fixed bug with shhh.flow from file path name in write functions, added "smart" featur...

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 40a4c8499a599207b56831c91e6f0f41c023eb2c..537821134edebcf9dcad70f8c1f38be0da39b121 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -23,7 +23,7 @@ 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,true); parameters.push_back(plookup);
+               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);
@@ -2152,7 +2152,7 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
-               string qualityFileName = thisOutputDir + flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.qual";
+               string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + ".shhh.qual";
 
                ofstream qualityFile;
                m->openOutputFile(qualityFileName, qualityFile);
@@ -2259,7 +2259,7 @@ void ShhherCommand::writeSequences(vector<int> otuCounts){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
-               string fastaFileName = thisOutputDir + flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.fasta";
+               string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + ".shhh.fasta";
                ofstream fastaFile;
                m->openOutputFile(fastaFileName, fastaFile);
                
@@ -2307,7 +2307,7 @@ void ShhherCommand::writeNames(vector<int> otuCounts){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
-               string nameFileName = thisOutputDir + flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
+               string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + ".shhh.names";
                ofstream nameFile;
                m->openOutputFile(nameFileName, nameFile);
                
@@ -2345,7 +2345,7 @@ void ShhherCommand::writeGroups(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
-               string fileRoot = thisOutputDir + flowFileName.substr(0,flowFileName.find_last_of('.'));
+               string fileRoot = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName));
                string groupFileName = fileRoot + ".shhh.groups";
                ofstream groupFile;
                m->openOutputFile(groupFileName, groupFile);
@@ -2370,7 +2370,7 @@ void ShhherCommand::writeClusters(vector<int> otuCounts){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
-               string otuCountsFileName = thisOutputDir + flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.counts";
+               string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + ".shhh.counts";
                ofstream otuCountsFile;
                m->openOutputFile(otuCountsFileName, otuCountsFile);