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added get.dists and remove.dists commands. fixed bug in trim.seqs win…
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…dows paralellization that caused blank groups in group file. added list and shared file to get.otulabels and remove.otulabels. added list file to list.otulabels.
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@mothur-westcott
mothur-westcott committed Jan 29, 2013
1 parent 14cddf8 commit 1f0e54b
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Showing 14 changed files with 1,861 additions and 28 deletions.
12 changes: 12 additions & 0 deletions Mothur.xcodeproj/project.pbxproj
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Expand Up @@ -17,6 +17,7 @@
A70056E6156A93D000924A2D /* getotulabelscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70056E5156A93D000924A2D /* getotulabelscommand.cpp */; };
A70056EB156AB6E500924A2D /* removeotulabelscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70056EA156AB6E500924A2D /* removeotulabelscommand.cpp */; };
A70332B712D3A13400761E33 /* makefile in Sources */ = {isa = PBXBuildFile; fileRef = A70332B512D3A13400761E33 /* makefile */; };
A7128B1D16B7002A00723BE4 /* getdistscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7128B1C16B7002600723BE4 /* getdistscommand.cpp */; };
A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBAB12DC7613000092AC /* readphylipvector.cpp */; };
A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */; };
A71CB160130B04A2001E7287 /* anosimcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71CB15E130B04A2001E7287 /* anosimcommand.cpp */; };
Expand Down Expand Up @@ -64,6 +65,7 @@
A7A32DAA14DC43B00001D2E5 /* sortseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */; };
A7A3C8C914D041AD00B1BFBE /* otuassociationcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A3C8C714D041AD00B1BFBE /* otuassociationcommand.cpp */; };
A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A61F2C130062E000E05B6B /* amovacommand.cpp */; };
A7B0231516B8244C006BA09E /* removedistscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B0231416B8244B006BA09E /* removedistscommand.cpp */; };
A7BF221414587886000AD524 /* myPerseus.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7BF221214587886000AD524 /* myPerseus.cpp */; };
A7BF2232145879B2000AD524 /* chimeraperseuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7BF2231145879B2000AD524 /* chimeraperseuscommand.cpp */; };
A7C3DC0B14FE457500FE1924 /* cooccurrencecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C3DC0914FE457500FE1924 /* cooccurrencecommand.cpp */; };
Expand Down Expand Up @@ -402,6 +404,8 @@
A70056E9156AB6D400924A2D /* removeotulabelscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeotulabelscommand.h; sourceTree = "<group>"; };
A70056EA156AB6E500924A2D /* removeotulabelscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeotulabelscommand.cpp; sourceTree = "<group>"; };
A70332B512D3A13400761E33 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
A7128B1A16B7001200723BE4 /* getdistscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getdistscommand.h; sourceTree = "<group>"; };
A7128B1C16B7002600723BE4 /* getdistscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getdistscommand.cpp; sourceTree = "<group>"; };
A713EBAA12DC7613000092AC /* readphylipvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylipvector.h; sourceTree = "<group>"; };
A713EBAB12DC7613000092AC /* readphylipvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylipvector.cpp; sourceTree = "<group>"; };
A713EBEB12DC7C5E000092AC /* nmdscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nmdscommand.h; sourceTree = "<group>"; };
Expand Down Expand Up @@ -499,6 +503,8 @@
A7A61F2B130062E000E05B6B /* amovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = amovacommand.h; sourceTree = "<group>"; };
A7A61F2C130062E000E05B6B /* amovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = amovacommand.cpp; sourceTree = "<group>"; };
A7AACFBA132FE008003D6C4D /* currentfile.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = currentfile.h; sourceTree = "<group>"; };
A7B0231416B8244B006BA09E /* removedistscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removedistscommand.cpp; sourceTree = "<group>"; };
A7B0231716B8245D006BA09E /* removedistscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removedistscommand.h; sourceTree = "<group>"; };
A7BF221214587886000AD524 /* myPerseus.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = myPerseus.cpp; sourceTree = "<group>"; };
A7BF221314587886000AD524 /* myPerseus.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = myPerseus.h; sourceTree = "<group>"; };
A7BF2230145879B2000AD524 /* chimeraperseuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraperseuscommand.h; sourceTree = "<group>"; };
Expand Down Expand Up @@ -1358,6 +1364,8 @@
219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */,
A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */,
A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */,
A7128B1A16B7001200723BE4 /* getdistscommand.h */,
A7128B1C16B7002600723BE4 /* getdistscommand.cpp */,
A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */,
A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */,
A7E9B6F512D37EC400DA6239 /* getgroupscommand.h */,
Expand Down Expand Up @@ -1466,6 +1474,8 @@
A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */,
A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */,
A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */,
A7B0231716B8245D006BA09E /* removedistscommand.h */,
A7B0231416B8244B006BA09E /* removedistscommand.cpp */,
A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */,
A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */,
A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */,
Expand Down Expand Up @@ -2316,6 +2326,8 @@
A7496D2E167B531B00CC7D7C /* kruskalwalliscommand.cpp in Sources */,
A79EEF8616971D4A0006DEC1 /* filtersharedcommand.cpp in Sources */,
A74C06E916A9C0A9008390A3 /* primerdesigncommand.cpp in Sources */,
A7128B1D16B7002A00723BE4 /* getdistscommand.cpp in Sources */,
A7B0231516B8244C006BA09E /* removedistscommand.cpp in Sources */,
);
runOnlyForDeploymentPostprocessing = 0;
};
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10 changes: 6 additions & 4 deletions catchallcommand.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -80,6 +80,7 @@ CatchAllCommand::CatchAllCommand(){
outputTypes["models"] = tempOutNames;
outputTypes["bubble"] = tempOutNames;
outputTypes["summary"] = tempOutNames;
outputTypes["sabund"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
Expand Down Expand Up @@ -118,6 +119,7 @@ CatchAllCommand::CatchAllCommand(string option) {
outputTypes["models"] = tempOutNames;
outputTypes["bubble"] = tempOutNames;
outputTypes["summary"] = tempOutNames;
outputTypes["sabund"] = tempOutNames;


