adding labels to list file.

[mothur.git] / sharedlistvector.cpp

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index 2ce250ba908b4b45fa200b845275af22c3ca3be6..8fabc5b605b40f06ea1e7217a766f36bc8bfded9 100644 (file)
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -35,16 +35,70 @@ SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numB
             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) {
@@ -79,7 +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){
@@ -237,6 +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++){
@@ -272,6 +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