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added kruskwalliscommand to Xcode project and fixed parameter issues.
[mothur.git] / shhhercommand.cpp
diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index c34f25de509c78b9e1b97b7c303142864e3c7e01..a859d145b49e261bace85fb973d3aa9466bc1123 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -12,18 +12,18 @@
 //**********************************************************************************************************************
 vector<string> ShhherCommand::setParameters(){ 
        try {
-               CommandParameter pflow("flow", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pflow);
-               CommandParameter pfile("file", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pfile);
-               CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plookup);
-               CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(pcutoff);
-               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-               CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "",false,false); parameters.push_back(pmaxiter);
-        CommandParameter plarge("large", "Number", "", "-1", "", "", "",false,false); parameters.push_back(plarge);
-               CommandParameter psigma("sigma", "Number", "", "60", "", "", "",false,false); parameters.push_back(psigma);
-               CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "",false,false); parameters.push_back(pmindelta);
-               CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pflow("flow", "InputTypes", "", "", "none", "fileflow", "none","fasta-name-group-counts-qfile",false,false,true); parameters.push_back(pflow);
+               CommandParameter pfile("file", "InputTypes", "", "", "none", "fileflow", "none","fasta-name-group-counts-qfile",false,false,true); parameters.push_back(pfile);
+               CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(plookup);
+               CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "","",false,false); parameters.push_back(pcutoff);
+               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+               CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(pmaxiter);
+        CommandParameter plarge("large", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(plarge);
+               CommandParameter psigma("sigma", "Number", "", "60", "", "", "","",false,false); parameters.push_back(psigma);
+               CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "","",false,false); parameters.push_back(pmindelta);
+               CommandParameter porder("order", "String", "", "", "", "", "","",false,false); parameters.push_back(porder);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -47,28 +47,23 @@ string ShhherCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string ShhherCommand::getOutputFileNameTag(string type, string inputName=""){  
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
-        
-        //is this a type this command creates
-        it = outputTypes.find(type);
-        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
-        else {
-            if (type == "fasta")            {   outputFileName =  "shhh.fasta";   }
-            else if (type == "name")    {   outputFileName =  "shhh.names";   }
-            else if (type == "group")        {   outputFileName =  "shhh.groups";   }
-            else if (type == "counts")        {   outputFileName =  "shhh.counts";   }
-            else if (type == "qfile")        {   outputFileName =  "shhh.qual";   }
-            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
-        }
-        return outputFileName;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ShhherCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+string ShhherCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "fasta")            {   pattern = "[filename],shhh.fasta";   }
+        else if (type == "name")    {   pattern = "[filename],shhh.names";   }
+        else if (type == "group")        {   pattern = "[filename],shhh.groups";   }
+        else if (type == "counts")        {   pattern = "[filename],shhh.counts";   }
+        else if (type == "qfile")        {   pattern = "[filename],shhh.qual";   }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ShhherCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 
@@ -776,8 +771,8 @@ int ShhherCommand::execute(){
 
                
                if(compositeFASTAFileName != ""){
-                       outputNames.push_back(compositeFASTAFileName);
-                       outputNames.push_back(compositeNamesFileName);
+                       outputNames.push_back(compositeFASTAFileName); outputTypes["fasta"].push_back(compositeFASTAFileName);
+                       outputNames.push_back(compositeNamesFileName); outputTypes["name"].push_back(compositeNamesFileName); 
                }
 
                m->mothurOutEndLine();
@@ -801,8 +796,9 @@ string ShhherCommand::createNamesFile(){
                for(int i=0;i<numSeqs;i++){
                        duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ',';
                }
-               
-               string nameFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name");
+               map<string, string> variables; 
+               variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+               string nameFileName = getOutputFileName("name",variables);
                
                ofstream nameFile;
                m->openOutputFile(nameFileName, nameFile);
@@ -1039,7 +1035,12 @@ void ShhherCommand::getFlowData(){
         
         float intensity;
         