//if the user changes the input directory command factory will send this info to us in the output parameter
Expand Down Expand Up @@ -237,7 +239,7 @@ int CatchAllCommand::execute() {
catchAllTest = m->getFullPathName(catchAllTest);

#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
catchAllCommandExe += "mono " + catchAllTest + " ";
catchAllCommandExe += "mono \"" + catchAllTest + "\" ";
#else
catchAllCommandExe += "\"" + catchAllTest + "\" ";
#endif
Expand Down Expand Up @@ -291,7 +293,7 @@ int CatchAllCommand::execute() {
//create system command
string catchAllCommand = "";
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + + "\" 1";
#else
//removes extra '\\' catchall doesnt like that
vector<string> tempNames;
Expand Down Expand Up @@ -354,7 +356,7 @@ int CatchAllCommand::execute() {
//create system command
string catchAllCommand = "";
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + + "\" 1";
#else
//removes extra '\\' catchall doesnt like that
vector<string> tempNames;
Expand Down Expand Up @@ -439,7 +441,7 @@ int CatchAllCommand::execute() {
//create system command
string catchAllCommand = "";
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + + "\" 1";
#else
//removes extra '\\' catchall doesnt like that
vector<string> tempNames;
Expand Down
12 changes: 11 additions & 1 deletion commandfactory.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -138,6 +138,8 @@
#include "classifysharedcommand.h"
#include "filtersharedcommand.h"
#include "primerdesigncommand.h"
#include "getdistscommand.h"
#include "removedistscommand.h"

/*******************************************************/

Expand Down Expand Up @@ -298,7 +300,9 @@ CommandFactory::CommandFactory(){
commands["quit"] = "MPIEnabled";
commands["classify.shared"] = "classify.shared";
commands["filter.shared"] = "filter.shared";
commands["primer.design"] = "primer.design";
commands["primer.design"] = "primer.design";
commands["get.dists"] = "get.dists";
commands["remove.dists"] = "remove.dists";


}
Expand Down Expand Up @@ -516,6 +520,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
else if(commandName == "classify.shared") { command = new ClassifySharedCommand(optionString); }
else if(commandName == "filter.shared") { command = new FilterSharedCommand(optionString); }
else if(commandName == "primer.design") { command = new PrimerDesignCommand(optionString); }
else if(commandName == "get.dists") { command = new GetDistsCommand(optionString); }
else if(commandName == "remove.dists") { command = new RemoveDistsCommand(optionString); }
else { command = new NoCommand(optionString); }

return command;
Expand Down Expand Up @@ -674,6 +680,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
else if(commandName == "classify.shared") { pipecommand = new ClassifySharedCommand(optionString); }
else if(commandName == "filter.shared") { pipecommand = new FilterSharedCommand(optionString); }
else if(commandName == "primer.design") { pipecommand = new PrimerDesignCommand(optionString); }
else if(commandName == "get.dists") { pipecommand = new GetDistsCommand(optionString); }
else if(commandName == "remove.dists") { pipecommand = new RemoveDistsCommand(optionString); }
else { pipecommand = new NoCommand(optionString); }

return pipecommand;
Expand Down Expand Up @@ -818,6 +826,8 @@ Command* CommandFactory::getCommand(string commandName){
else if(commandName == "classify.shared") { shellcommand = new ClassifySharedCommand(); }
else if(commandName == "filter.shared") { shellcommand = new FilterSharedCommand(); }
else if(commandName == "primer.design") { shellcommand = new PrimerDesignCommand(); }
else if(commandName == "get.dists") { shellcommand = new GetDistsCommand(); }
else if(commandName == "remove.dists") { shellcommand = new RemoveDistsCommand(); }
else { shellcommand = new NoCommand(); }

return shellcommand;
Expand Down
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