line and label no longer persist between commands. Added phylip formated output...

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 6eb7d576833e0ba944d8f445ff662f2e1d86e661..e2ca937ed971e87194fd3623c48aec343d2f3ca5 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -80,30 +80,43 @@ int DistanceCommand::execute(){
                cutoff += 0.005;
                
                string distFile = getRootName(globaldata->getFastaFile()) + "dist";
+               string phylipFile = getRootName(globaldata->getFastaFile()) + "phylip.dist";
                
+               remove(phylipFile.c_str());
                remove(distFile.c_str());
                
+               //output numSeqs to phylip formatted dist file
+               openOutputFile(phylipFile, phylipOut);
+               phylipOut << numSeqs << endl;
+               phylipOut.close();
+               
                //#     if defined (_WIN32)
                //figure out how to implement the fork and wait commands in windows
-               //      driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
+               //      driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile, cutoff);
                //#     endif
                
 #if defined (__APPLE__) || (__MACH__)
                if(processors == 1){
-                       driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);    
+                       driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff);
+                       appendFiles((phylipFile + "tempPhylipA"), phylipFile);
+                       remove((phylipFile + "tempPhylipA").c_str());   
                }       
                else if(processors == 2){
                        
                        int pid = fork();
                        if(pid > 0){
-                               driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", cutoff);        
+                               driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff);    
                                appendFiles((distFile+"tempa"), distFile);
-                               remove((distFile + "tempa").c_str());   
+                               remove((distFile + "tempa").c_str());
+                               appendFiles((phylipFile + "tempPhylipA"), phylipFile);
+                               remove((phylipFile + "tempPhylipA").c_str());
                        }
                        else{
-                               driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", cutoff);  
+                               driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff);      
                                appendFiles((distFile+"tempb"), distFile);
-                               remove((distFile + "tempb").c_str());   
+                               remove((distFile + "tempb").c_str());
+                               appendFiles((phylipFile + "tempPhylipB"), phylipFile);
+                               remove((phylipFile + "tempPhylipB").c_str());   
                        }
                        wait(NULL);
                        
@@ -113,21 +126,27 @@ int DistanceCommand::execute(){
                        if(pid1 > 0){
                                int pid2 = fork();
                                if(pid2 > 0){
-                                       driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", cutoff);
+                                       driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", phylipFile + "tempPhylipA", cutoff);
                                        appendFiles(distFile+"tempa", distFile);
-                                       remove((distFile + "tempa").c_str());   
+                                       appendFiles((phylipFile + "tempPhylipA"), phylipFile);
+                                       remove((distFile + "tempa").c_str());
+                                       remove((phylipFile + "tempPhylipA").c_str());   
                                }
                                else{
-                                       driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", cutoff);        
+                                       driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", phylipFile + "tempPhylipB", cutoff);    
                                        appendFiles(distFile+"tempb", distFile);
-                                       remove((distFile + "tempb").c_str());                           
+                                       appendFiles((phylipFile + "tempPhylipB"), phylipFile);
+                                       remove((distFile + "tempb").c_str());   
+                                       remove((phylipFile + "tempPhylipB").c_str());                   
                                }
                                wait(NULL);
                        }
                        else{
-                               driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", cutoff);      
+                               driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", phylipFile + "tempPhylipC", cutoff);  
                                appendFiles(distFile+"tempc", distFile);
-                               remove((distFile + "tempc").c_str());                   
+                               appendFiles((phylipFile + "tempPhylipC"), phylipFile);
+                               remove((distFile + "tempc").c_str());   
+                               remove((phylipFile + "tempPhylipC").c_str());           
                        }
                        wait(NULL);
                }
@@ -136,28 +155,37 @@ int DistanceCommand::execute(){
                        if(pid1 > 0){
                                int pid2 = fork();
                                if(pid2 > 0){
-                                       driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", cutoff);      
+                                       driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", phylipFile + "tempPhylipA", cutoff);  
                                        appendFiles(distFile+"tempa", distFile);
-                                       remove((distFile + "tempa").c_str());                   
+                                       appendFiles((phylipFile + "tempPhylipA"), phylipFile);
+                                       remove((distFile + "tempa").c_str());
+                                       remove((phylipFile + "tempPhylipA").c_str());                   
                                }
                                else{
-                                       driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", cutoff);      
+                                       driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", phylipFile + "tempPhylipB", cutoff);  
                                        appendFiles(distFile+"tempb", distFile);
-                                       remove((distFile + "tempb").c_str());                           
+                                       appendFiles((phylipFile + "tempPhylipB"), phylipFile);
+                                       remove((distFile + "tempb").c_str());
+                                       remove((phylipFile + "tempPhylipB").c_str());                           
                                }
                                wait(NULL);
                        }
                        else{
                                int pid3 = fork();
                                if(pid3 > 0){
-                                       driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", cutoff);  
+                                       driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", phylipFile + "tempPhylipC", cutoff);      
                                        appendFiles(distFile+"tempc", distFile);
-                                       remove((distFile + "tempc").c_str());                           
+                                       appendFiles((phylipFile + "tempPhylipC"), phylipFile);
+                                       remove((distFile + "tempc").c_str());
+                                       remove((phylipFile + "tempPhylipC").c_str());   
+                                                               
                                }
                                else{
-                                       driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", cutoff);    
+                                       driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", phylipFile + "tempPhylipD", cutoff);        
                                        appendFiles(distFile+"tempd", distFile);
-                                       remove((distFile + "tempd").c_str());                           
+                                       appendFiles((phylipFile + "tempPhylipD"), phylipFile);
+                                       remove((distFile + "tempd").c_str());   
+                                       remove((phylipFile + "tempPhylipD").c_str());                   
                                }
                                wait(NULL);
                        }
@@ -166,20 +194,27 @@ int DistanceCommand::execute(){
                wait(NULL);
 #elif (linux) || (__linux)
                if(processors == 1){
-                       driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);    
+                       driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff);
+                       appendFiles((phylipFile + "tempPhylipA"), phylipFile);  
+                       remove((phylipFile + "tempPhylipA").c_str());   
                }       
                else if(processors == 2){
                        
