added compile time default path

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index e5c04949905d7edd6ba5ec45f4fd5a8214053471..a20a383b6125e135fc1aefeec47e2bc6b892f1e9 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -107,7 +107,17 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                        #endif
                                        
                                        ifstream in;
-                                       ableToOpen = openInputFile(fastaFileNames[i], in);
+                                       ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+                               
+                                       //if you can't open it, try default location
+                                       if (ableToOpen == 1) {
+                                               if (m->getDefaultPath() != "") { //default path is set
+                                                       string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
+                                                       m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       fastaFileNames[i] = tryPath;
+                                               }
+                                       }
                                        in.close();
                                        
                                        #ifdef USE_MPI  
@@ -122,7 +132,7 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                        #endif
                                        
                                        if (ableToOpen == 1) { 
-                                               m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine(); 
+                                               m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
                                                //erase from file list
                                                fastaFileNames.erase(fastaFileNames.begin()+i);
                                                i--;
@@ -168,7 +178,17 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                        #endif
 
                                        ifstream in;
-                                       ableToOpen = openInputFile(namefileNames[i], in);
+                                       ableToOpen = openInputFile(namefileNames[i], in, "noerror");
+                               
+                                       //if you can't open it, try default location
+                                       if (ableToOpen == 1) {
+                                               if (m->getDefaultPath() != "") { //default path is set
+                                                       string tryPath = m->getDefaultPath() + getSimpleName(namefileNames[i]);
+                                                       m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       namefileNames[i] = tryPath;
+                                               }
+                                       }
                                        in.close();
                                        
                                        #ifdef USE_MPI  
@@ -181,8 +201,14 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                                }
                                                
                                        #endif
-                                       if (ableToOpen == 1) {  m->mothurOut("Unable to match name file with fasta file."); m->mothurOutEndLine(); abort = true;        }
                                        
+                                       if (ableToOpen == 1) { 
+                                               m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();  abort = true;
+                                               //erase from file list
+                                               namefileNames.erase(namefileNames.begin()+i);
+                                               i--;
+                                       }
+
                                }
                        }
 
@@ -213,7 +239,17 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                        #endif
 
                                        ifstream in;
-                                       ableToOpen = openInputFile(groupfileNames[i], in);
+                                       ableToOpen = openInputFile(groupfileNames[i], in, "noerror");
+                               
+                                       //if you can't open it, try default location
+                                       if (ableToOpen == 1) {
+                                               if (m->getDefaultPath() != "") { //default path is set
+                                                       string tryPath = m->getDefaultPath() + getSimpleName(groupfileNames[i]);
+                                                       m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       groupfileNames[i] = tryPath;
+                                               }
+                                       }
                                        in.close();
                                        
                                        #ifdef USE_MPI  
@@ -226,8 +262,13 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                                }
                                                
                                        #endif
-                                       if (ableToOpen == 1) {  m->mothurOut("Unable to match group file with fasta file, not using " + groupfileNames[i] + "."); m->mothurOutEndLine(); groupfileNames[i] = "";        }
                                        
+                                       if (ableToOpen == 1) { 
+                                               m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
+                                               //erase from file list
+                                               groupfileNames.erase(groupfileNames.begin()+i);
+                                               i--;
+                                       }
                                }
                        }
 
@@ -470,7 +511,7 @@ int ClassifySeqsCommand::execute(){
                        if(processors == 1){
                                ifstream inFASTA;
                                openInputFile(fastaFileNames[s], inFASTA);
-                               numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                               getNumSeqs(inFASTA, numFastaSeqs);
                                inFASTA.close();
                                
                                lines.push_back(new linePair(0, numFastaSeqs));
@@ -478,7 +519,7 @@ int ClassifySeqsCommand::execute(){
                                driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
                        }
                        else{
-                               vector<int> positions;
+                               vector<unsigned long int> positions;
                                processIDS.resize(0);
                                
                                ifstream inFASTA;
@@ -488,7 +529,7 @@ int ClassifySeqsCommand::execute(){
                                while(!inFASTA.eof()){
                                        input = getline(inFASTA);
                                        if (input.length() != 0) {
-                                               if(input[0] == '>'){    int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);       }
+                                               if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
                                        }
                                }
                                inFASTA.close();
@@ -496,9 +537,9 @@ int ClassifySeqsCommand::execute(){
                                numFastaSeqs = positions.size();
                                
                                int numSeqsPerProcessor = numFastaSeqs / processors;
-                               
+       
                                for (int i = 0; i < processors; i++) {
-                                       int startPos = positions[ i * numSeqsPerProcessor ];
+                                       unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
                                        if(i == processors - 1){
                                                numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
                                        }
@@ -520,7 +561,7 @@ int ClassifySeqsCommand::execute(){
        #else
                        ifstream inFASTA;
                        openInputFile(fastaFileNames[s], inFASTA);
-                       numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                       getNumSeqs(inFASTA, numFastaSeqs);
                        inFASTA.close();
                        
                        lines.push_back(new linePair(0, numFastaSeqs));
@@ -761,9 +802,9 @@ int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFNa
 
                for(int i=0;i<line->numSeqs;i++){
                        if (m->control_pressed) { return 0; }
-                       
-                       Sequence* candidateSeq = new Sequence(inFASTA);
-                       
+               
+                       Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
+               
                        if (candidateSeq->getName() != "") {
                                taxonomy = classify->getTaxonomy(candidateSeq);