added tempdefault to set.dir and fixed bug with padding type in sffinfo.

diff --git a/makefile b/makefile
index b3bc136f1b57cbf5f4e96954a4d7350452cbbef6..974890d363ee400ec3a243aecc23e1f4ff79c9a5 100644 (file)
--- a/makefile
+++ b/makefile
@@ -13,7 +13,7 @@
 
 CXXFLAGS += -O3
 
-MOTHUR_FILES = "\"/Users/SarahsWork/desktop//Release\""
+MOTHUR_FILES = "\"/Users/SarahsWork/desktop/Release\""
 ifeq  ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
 else
        CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}

diff --git a/mothur.cpp b/mothur.cpp
index cb8d1e8715e518ed0d307fc2d50ab46961e21f92..6e61f8796b9d2256de9773d9621174cc677c8ad2 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -87,9 +87,9 @@ int main(int argc, char *argv[]){
                #endif
                
                //header
-               m->mothurOut("mothur v.1.11.0");
+               m->mothurOut("mothur v.1.12.0");
                m->mothurOutEndLine();          
-               m->mothurOut("Last updated: 6/18/2010");
+               m->mothurOut("Last updated: 7/23/2010");
                m->mothurOutEndLine();  
                m->mothurOutEndLine();          
                m->mothurOut("by");

diff --git a/setdircommand.cpp b/setdircommand.cpp
index 238ffa5ff227eb85bae8dff594a7d1f97d357280..1bc78bdf13cd69ee3be268bef006fc74d69dce9e 100644 (file)
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -20,7 +20,7 @@ SetDirectoryCommand::SetDirectoryCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"output","input","outputdir","inputdir"};
+                       string Array[] =  {"output","input","tempdefault","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -37,9 +37,12 @@ SetDirectoryCommand::SetDirectoryCommand(string option)  {
                        
                        input = validParameter.validFile(parameters, "input", false);                   
                        if (input == "not found") {  input = "";  }
+                       
+                       tempdefault = validParameter.validFile(parameters, "tempdefault", false);                       
+                       if (tempdefault == "not found") {  tempdefault = "";  }
                                
-                       if ((input == "") && (output == "")) {  
-                               m->mothurOut("You must provide either an input or output for the set.outdir command."); m->mothurOutEndLine(); abort = true;
+                       if ((input == "") && (output == "") && (tempdefault == "")) {   
+                               m->mothurOut("You must provide either an input, output or tempdefault for the set.outdir command."); m->mothurOutEndLine(); abort = true;
                        }
                }
        }
@@ -54,10 +57,12 @@ void SetDirectoryCommand::help(){
        try {
                m->mothurOut("The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n");
                m->mothurOut("The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n");
-               m->mothurOut("The set.dir command parameter is output and is required.\n");
+               m->mothurOut("The set.dir command can also be used to override or set the default location mothur will look for files if it is unable to find them, the directory must exist.\n");
+               m->mothurOut("The set.dir command parameters are input, output and tempdefault and one is required.\n");
                m->mothurOut("To return the output to the same directory as the input files you may enter: output=clear.\n");
                m->mothurOut("To return the input to the same directory as the mothur.exe you may enter: input=clear.\n");
-               m->mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory).\n");
+               m->mothurOut("To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n");
+               m->mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory, tempdefault=yourTempDefault).\n");
                m->mothurOut("Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n");
        }
@@ -130,6 +135,42 @@ int SetDirectoryCommand::execute(){
                                commandFactory->setInputDirectory(input); 
                        }
                }
+               
+               //set default
+               if (tempdefault == "clear") {  
+                       #ifdef MOTHUR_FILES
+                               string temp = MOTHUR_FILES; 
+                               m->mothurOut("Resetting default directory to " + temp); m->mothurOutEndLine();  
+                               m->setDefaultPath(temp);
+                       #else
+                               string temp = ""; 
+                               m->mothurOut("No default directory defined at compile time."); m->mothurOutEndLine();  
+                               m->setDefaultPath(temp);
+                       #endif
+               }else if (tempdefault == "") {  //do nothing
+               }else {
+                       //add / to name if needed
+                       string lastChar = tempdefault.substr(tempdefault.length()-1);
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                               if (lastChar != "/") { tempdefault += "/"; }
+                       #else
+                               if (lastChar != "\\") { tempdefault += "\\"; }  
+                       #endif
+                       
+                       //test to make sure directory exists
+                       tempdefault = getFullPathName(tempdefault);
+                       string inTemp = tempdefault + "temp";
+                       ofstream in;
+                       in.open(inTemp.c_str(), ios::trunc);
+                       if(!in) {
+                               m->mothurOut(tempdefault + " directory does not exist or is not writable."); m->mothurOutEndLine(); 
+                       }else{
+                               in.close();
+                               remove(inTemp.c_str());
+                               m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();  
+                               m->setDefaultPath(tempdefault);
+                       }
+               }
 
                return 0;
        }

diff --git a/setdircommand.h b/setdircommand.h
index 663496523e55a9cd2e2a8999043a8eeb743a8b7b..565b839aadb6ce8f2f440e6bd8b75be44afba227 100644 (file)
--- a/setdircommand.h
+++ b/setdircommand.h
@@ -25,7 +25,7 @@ public:
        
 private:
        CommandFactory* commandFactory;
-       string output, input;
+       string output, input, tempdefault;
        bool abort;
                
 };

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 07334f656d3aaff14c653a14a38d1e0eac38bba9..01338ca34be42556131b15a0ead73c0ef9952858 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -363,8 +363,8 @@ int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
                        if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength);  }
                                
                        /* Pad to 8 chars */
-                       int spotInFile = in.tellg();
-                       int spot = (spotInFile + 7)& ~7;  // ~ inverts
+                       unsigned long int spotInFile = in.tellg();
+                       unsigned long int spot = (spotInFile + 7)& ~7;  // ~ inverts
                        in.seekg(spot);
                        
                }else{
@@ -426,8 +426,8 @@ int SffInfoCommand::readHeader(ifstream& in, Header& header){
                        if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength);  }
                        
                        /* Pad to 8 chars */
-                       int spotInFile = in.tellg();
-                       int spot = (spotInFile + 7)& ~7;
+                       unsigned long int spotInFile = in.tellg();
+                       unsigned long int spot = (spotInFile + 7)& ~7;
                        in.seekg(spot);
                        
                }else{
@@ -478,8 +478,8 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, i
                        }
                
                        /* Pad to 8 chars */
-                       int spotInFile = in.tellg();
-                       int spot = (spotInFile + 7)& ~7;
+                       unsigned long int spotInFile = in.tellg();
+                       unsigned long int spot = (spotInFile + 7)& ~7;
                        in.seekg(spot);
                        
                }else{