changed raredisplay to use vectors instead of files

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index a0ba7c2d551cd765ce82ab5ea53362a3191434a6..75ef0d57dda26943c7a2da0c295369cd501c8ed1 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -199,9 +199,9 @@
                370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getoturepcommand.cpp; sourceTree = SOURCE_ROOT; };
                371B30B20FD7EE67000414CA /* screenseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = screenseqscommand.cpp; sourceTree = SOURCE_ROOT; };
                371B30B30FD7EE67000414CA /* screenseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = screenseqscommand.h; sourceTree = SOURCE_ROOT; };
-               372095C1103196D70004D347 /* chimera.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimera.cpp; sourceTree = "<group>"; };
-               372A55531017922B00C5194B /* decalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = decalc.h; sourceTree = "<group>"; };
-               372A55541017922B00C5194B /* decalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = decalc.cpp; sourceTree = "<group>"; };
+               372095C1103196D70004D347 /* chimera.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimera.cpp; sourceTree = SOURCE_ROOT; };
+               372A55531017922B00C5194B /* decalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = decalc.h; sourceTree = SOURCE_ROOT; };
+               372A55541017922B00C5194B /* decalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = decalc.cpp; sourceTree = SOURCE_ROOT; };
                372E126E0F26365B0095CF7E /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = SOURCE_ROOT; };
                372E126F0F26365B0095CF7E /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = SOURCE_ROOT; };
                372E12940F263D5A0095CF7E /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = SOURCE_ROOT; };
@@ -251,11 +251,11 @@
                3749271C0FD58C840031C06B /* getsabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsabundcommand.cpp; sourceTree = SOURCE_ROOT; };
                3749273D0FD5956B0031C06B /* getrabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrabundcommand.h; sourceTree = SOURCE_ROOT; };
                3749273E0FD5956B0031C06B /* getrabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrabundcommand.cpp; sourceTree = SOURCE_ROOT; };
-               374F2FD51006320200E97C66 /* chimera.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimera.h; sourceTree = "<group>"; };
-               374F2FE9100634B600E97C66 /* bellerophon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bellerophon.h; sourceTree = "<group>"; };
-               374F2FEA100634B600E97C66 /* bellerophon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bellerophon.cpp; sourceTree = "<group>"; };
-               374F301110063B6F00E97C66 /* pintail.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pintail.h; sourceTree = "<group>"; };
-               374F301210063B6F00E97C66 /* pintail.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pintail.cpp; sourceTree = "<group>"; };
+               374F2FD51006320200E97C66 /* chimera.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimera.h; sourceTree = SOURCE_ROOT; };
+               374F2FE9100634B600E97C66 /* bellerophon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bellerophon.h; sourceTree = SOURCE_ROOT; };
+               374F2FEA100634B600E97C66 /* bellerophon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bellerophon.cpp; sourceTree = SOURCE_ROOT; };
+               374F301110063B6F00E97C66 /* pintail.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pintail.h; sourceTree = SOURCE_ROOT; };
+               374F301210063B6F00E97C66 /* pintail.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pintail.cpp; sourceTree = SOURCE_ROOT; };
                37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = SOURCE_ROOT; };
                37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = SOURCE_ROOT; };
                37519A9F0F810D0200FED5E8 /* venncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venncommand.h; sourceTree = SOURCE_ROOT; };
@@ -323,9 +323,9 @@
                3799A94D0FD6A58C00E33EDE /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; sourceTree = SOURCE_ROOT; };
                3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqsummarycommand.cpp; sourceTree = SOURCE_ROOT; };
                3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqsummarycommand.h; sourceTree = SOURCE_ROOT; };
-               379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraseqscommand.h; sourceTree = "<group>"; };
-               379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraseqscommand.cpp; sourceTree = "<group>"; };
-               379D3D6B0FF917F40068C1C0 /* filters.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filters.h; sourceTree = "<group>"; };
+               379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraseqscommand.h; sourceTree = SOURCE_ROOT; };
+               379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraseqscommand.cpp; sourceTree = SOURCE_ROOT; };
+               379D3D6B0FF917F40068C1C0 /* filters.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filters.h; sourceTree = SOURCE_ROOT; };
                37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = SOURCE_ROOT; };
                37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = SOURCE_ROOT; };
                37AD4DB90F28E2FE00AA2D49 /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = SOURCE_ROOT; };
@@ -336,14 +336,14 @@
                37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobscollectsummary.cpp; sourceTree = SOURCE_ROOT; };
                37B28F660F27590100808A62 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = SOURCE_ROOT; };
                37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = SOURCE_ROOT; };
-               37B73C741004BEFD008C4B41 /* listseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listseqscommand.h; sourceTree = "<group>"; };
-               37B73C751004BEFD008C4B41 /* listseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listseqscommand.cpp; sourceTree = "<group>"; };
-               37B73CA41004D89A008C4B41 /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = "<group>"; };
-               37B73CA51004D89A008C4B41 /* getseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getseqscommand.cpp; sourceTree = "<group>"; };
-               37B73CBE1004EB38008C4B41 /* removeseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeseqscommand.h; sourceTree = "<group>"; };
-               37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeseqscommand.cpp; sourceTree = "<group>"; };
-               37B73CCD1004F5E0008C4B41 /* systemcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = systemcommand.h; sourceTree = "<group>"; };
-               37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = systemcommand.cpp; sourceTree = "<group>"; };
+               37B73C741004BEFD008C4B41 /* listseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listseqscommand.h; sourceTree = SOURCE_ROOT; };
+               37B73C751004BEFD008C4B41 /* listseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listseqscommand.cpp; sourceTree = SOURCE_ROOT; };
+               37B73CA41004D89A008C4B41 /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = SOURCE_ROOT; };
+               37B73CA51004D89A008C4B41 /* getseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getseqscommand.cpp; sourceTree = SOURCE_ROOT; };
+               37B73CBE1004EB38008C4B41 /* removeseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeseqscommand.h; sourceTree = SOURCE_ROOT; };
+               37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeseqscommand.cpp; sourceTree = SOURCE_ROOT; };
+               37B73CCD1004F5E0008C4B41 /* systemcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = systemcommand.h; sourceTree = SOURCE_ROOT; };
+               37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = systemcommand.cpp; sourceTree = SOURCE_ROOT; };
                37C1D9710F86506E0059E3F0 /* binsequencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = binsequencecommand.h; sourceTree = SOURCE_ROOT; };
                37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = binsequencecommand.cpp; sourceTree = SOURCE_ROOT; };
                37C753CC0FB3415200DBD02E /* distancecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distancecommand.h; sourceTree = SOURCE_ROOT; };
@@ -515,10 +515,10 @@
                A70B53A70F4CD7AD0064797E /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = SOURCE_ROOT; };
                A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlinecommand.cpp; sourceTree = SOURCE_ROOT; };
                A70B53A90F4CD7AD0064797E /* getlinecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlinecommand.h; sourceTree = SOURCE_ROOT; };
-               A75B8879104C16860083C454 /* alignedsimilarity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignedsimilarity.cpp; sourceTree = "<group>"; };
-               A75B887A104C16860083C454 /* alignedsimilarity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = alignedsimilarity.h; sourceTree = "<group>"; };
-               A75B887B104C16860083C454 /* ccode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ccode.cpp; sourceTree = "<group>"; };
-               A75B887C104C16860083C454 /* ccode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ccode.h; sourceTree = "<group>"; };
+               A75B8879104C16860083C454 /* alignedsimilarity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignedsimilarity.cpp; sourceTree = SOURCE_ROOT; };
+               A75B887A104C16860083C454 /* alignedsimilarity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = alignedsimilarity.h; sourceTree = SOURCE_ROOT; };
+               A75B887B104C16860083C454 /* ccode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ccode.cpp; sourceTree = SOURCE_ROOT; };
+               A75B887C104C16860083C454 /* ccode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ccode.h; sourceTree = SOURCE_ROOT; };
                C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = "<group>"; };
                EB1216860F619B83004A865F /* bergerparker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bergerparker.h; sourceTree = SOURCE_ROOT; };
                EB1216870F619B83004A865F /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = SOURCE_ROOT; };

