp;h=90df802cfea64f2894733bcd377936b4476ac05b;hp=6e008074a86dd849261401e45deb26fbcb506bc7;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2

diff --git a/listvector.cpp b/listvector.cpp
index 6e00807..90df802 100644
--- a/listvector.cpp
+++ b/listvector.cpp
@@ -13,6 +13,27 @@
 #include "ordervector.hpp"
 #include "listvector.hpp"
 
+//sorts highest to lowest
+/***********************************************************************/
+inline bool abundNamesSort(string left, string right){
+    
+    int countLeft = 0;
+    if(left != ""){
+        countLeft = 1;
+        for(int i=0;i<left.size();i++){  if(left[i] == ','){  countLeft++;  }  }
+    }
+    
+    int countRight = 0;
+    if(right != ""){
+        countRight = 1;
+        for(int i=0;i<right.size();i++){  if(right[i] == ','){  countRight++;  }  }
+    }
+    
+	if (countLeft > countRight) {
+        return true;
+    }
+    return false;	
+} 
 
 /***********************************************************************/
 
@@ -28,7 +49,7 @@ ListVector::ListVector(string id, vector<string> lv) : DataVector(id), data(lv){
 	try {
 		for(int i=0;i<data.size();i++){
 			if(data[i] != ""){
-				int binSize = getNumNames(data[i]);
+				int binSize = m->getNumNames(data[i]);
 				numBins = i+1;
 				if(binSize > maxRank)	{	maxRank = binSize;	}
 				numSeqs += binSize;
@@ -36,7 +57,7 @@ ListVector::ListVector(string id, vector<string> lv) : DataVector(id), data(lv){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "ListVector");
+		m->errorOut(e, "ListVector", "ListVector");
 		exit(1);
 	}
 }
@@ -46,8 +67,59 @@ ListVector::ListVector(string id, vector<string> lv) : DataVector(id), data(lv){
 ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
 	try {
 		int hold;
-		f >> label >> hold;
+        
+        //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 "numOtus"
+				f >> label; m->gobble(f);
+				
+				//eat rest of line
+				label = m->getline(f); m->gobble(f);
+				
+				//parse labels to save
+				istringstream iStringStream(label);
+				m->listBinLabelsInFile.clear();
+				while(!iStringStream.eof()){
+					if (m->control_pressed) { break; }
+					string temp;
+					iStringStream >> temp;  m->gobble(iStringStream);
+                    
+					m->listBinLabelsInFile.push_back(temp);
+				}
+				
+				f >> label >> hold;
+			}else {
+                //read in first row
+                f >> hold;
+                
+                //make binlabels because we don't have any
+                string snumBins = toString(hold);
+                m->listBinLabelsInFile.clear();
+                for (int i = 0; i < hold; 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->listBinLabelsInFile.push_back(binLabel);
+                }
+            }
+            m->saveNextLabel = label;
+		}else {
+            f >> label >> hold;
+            m->saveNextLabel = label;
+        }
 	
+        binLabels.assign(m->listBinLabelsInFile.begin(), m->listBinLabelsInFile.begin()+hold);
+		
 		data.assign(hold, "");
 		string inputData = "";
 	
@@ -55,9 +127,12 @@ ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numS
 			f >> inputData;
 			set(i, inputData);
 		}
+		m->gobble(f);
+        
+        if (f.eof()) { m->saveNextLabel = ""; }
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "ListVector");
+		m->errorOut(e, "ListVector", "ListVector");
 		exit(1);
 	}
 }
@@ -66,9 +141,9 @@ ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numS
 
 void ListVector::set(int binNumber, string seqNames){
 	try {
-		int nNames_old = getNumNames(data[binNumber]);
+		int nNames_old = m->getNumNames(data[binNumber]);
 		data[binNumber] = seqNames;
-		int nNames_new = getNumNames(seqNames);
+		int nNames_new = m->getNumNames(seqNames);
 	
 		if(nNames_old == 0)			{	numBins++;				}
 		if(nNames_new == 0)			{	numBins--;				}
@@ -77,7 +152,7 @@ void ListVector::set(int binNumber, string seqNames){
 		numSeqs += (nNames_new - nNames_old);
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "set");
+		m->errorOut(e, "ListVector", "set");
 		exit(1);
 	}
 }
@@ -87,13 +162,67 @@ void ListVector::set(int binNumber, string seqNames){
 string ListVector::get(int index){
 	return data[index];
 }
+/***********************************************************************/
+
+void ListVector::setLabels(vector<string> labels){
+	try {
+		binLabels = labels;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ListVector", "setLabels");
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+//could potentially end up with duplicate binlabel names with code below.
+//we don't currently use them in a way that would do that.
+//if you had a listfile that had been subsampled and then added to it, dup names would be possible.
+vector<string> ListVector::getLabels(){
+    try {
+        
+        string tagHeader = "Otu";
+        if (m->sharedHeaderMode == "tax") { tagHeader = "PhyloType"; }
+        
+        if (binLabels.size() < data.size()) {
+            string snumBins = toString(numBins);
+            
+            for (int i = 0; i < numBins; i++) {
+                string binLabel = tagHeader;
+                
+                if (i < binLabels.size()) { //label exists, check leading zeros length
+                    string sbinNumber = m->getSimpleLabel(binLabels[i]);
+                    if (sbinNumber.length() < snumBins.length()) {
+                        int diff = snumBins.length() - sbinNumber.length();
+                        for (int h = 0; h < diff; h++) { binLabel += "0"; }
+                    }
+                    binLabel += sbinNumber;
+                    binLabels[i] = binLabel;
+                }else{
+                    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;
+                    binLabels.push_back(binLabel);
+                }
+            }
+        }
+        return binLabels;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "ListVector", "getLabels");
+		exit(1);
+	}
+}
 