-        flowFile >> numFlowCells;
+        string numFlowTest;
+        flowFile >> numFlowTest;
+        
+        if (!m->isContainingOnlyDigits(numFlowTest)) { m->mothurOut("[ERROR]: expected a number and got " + numFlowTest + ", quitting. Did you use the flow parameter instead of the file parameter?"); m->mothurOutEndLine(); exit(1); }
+        else { convert(numFlowTest, numFlowCells); }
+        
         int index = 0;//pcluster
         while(!flowFile.eof()){
             
@@ -1376,17 +1377,17 @@ string ShhherCommand::cluster(string distFileName, string namesFileName){
     try {
         
         ReadMatrix* read = new ReadColumnMatrix(distFileName);         
-        read->setCutoff(cutoff);
-        
-        NameAssignment* clusterNameMap = new NameAssignment(namesFileName);
-        clusterNameMap->readMap();
-        read->read(clusterNameMap);
-        
-        ListVector* list = read->getListVector();
-        SparseMatrix* matrix = read->getMatrix();
+               read->setCutoff(cutoff);
+               
+               NameAssignment* clusterNameMap = new NameAssignment(namesFileName);
+               clusterNameMap->readMap();
+               read->read(clusterNameMap);
         
-        delete read; 
-        delete clusterNameMap; 
+               ListVector* list = read->getListVector();
+               SparseDistanceMatrix* matrix = read->getDMatrix();
+               
+               delete read; 
+               delete clusterNameMap; 
         
         RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
         
@@ -1646,7 +1647,9 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
     try {
         string thisOutputDir = outputDir;
         if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
-        string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("qfile");
+        map<string, string> variables; 
+               variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+        string qualityFileName = getOutputFileName("qfile",variables);
         
         ofstream qualityFile;
         m->openOutputFile(qualityFileName, qualityFile);
@@ -1738,7 +1741,7 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
             }
         }
         qualityFile.close();
-        outputNames.push_back(qualityFileName);
+        outputNames.push_back(qualityFileName); outputTypes["qfile"].push_back(qualityFileName);
         
     }
     catch(exception& e) {
@@ -1753,7 +1756,9 @@ void ShhherCommand::writeSequences(vector<int> otuCounts){
     try {
         string thisOutputDir = outputDir;
         if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
-        string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta");
+        map<string, string> variables; 
+               variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName));
+        string fastaFileName = getOutputFileName("fasta",variables);
         ofstream fastaFile;
         m->openOutputFile(fastaFileName, fastaFile);
         
@@ -1783,7 +1788,7 @@ void ShhherCommand::writeSequences(vector<int> otuCounts){
         }
         fastaFile.close();
         
-        outputNames.push_back(fastaFileName);
+        outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
         
         if(compositeFASTAFileName != ""){
             m->appendFiles(fastaFileName, compositeFASTAFileName);
@@ -1801,7 +1806,9 @@ void ShhherCommand::writeNames(vector<int> otuCounts){
     try {
         string thisOutputDir = outputDir;
         if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
-        string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name");
+        map<string, string> variables; 
+               variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName));
+        string nameFileName = getOutputFileName("name",variables);
         ofstream nameFile;
         m->openOutputFile(nameFileName, nameFile);
         
@@ -1820,7 +1827,7 @@ void ShhherCommand::writeNames(vector<int> otuCounts){
             }
         }
         nameFile.close();
-        outputNames.push_back(nameFileName);
+        outputNames.push_back(nameFileName); outputTypes["name"].push_back(nameFileName);
         
         
         if(compositeNamesFileName != ""){
@@ -1843,7 +1850,9 @@ void ShhherCommand::writeGroups(){
         int pos = fileRoot.find_first_of('.');
         string fileGroup = fileRoot;
         if (pos != string::npos) {  fileGroup = fileRoot.substr(pos+1, (fileRoot.length()-1-(pos+1)));  }
-        string groupFileName = thisOutputDir + fileRoot + getOutputFileNameTag("group");
+        map<string, string> variables; 
+               variables["[filename]"] = thisOutputDir + fileRoot;
+        string groupFileName = getOutputFileName("group",variables);
         ofstream groupFile;
         m->openOutputFile(groupFileName, groupFile);
         