diff --git a/listvector.cpp b/listvector.cpp
index 6e008074a86dd849261401e45deb26fbcb506bc7..e123298930f706f9bf19d267e0ee17a5ddb41243 100644 (file)
--- a/listvector.cpp
+++ b/listvector.cpp
@@ -55,6 +55,8 @@ ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numS
                        f >> inputData;
                        set(i, inputData);
                }
+               
+               gobble(f);
        }
        catch(exception& e) {
                errorOut(e, "ListVector", "ListVector");

diff --git a/raredisplay.cpp b/raredisplay.cpp
index b86312bc4411e8cdd2faca9934aab3abf5c96c52..6c5a5e5f6d5c22a08d609681d88f5539460881ac 100644 (file)
--- a/raredisplay.cpp
+++ b/raredisplay.cpp
@@ -14,14 +14,6 @@
 void RareDisplay::init(string label){
        try {
                this->label = label;
-               if(nIters != 1){
-                       tempInFile.clear();
-                       openOutputFile(tempOutName, tempOutFile);
-                       openInputFile(tempInName, tempInFile);
-               }
-               else{
-                       openOutputFile(tempOutName, tempOutFile);
-               }
        }
        catch(exception& e) {
                errorOut(e, "RareDisplay", "init");
@@ -38,20 +30,22 @@ void RareDisplay::update(SAbundVector* rank){
 
                if(nIters != 1){
 
-                       double oldNSeqs, oldMean, oldVar;
-               
-                       tempInFile >> oldNSeqs >> oldMean >> oldVar;
-               
-                       double oldS = oldVar * ( nIters - 2 );
-                       double delta = data[0] - oldMean;
-                       double newMean = oldMean + delta / nIters;
+                       double oldS = var[index] * ( nIters - 2 );
+                       double delta = data[0] - results[index];
+                       double newMean = results[index] + delta / nIters;
                        double newS = oldS + delta * ( data[0] - newMean );
                        double newVar = newS / ( nIters - 1 );
 
