added keep dots to pcr.seqs. fixed pre.cluster name file name when group option is...

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index cf4256851eb583a78b78fd5ab800bbfa5d46f5e8..f2fbc80088b1adf2927ee78d5b1e02fbf9691cb1 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -147,7 +147,7 @@ PreClusterCommand::PreClusterCommand(string option) {
                        // ...at some point should added some additional type checking...
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not found") { namefile =  "";  }
-                       else if (namefile == "not open") { abort = true; }      
+                       else if (namefile == "not open") { namefile = ""; abort = true; }       
                        else {  m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
@@ -156,13 +156,16 @@ PreClusterCommand::PreClusterCommand(string option) {
                        else {   m->setGroupFile(groupfile); bygroup = true;  }
                        
                        string temp     = validParameter.validFile(parameters, "diffs", false);         if(temp == "not found"){        temp = "1"; }
-                       convert(temp, diffs); 
+                       m->mothurConvert(temp, diffs); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
-                       
+                       m->mothurConvert(temp, processors);
                        
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(fastafile);
+                               parser.getNameFile(files);
+                       }
                }
                                
        }
@@ -214,17 +217,19 @@ int PreClusterCommand::execute(){
                        m->mothurOutEndLine(); 
                        m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
                        m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); 
-                       
+                       m->mothurCalling = true;
+            
                        Command* uniqueCommand = new DeconvoluteCommand(inputString);
                        uniqueCommand->execute();
                        
                        map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
                        
                        delete uniqueCommand;
-                       
+                       m->mothurCalling = false;
                        m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
                        
                        m->renameFile(filenames["fasta"][0], newFastaFile);
+            m->renameFile(filenames["name"][0], newNamesFile);
                        
                        m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine(); 
                                
@@ -299,7 +304,7 @@ int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newF
                        lines.push_back(linePair(startIndex, endIndex));
                }
                
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)          
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)         
                
                //loop through and create all the processes you want
                while (process != processors) {
@@ -372,6 +377,9 @@ int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newF
                
                //append output files
                for(int i=0;i<processIDS.size();i++){
+                       //newFName = m->getFullPathName(".\\" + newFName);
+                       //newNName = m->getFullPathName(".\\" + newNName);
+                       
                        m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
                        m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));
                        
@@ -508,7 +516,7 @@ int PreClusterCommand::readFASTA(){
                m->openInputFile(fastafile, inFasta);
                
                //string firstCol, secondCol, nameString;
-               length = 0;
+               set<int> lengths;
                
                while (!inFasta.eof()) {
                        
@@ -534,17 +542,21 @@ int PreClusterCommand::readFASTA(){
                                        else{
                                                seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
                                                alignSeqs.push_back(tempNode);
-                                               if (seq.getAligned().length() > length) {  length = seq.getAligned().length();  }
+                                               lengths.insert(seq.getAligned().length());
                                        }       
                                }else { //no names file, you are identical to yourself 
                                        seqPNode tempNode(1, seq, seq.getName());
                                        alignSeqs.push_back(tempNode);
-                                       if (seq.getAligned().length() > length) {  length = seq.getAligned().length();  }
+                                       lengths.insert(seq.getAligned().length());
                                }
                        }
                }
                inFasta.close();
                //inNames.close();
+        
+        if (lengths.size() > 1) { m->control_pressed = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
+        else if (lengths.size() == 1) { length = *(lengths.begin()); }
+        
                return alignSeqs.size();
        }
        
@@ -556,7 +568,7 @@ int PreClusterCommand::readFASTA(){
 /**************************************************************************************************/
 int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>& thisSeqs){
        try {
-               length = 0;
+               set<int> lengths;
                alignSeqs.clear();
                map<string, string>::iterator it;
                bool error = false;
@@ -579,15 +591,18 @@ int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>&
                                        
                                        seqPNode tempNode(numReps, thisSeqs[i], it->second);
                                        alignSeqs.push_back(tempNode);
-                                       if (thisSeqs[i].getAligned().length() > length) {  length = thisSeqs[i].getAligned().length();  }
+                    lengths.insert(thisSeqs[i].getAligned().length());
                                }       
                        }else { //no names file, you are identical to yourself 
                                seqPNode tempNode(1, thisSeqs[i], thisSeqs[i].getName());
                                alignSeqs.push_back(tempNode);
-                               if (thisSeqs[i].getAligned().length() > length) {  length = thisSeqs[i].getAligned().length();  }
+                               lengths.insert(thisSeqs[i].getAligned().length());
                        }
                }
                
+        if (lengths.size() > 1) { error = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
+        else if (lengths.size() == 1) { length = *(lengths.begin()); }
+        
                //sanity check
                if (error) { m->control_pressed = true; }