From fbaa6c7ac44f857c1ece7c8199e9e7e09b4bbe74 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Tue, 20 Jul 2010 14:40:07 +0000
Subject: [PATCH] added tempdefault to set.dir and fixed bug with padding type
in sffinfo.
---
makefile | 2 +-
mothur.cpp | 4 ++--
setdircommand.cpp | 51 +++++++++++++++++++++++++++++++++++++++++-----
setdircommand.h | 2 +-
sffinfocommand.cpp | 12 +++++------
5 files changed, 56 insertions(+), 15 deletions(-)
diff --git a/makefile b/makefile
index b3bc136..974890d 100644
--- 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 cb8d1e8..6e61f87 100644
--- 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 238ffa5..1bc78bd 100644
--- 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 6634965..565b839 100644
--- 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 07334f6..01338ca 100644
--- 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{
--
2.39.5