-                       tempOutFile << newNSeqs << '\t' << newMean << '\t' << newVar << endl;
+                       seqs[index] = newNSeqs;
+                       results[index] = newMean; 
+                       var[index] = newVar;
+                       
+                       index++;  
                }
                else{
-                       tempOutFile << newNSeqs << '\t' << data[0] << '\t' << 0 << endl;
+                       seqs.push_back(newNSeqs); 
+                       results.push_back(data[0]);
+                       var.push_back(0.0);
                }
        }
        catch(exception& e) {
@@ -67,20 +61,24 @@ void RareDisplay::update(vector<SharedRAbundVector*> shared, int numSeqs, int nu
                double newNSeqs = data[0];
                
                if(nIters != 1){
-                       double oldNSeqs, oldMean, oldVar;
                
-                       tempInFile >> oldNSeqs >> oldMean >> oldVar;
-               
-                       double oldS = oldVar * ( nIters - 2 );
-                       double delta = data[0] - oldMean;
-                       double newMean = oldMean + delta / nIters;
+                       double oldS = var[index] * ( nIters - 2 );
+                       double delta = data[0] - results[index];
+                       double newMean = results[index] + delta / nIters;
                        double newS = oldS + delta * ( data[0] - newMean );
                        double newVar = newS / ( nIters - 1 );
-
-                       tempOutFile << newNSeqs << '\t' << newMean << '\t' << newVar << endl;
+                       seqs[index] = newNSeqs;
+                       results[index] = newMean; 
+                       var[index] = newVar;
+                       
+                       index++;  
                }
                else{
-                       tempOutFile << newNSeqs << '\t' << data[0] << '\t' << 0 << endl;
+                       
+                       seqs.push_back(newNSeqs); 
+                       results.push_back(data[0]);
+                       var.push_back(0.0);
+
                }
        }
        catch(exception& e) {
@@ -93,21 +91,8 @@ void RareDisplay::update(vector<SharedRAbundVector*> shared, int numSeqs, int nu
 
 void RareDisplay::reset(){
        try {
-               if(nIters != 1){
-                       tempOutFile.close();
-                       tempInFile.close();
-               }
-               else{
-                       tempOutFile.close();
-               }
-       
                nIters++;
-       
-               remove(tempInName.c_str());
-               renameOk = rename(tempOutName.c_str(), tempInName.c_str());     
-               
-               //checks to make sure user was able to rename and remove successfully
-               if (renameOk != 0) { mothurOut("Unable to rename the necessary temp files."); mothurOutEndLine(); }
+               index = 0;
        }
        catch(exception& e) {
                errorOut(e, "RareDisplay", "reset");
@@ -122,32 +107,27 @@ void RareDisplay::close(){
                
                output->initFile(label);
        
-               openInputFile(tempInName, tempInFile);
-       
-               while(!tempInFile.eof()){
-                       int nSeqs;
-                       tempInFile >> nSeqs;
+               for (int i = 0; i < seqs.size(); i++) {
                
                        vector<double> data(3,0);
-                       double variance = 0;
-               
-                       tempInFile >> data[0];
-                       tempInFile >> variance;
-               
+                       double variance = var[i];
+                       
+                       data[0] = results[i];
+                       
                        double ci = 1.96 * pow(variance, 0.5);
                        data[1] = data[0] - ci;
                        data[2] = data[0] + ci;
                
-                       output->output(nSeqs, data);
-               
-                       gobble(tempInFile);
+                       output->output(seqs[i], data);
                }
-               tempInFile.close();
-       
-               remove(tempInName.c_str());
-               remove(tempOutName.c_str());
                
                nIters = 1;
+               index = 0;
+               
+               seqs.clear();
+               results.clear();
+               var.clear();
+               
                output->resetFile();
        }
        catch(exception& e) {

diff --git a/raredisplay.h b/raredisplay.h
index c9067060820eece4446921011634c1515c44b812..72147ade3a9a37e3b865cb5166473b65f8f7777d 100644 (file)
--- a/raredisplay.h
+++ b/raredisplay.h
@@ -11,8 +11,7 @@
 class RareDisplay : public Display {
        
 public:
-       RareDisplay(Calculator* calc, FileOutput* file) : estimate(calc), output(file), nIters(1),
-                                                       tempInName(getPathName(output->getFileName()) + ".tempin"), tempOutName(getPathName(output->getFileName()) + ".tempout") {};
+       RareDisplay(Calculator* calc, FileOutput* file) : estimate(calc), output(file), nIters(1), index(0) {};
        ~RareDisplay()                                  {       delete estimate; delete output;         };
        void init(string);
        void reset();
@@ -25,12 +24,10 @@ private:
        Calculator* estimate;
        FileOutput* output;
        string label;
-       int nIters;
-       string tempInName, tempOutName;
-       ifstream tempInFile;
-       ofstream tempOutFile;
-       int renameOk;
-
+       vector<int> seqs;  
+       vector<double> results;
+       vector<double> var;
+       int index, nIters;
 };
 
 #endif