fixes while testing 1.33.0

[mothur.git] / listvector.cpp

diff --git a/listvector.cpp b/listvector.cpp
index 2758c94264a1ba527e8d7c3970e0bac53254579b..90df802cfea64f2894733bcd377936b4476ac05b 100644 (file)
--- a/listvector.cpp
+++ b/listvector.cpp
@@ -67,8 +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 = "";
        
@@ -77,6 +128,8 @@ ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numS
                        set(i, inputData);
                }
                m->gobble(f);
+        
+        if (f.eof()) { m->saveNextLabel = ""; }
        }
        catch(exception& e) {
                m->errorOut(e, "ListVector", "ListVector");
@@ -109,6 +162,60 @@ 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);
+       }
+}
 
 /***********************************************************************/
 
@@ -150,6 +257,52 @@ 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){