X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedlistvector.cpp;h=8fabc5b605b40f06ea1e7217a766f36bc8bfded9;hp=2cecb5de49d2aca77c33f21b77d584d6c15f893e;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=d70a1c2d70c5a516e74880709e3b48cfc1ce0321

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index 2cecb5d..8fabc5b 100644
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -25,25 +25,80 @@ SharedListVector::SharedListVector(int n):	DataVector(), data(n, "") , maxRank(0
 /***********************************************************************/
 SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
 	try {
+        groupmap = NULL; countTable = NULL;
 		//set up groupmap for later.
         if (m->groupMode == "group") {
             groupmap = new GroupMap(m->getGroupFile());
             groupmap->readMap(); 
         }else {
             countTable = new CountTable();
-            countTable->readTable(m->getCountTableFile());
+            countTable->readTable(m->getCountTableFile(), true, false);
         }
 
-		int hold;
-		string inputData;
-		f >> label >> hold;
-	
-		data.assign(hold, "");
+        int 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 = "";
+        
 		for(int i=0;i<hold;i++){
 			f >> inputData;
 			set(i, inputData);
 		}
+		m->gobble(f);
+        
+        if (f.eof()) { m->saveNextLabel = ""; }
 		
 	}
 	catch(exception& e) {
@@ -78,7 +133,59 @@ void SharedListVector::set(int binNumber, string seqNames){
 string SharedListVector::get(int index){
 	return data[index];
 }
+/***********************************************************************/
+
+void SharedListVector::setLabels(vector<string> labels){
+	try {
+		binLabels = labels;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SharedListVector", "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> SharedListVector::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, "SharedListVector", "getLabels");
+		exit(1);
+	}
+}
 /***********************************************************************/
 
 void SharedListVector::push_back(string seqNames){
@@ -236,6 +343,8 @@ SharedOrderVector* SharedListVector::getSharedOrderVector(){
 /***********************************************************************/
 SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
 	try {
+        m->currentSharedBinLabels = binLabels;
+        
 		SharedRAbundVector rav(data.size());
 		
 		for(int i=0;i<numBins;i++){
@@ -271,6 +380,8 @@ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
 /***********************************************************************/
 vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
 	try {
+        m->currentSharedBinLabels = binLabels;
+        
 		SharedUtil* util;
 		util = new SharedUtil();
 		vector<SharedRAbundVector*> lookup;  //contains just the groups the user selected