                        int pid = fork();
                        if(pid > 0){
-                               driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", cutoff);        
+                               driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff);    
                                appendFiles((distFile+"tempa"), distFile);
+                               appendFiles((phylipFile + "tempPhylipA"), phylipFile);
                                remove((distFile + "tempa").c_str());   
+                               remove((phylipFile + "tempPhylipA").c_str());
+
                        }
                        else{
-                               driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", cutoff);  
+                               driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff);      
                                appendFiles((distFile+"tempb"), distFile);
-                               remove((distFile + "tempb").c_str());   
+                               appendFiles((phylipFile + "tempPhylipB"), phylipFile);
+                               remove((distFile + "tempb").c_str());
+                               remove((phylipFile + "tempPhylipB").c_str());   
                        }
                        wait();
                        
@@ -189,21 +224,28 @@ int DistanceCommand::execute(){
                        if(pid1 > 0){
                                int pid2 = fork();
                                if(pid2 > 0){
-                                       driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", cutoff);
-                                       appendFiles(distFile+"tempa", distFile);
+                                       driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff);    
+                                       appendFiles((distFile+"tempa"), distFile);
+                                       appendFiles((phylipFile + "tempPhylipA"), phylipFile);
                                        remove((distFile + "tempa").c_str());   
+                                       remove((phylipFile + "tempPhylipA").c_str());
+
                                }
                                else{
-                                       driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", cutoff);        
-                                       appendFiles(distFile+"tempb", distFile);
-                                       remove((distFile + "tempb").c_str());                           
+                                       driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff);      
+                                       appendFiles((distFile+"tempb"), distFile);
+                                       appendFiles((phylipFile + "tempPhylipB"), phylipFile);
+                                       remove((distFile + "tempb").c_str());
+                                       remove((phylipFile + "tempPhylipB").c_str());   
                                }
                                wait();
                        }
                        else{
-                               driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", cutoff);      
+                               driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", phylipFile + "tempPhylipC", cutoff);  
                                appendFiles(distFile+"tempc", distFile);
-                               remove((distFile + "tempc").c_str());                   
+                               appendFiles((phylipFile + "tempPhylipC"), phylipFile);
+                               remove((distFile + "tempc").c_str());   
+                               remove((phylipFile + "tempPhylipC").c_str());                           
                        }
                        wait();
                }
@@ -212,28 +254,36 @@ int DistanceCommand::execute(){
                        if(pid1 > 0){
                                int pid2 = fork();
                                if(pid2 > 0){
-                                       driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", cutoff);      
-                                       appendFiles(distFile+"tempa", distFile);
-                                       remove((distFile + "tempa").c_str());                   
+                                       driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff);    
+                                       appendFiles((distFile+"tempa"), distFile);
+                                       appendFiles((phylipFile + "tempPhylipA"), phylipFile);
+                                       remove((distFile + "tempa").c_str());   
+                                       remove((phylipFile + "tempPhylipA").c_str());
                                }
                                else{
-                                       driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", cutoff);      
-                                       appendFiles(distFile+"tempb", distFile);
-                                       remove((distFile + "tempb").c_str());                           
+                                       driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff);      
+                                       appendFiles((distFile+"tempb"), distFile);
+                                       appendFiles((phylipFile + "tempPhylipB"), phylipFile);
+                                       remove((distFile + "tempb").c_str());
+                                       remove((phylipFile + "tempPhylipB").c_str());   
                                }
                                wait();
                        }
                        else{
                                int pid3 = fork();
                                if(pid3 > 0){
-                                       driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", cutoff);  
+                                       driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", phylipFile + "tempPhylipC", cutoff);  
                                        appendFiles(distFile+"tempc", distFile);
-                                       remove((distFile + "tempc").c_str());                           
+                                       appendFiles((phylipFile + "tempPhylipC"), phylipFile);
+                                       remove((distFile + "tempc").c_str());   
+                                       remove((phylipFile + "tempPhylipC").c_str());                                   
                                }
                                else{
-                                       driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", cutoff);    
+                                       driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", phylipFile + "tempPhylipD", cutoff);        
                                        appendFiles(distFile+"tempd", distFile);
-                                       remove((distFile + "tempd").c_str());                           
+                                       appendFiles((phylipFile + "tempPhylipD"), phylipFile);
+                                       remove((distFile + "tempd").c_str());   
+                                       remove((phylipFile + "tempPhylipD").c_str());                           
                                }
                                wait();
                        }
@@ -242,7 +292,9 @@ int DistanceCommand::execute(){
                wait();
                