 /***********************************************************************/
 
 void ListVector::push_back(string seqNames){
 	try {
 		data.push_back(seqNames);
-		int nNames = getNumNames(seqNames);
+		int nNames = m->getNumNames(seqNames);
 	
 		numBins++;
 	
@@ -102,7 +231,7 @@ void ListVector::push_back(string seqNames){
 		numSeqs += nNames;
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "push_back");
+		m->errorOut(e, "ListVector", "push_back");
 		exit(1);
 	}
 }
@@ -128,21 +257,70 @@ void ListVector::clear(){
 	
 }
 
+/***********************************************************************/
+void ListVector::printHeaders(ostream& output){
+	try {
+		string snumBins = toString(numBins);
+		output << "label\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";
+				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 < binLabels.size()) {  binLabel = binLabels[i]; }
+				
+				output << binLabel << '\t';
+			}
+			output << endl;
+		}else {
+			for (int i = 0; i < numBins; 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;
+				if (i < binLabels.size()) {  binLabel = binLabels[i]; }
+				
+				output << binLabel << '\t';
+			}
+			
+			output << endl;
+		}
+		m->printedListHeaders = true;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ListVector", "printHeaders");
+		exit(1);
+	}
+}
+
 /***********************************************************************/
 
 void ListVector::print(ostream& output){
 	try {
 		output << label << '\t' << numBins << '\t';
 	
-		for(int i=0;i<data.size();i++){
-			if(data[i] != ""){
-				output << data[i] << '\t';
+        vector<string> hold = data;
+        sort(hold.begin(), hold.end(), abundNamesSort);
+        
+		for(int i=0;i<hold.size();i++){
+			if(hold[i] != ""){
+				output << hold[i] << '\t';
 			}
 		}
 		output << endl;
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "print");
+		m->errorOut(e, "ListVector", "print");
 		exit(1);
 	}
 }
@@ -155,7 +333,7 @@ RAbundVector ListVector::getRAbundVector(){
 		RAbundVector rav;
 	
 		for(int i=0;i<data.size();i++){
-			int binSize = getNumNames(data[i]);
+			int binSize = m->getNumNames(data[i]);
 			rav.push_back(binSize);
 		}
 	
@@ -173,7 +351,7 @@ RAbundVector ListVector::getRAbundVector(){
 		return rav;
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "getRAbundVector");
+		m->errorOut(e, "ListVector", "getRAbundVector");
 		exit(1);
 	}
 }
@@ -185,7 +363,7 @@ SAbundVector ListVector::getSAbundVector(){
 		SAbundVector sav(maxRank+1);
 	
 		for(int i=0;i<data.size();i++){
-			int binSize = getNumNames(data[i]);	
+			int binSize = m->getNumNames(data[i]);	
 			sav.set(binSize, sav.get(binSize) + 1);	
 		}
 		sav.set(0, 0);
@@ -194,7 +372,7 @@ SAbundVector ListVector::getSAbundVector(){
 		return sav;
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "getSAbundVector");
+		m->errorOut(e, "ListVector", "getSAbundVector");
 		exit(1);
 	}
 }
@@ -208,7 +386,7 @@ OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 			OrderVector ov;
 		
 			for(int i=0;i<data.size();i++){
-				int binSize = getNumNames(data[i]);		
+				int binSize = m->getNumNames(data[i]);		
 				for(int j=0;j<binSize;j++){
 					ov.push_back(i);
 				}
@@ -236,7 +414,7 @@ OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 					}
 					else{
 						if(orderMap->count(seqName) == 0){
-							mothurOut(seqName + " not found, check *.names file\n");
+							m->mothurOut(seqName + " not found, check *.names file\n");
 							exit(1);
 						}
 					
@@ -246,7 +424,7 @@ OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 				}
 			
 				if(orderMap->count(seqName) == 0){
-					mothurOut(seqName + " not found, check *.names file\n");
+					m->mothurOut(seqName + " not found, check *.names file\n");
 					exit(1);
 				}
 				ov.set((*orderMap)[seqName], i);	
@@ -259,7 +437,7 @@ OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "ListVector", "getOrderVector");
+		m->errorOut(e, "ListVector", "getOrderVector");
 		exit(1);
 	}
 }