@@ -1852,7 +1861,7 @@ void ShhherCommand::writeGroups(){
             groupFile << seqNameVector[i] << '\t' << fileGroup << endl;
         }
         groupFile.close();
-        outputNames.push_back(groupFileName);
+        outputNames.push_back(groupFileName); outputTypes["group"].push_back(groupFileName);
         
     }
     catch(exception& e) {
@@ -1867,7 +1876,9 @@ void ShhherCommand::writeClusters(vector<int> otuCounts){
     try {
         string thisOutputDir = outputDir;
         if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
-        string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) +getOutputFileNameTag("counts");
+        map<string, string> variables; 
+               variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName));
+        string otuCountsFileName = getOutputFileName("counts",variables);
         ofstream otuCountsFile;
         m->openOutputFile(otuCountsFileName, otuCountsFile);
         
@@ -1912,7 +1923,7 @@ void ShhherCommand::writeClusters(vector<int> otuCounts){
             }
         }
         otuCountsFile.close();
-        outputNames.push_back(otuCountsFileName);
+        outputNames.push_back(otuCountsFileName); outputTypes["counts"].push_back(otuCountsFileName);
         
     }
     catch(exception& e) {
@@ -1926,7 +1937,7 @@ void ShhherCommand::writeClusters(vector<int> otuCounts){
 
 int ShhherCommand::execute(){
        try {
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                getSingleLookUp();      if (m->control_pressed) { return 0; }
                getJointLookUp();       if (m->control_pressed) { return 0; }
@@ -1943,8 +1954,8 @@ int ShhherCommand::execute(){
 #endif
         
                if(compositeFASTAFileName != ""){
-                       outputNames.push_back(compositeFASTAFileName);
-                       outputNames.push_back(compositeNamesFileName);
+                       outputNames.push_back(compositeFASTAFileName); outputTypes["fasta"].push_back(compositeFASTAFileName);
+                       outputNames.push_back(compositeNamesFileName); outputTypes["name"].push_back(compositeNamesFileName);
                }
 
                m->mothurOutEndLine();
@@ -2029,7 +2040,7 @@ int ShhherCommand::createProcesses(vector<string> filenames){
                //Windows version shared memory, so be careful when passing variables through the shhhFlowsData struct. 
                //Above fork() will clone, so memory is separate, but that's not the case with windows, 
                //////////////////////////////////////////////////////////////////////////////////////////////////////
-               
+               /*
                vector<shhhFlowsData*> pDataArray; 
                DWORD   dwThreadIdArray[processors-1];
                HANDLE  hThreadArray[processors-1]; 
@@ -2060,7 +2071,7 @@ int ShhherCommand::createProcesses(vector<string> filenames){
                        CloseHandle(hThreadArray[i]);
                        delete pDataArray[i];
                }
-               
+               */
         #endif
         
         for (int i=0;i<processIDS.size();i++) { 
@@ -2318,15 +2329,17 @@ int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFil
                 if ((large) && (g == 0)) {  flowFileName = filenames[i]; theseFlowFileNames[0] = filenames[i]; }
                 string thisOutputDir = outputDir;
                 if (outputDir == "") {  thisOutputDir = m->hasPath(flowFileName);  }
-                string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("qfile");
-                string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta");
-                string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name");
-                string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("counts");
+                map<string, string> variables; 
+                variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName));
+                string qualityFileName = getOutputFileName("qfile",variables);
+                string fastaFileName = getOutputFileName("fasta",variables);
+                string nameFileName = getOutputFileName("name",variables);
+                string otuCountsFileName = getOutputFileName("counts",variables);
                 string fileRoot = m->getRootName(m->getSimpleName(flowFileName));
                 int pos = fileRoot.find_first_of('.');
                 string fileGroup = fileRoot;
                 if (pos != string::npos) {  fileGroup = fileRoot.substr(pos+1, (fileRoot.length()-1-(pos+1)));  }
-                string groupFileName = thisOutputDir + fileRoot + getOutputFileNameTag("group");
+                string groupFileName = getOutputFileName("group",variables);
 