 #else
-               driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
+               driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff);
+               appendFiles((phylipFile + "tempPhylipA"), phylipFile);  
+               remove((phylipFile + "tempPhylipA").c_str());
 #endif
                
                delete distCalculator;
@@ -262,14 +314,20 @@ int DistanceCommand::execute(){
 
 /**************************************************************************************************/
 /////// need to fix to work with calcs and sequencedb
-int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLine, int endLine, string dFileName, float cutoff){
+int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLine, int endLine, string dFileName, string pFilename, float cutoff){
        try {
                int startTime = time(NULL);
                
+               //column file
                ofstream distFile(dFileName.c_str(), ios::trunc);
                distFile.setf(ios::fixed, ios::showpoint);
                distFile << setprecision(4);
                
+               //column file
+               ofstream philFile(pFilename.c_str(), ios::trunc);
+               philFile.setf(ios::fixed, ios::showpoint);
+               philFile << setprecision(4);
+               
                for(int i=startLine;i<endLine;i++){
                        
                        for(int j=0;j<i;j++){
@@ -279,8 +337,11 @@ int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLi
                                if(dist <= cutoff){
                                        distFile << align->get(i)->getName() << ' ' << align->get(j)->getName() << ' ' << dist << endl;
                                }
-                               
+                               philFile << dist << '\t';
                        }
+                       
+                       philFile << endl;
+                       
                        if(i % 100 == 0){
                                cout << i << '\t' << time(NULL) - startTime << endl;
                        }
@@ -288,6 +349,9 @@ int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLi
                }
                cout << endLine-1 << '\t' << time(NULL) - startTime << endl;
                
+               //philFile.close();
+               //distFile.close();
+               
                return 1;
        }
        catch(exception& e) {

diff --git a/distancecommand.h b/distancecommand.h
index c99e5c2cf8b7a56c4cd9b74d7563619a80b8f421..1f43856f43a033473a62c420e5c0bfce191fb182 100644 (file)
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -29,7 +29,7 @@ private:
        ValidCalculators* validCalculator;
        Dist* distCalculator;
        SequenceDB* seqDB;
-       ofstream out;
+       ofstream out, phylipOut;
        ifstream in;
        string outputFileName;
        string countends;
@@ -37,7 +37,7 @@ private:
        float cutoff;
        
        void appendFiles(string, string);
-       int driver(Dist*, SequenceDB*, int, int, string, float);
+       int driver(Dist*, SequenceDB*, int, int, string, string, float);
 
 };
 

diff --git a/globaldata.cpp b/globaldata.cpp
index b446d676fdb702aa0cb4a836dcb757a0e541fd0c..6138e2cc1b8f4fc70b8febc1105fcecca0448306 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -424,6 +424,8 @@ void GlobalData::clear() {
 
 /******************************************************/
 void GlobalData::reset() {
+       label                   =       "";
+       line                    =   "";
        cutoff                  =       "10.00";
        precision               =       "100";
        iters                   =       "1000"; 

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 0a742ea562852e8097485bea5a67200f6d8524c8..6a09ada5d3e8e4141c56a0c0ef4943beae6ef815 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -164,6 +164,11 @@ int SummarySharedCommand::execute(){
                        outputFileHandle.close();  remove(outputFileName.c_str());
                        if (mult == true) {  outAll.close();  remove(outAllFileName.c_str());  }
                        return 0;
+               //if you only have 2 groups you don't need a .sharedmultiple file
+               }else if ((lookup.size() == 2) && (mult == true)) { 
+                       mult = false;
+                       outAll.close();  
+                       remove(outAllFileName.c_str());
                }
                                        
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.