                 
                 writeQualities(numOTUs, numFlowCells, qualityFileName, otuCounts, nSeqsPerOTU, seqNumber, singleTau, flowDataIntI, uniqueFlowgrams, cumNumSeqs, mapUniqueToSeq, seqNameVector, centroids, aaI); if (m->control_pressed) { break; }
@@ -2337,15 +2350,16 @@ int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFil
                 
                 if (large) {
                     if (g > 0) {
-                        m->appendFiles(qualityFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("qfile")));
+                        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0]));
+                        m->appendFiles(qualityFileName, getOutputFileName("qfile",variables));
                         m->mothurRemove(qualityFileName);
-                        m->appendFiles(fastaFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("fasta")));
+                        m->appendFiles(fastaFileName, getOutputFileName("fasta",variables));
                         m->mothurRemove(fastaFileName);
-                        m->appendFiles(nameFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("name")));
+                        m->appendFiles(nameFileName, getOutputFileName("name",variables));
                         m->mothurRemove(nameFileName);
-                        m->appendFiles(otuCountsFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("counts")));
+                        m->appendFiles(otuCountsFileName, getOutputFileName("counts",variables));
                         m->mothurRemove(otuCountsFileName);
-                        m->appendFiles(groupFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("group")));
+                        m->appendFiles(groupFileName, getOutputFileName("group",variables));
                         m->mothurRemove(groupFileName);
                     }
                     m->mothurRemove(theseFlowFileNames[g]);
@@ -2382,7 +2396,12 @@ int ShhherCommand::getFlowData(string filename, vector<string>& thisSeqNameVecto
                thisFlowDataIntI.clear();
                thisNameMap.clear();
                
-               flowFile >> numFlowCells;
+               string numFlowTest;
+        flowFile >> numFlowTest;
+        
+        if (!m->isContainingOnlyDigits(numFlowTest)) { m->mothurOut("[ERROR]: expected a number and got " + numFlowTest + ", quitting. Did you use the flow parameter instead of the file parameter?"); m->mothurOutEndLine(); exit(1); }
+        else { convert(numFlowTest, numFlowCells); }
+        
         if (m->debug) { m->mothurOut("[DEBUG]: numFlowCells = " + toString(numFlowCells) + ".\n"); }
                int index = 0;//pcluster
                while(!flowFile.eof()){
@@ -3256,7 +3275,7 @@ void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string quality
                        }
                }
                qualityFile.close();
-               outputNames.push_back(qualityFileName);
+               outputNames.push_back(qualityFileName); outputTypes["qfile"].push_back(qualityFileName);
         
        }
        catch(exception& e) {
@@ -3300,7 +3319,7 @@ void ShhherCommand::writeSequences(string thisCompositeFASTAFileName, int numOTU
                }
                fastaFile.close();
         
-               outputNames.push_back(fastaFileName);
+               outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
         
                if(thisCompositeFASTAFileName != ""){
                        m->appendFiles(fastaFileName, thisCompositeFASTAFileName);
@@ -3335,7 +3354,7 @@ void ShhherCommand::writeNames(string thisCompositeNamesFileName, int numOTUs, s
                        }
                }
                nameFile.close();
-               outputNames.push_back(nameFileName);
+               outputNames.push_back(nameFileName); outputTypes["name"].push_back(nameFileName);
                
                
                if(thisCompositeNamesFileName != ""){
@@ -3360,7 +3379,7 @@ void ShhherCommand::writeGroups(string groupFileName, string fileRoot, int numSe
                        groupFile << seqNameVector[i] << '\t' << fileRoot << endl;
                }
                groupFile.close();
-               outputNames.push_back(groupFileName);
+               outputNames.push_back(groupFileName); outputTypes["group"].push_back(groupFileName);
         
        }
        catch(exception& e) {
@@ -3419,7 +3438,7 @@ void ShhherCommand::writeClusters(string otuCountsFileName, int numOTUs, int num
                        }
                }
                otuCountsFile.close();
-               outputNames.push_back(otuCountsFileName);
+               outputNames.push_back(otuCountsFileName); outputTypes["counts"].push_back(otuCountsFileName);
         
        }
        catch(exception& e) {
Mothur--16S microbiota sequencing software; mirror of main repository with my branches