Updates to unique.seqs

Includes filename changes from deconvolute to unique.seqs #792 #807
mothur · Jan 3, 2022 · 31f557a · 31f557a
1 parent 457517b
commit 31f557a
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Showing 22 changed files with 517 additions and 456 deletions.
diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
@@ -179,7 +179,7 @@
 		481FB5AD1AC1B7300076CFF3 /* countgroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A795840C13F13CD900F201D5 /* countgroupscommand.cpp */; };
 		481FB5AE1AC1B7300076CFF3 /* countseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7730EFE13967241007433A3 /* countseqscommand.cpp */; };
 		481FB5AF1AC1B7300076CFF3 /* createdatabasecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A77EBD2E1523709100ED407C /* createdatabasecommand.cpp */; };
-		481FB5B01AC1B7300076CFF3 /* deconvolutecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */; };
+		481FB5B01AC1B7300076CFF3 /* uniqueseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6C312D37EC400DA6239 /* uniqueseqscommand.cpp */; };
 		481FB5B11AC1B7300076CFF3 /* degapseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */; };
 		481FB5B21AC1B7300076CFF3 /* deuniqueseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */; };
 		481FB5B31AC1B7300076CFF3 /* deuniquetreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A77A221E139001B600B0BE70 /* deuniquetreecommand.cpp */; };
@@ -640,7 +640,7 @@
 		A7E9B8B512D37EC400DA6239 /* corraxescommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */; };
 		A7E9B8B612D37EC400DA6239 /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6BB12D37EC400DA6239 /* coverage.cpp */; };
 		A7E9B8B812D37EC400DA6239 /* decalc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6C112D37EC400DA6239 /* decalc.cpp */; };
-		A7E9B8B912D37EC400DA6239 /* deconvolutecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */; };
+		A7E9B8B912D37EC400DA6239 /* uniqueseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6C312D37EC400DA6239 /* uniqueseqscommand.cpp */; };
 		A7E9B8BA12D37EC400DA6239 /* degapseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */; };
 		A7E9B8BB12D37EC400DA6239 /* deuniqueseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */; };
 		A7E9B8BC12D37EC400DA6239 /* distancecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */; };
@@ -1383,8 +1383,8 @@
 		A7E9B6C012D37EC400DA6239 /* dayhoff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = dayhoff.h; path = source/calculators/dayhoff.h; sourceTree = SOURCE_ROOT; };
 		A7E9B6C112D37EC400DA6239 /* decalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = decalc.cpp; path = source/chimera/decalc.cpp; sourceTree = SOURCE_ROOT; };
 		A7E9B6C212D37EC400DA6239 /* decalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; lineEnding = 0; name = decalc.h; path = source/chimera/decalc.h; sourceTree = SOURCE_ROOT; xcLanguageSpecificationIdentifier = xcode.lang.objcpp; };
-		A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = deconvolutecommand.cpp; path = source/commands/deconvolutecommand.cpp; sourceTree = SOURCE_ROOT; };
-		A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = deconvolutecommand.h; path = source/commands/deconvolutecommand.h; sourceTree = SOURCE_ROOT; };
+		A7E9B6C312D37EC400DA6239 /* uniqueseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = uniqueseqscommand.cpp; path = source/commands/uniqueseqscommand.cpp; sourceTree = SOURCE_ROOT; };
+		A7E9B6C412D37EC400DA6239 /* uniqueseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = uniqueseqscommand.h; path = source/commands/uniqueseqscommand.h; sourceTree = SOURCE_ROOT; };
 		A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; name = degapseqscommand.cpp; path = source/commands/degapseqscommand.cpp; sourceTree = SOURCE_ROOT; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
 		A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = degapseqscommand.h; path = source/commands/degapseqscommand.h; sourceTree = SOURCE_ROOT; };
 		A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = deuniqueseqscommand.cpp; path = source/commands/deuniqueseqscommand.cpp; sourceTree = SOURCE_ROOT; };
@@ -2496,8 +2496,6 @@
 				A7730EFE13967241007433A3 /* countseqscommand.cpp */,
 				A77EBD2C1523707F00ED407C /* createdatabasecommand.h */,
 				A77EBD2E1523709100ED407C /* createdatabasecommand.cpp */,
-				A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */,
-				A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */,
 				A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */,
 				A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */,
 				A7E9B6C812D37EC400DA6239 /* deuniqueseqscommand.h */,
@@ -2718,6 +2716,8 @@
 				A7E9B86C12D37EC400DA6239 /* unifracunweightedcommand.cpp */,
 				A7E9B86F12D37EC400DA6239 /* unifracweightedcommand.h */,
 				A7E9B86E12D37EC400DA6239 /* unifracweightedcommand.cpp */,
+				A7E9B6C412D37EC400DA6239 /* uniqueseqscommand.h */,
+				A7E9B6C312D37EC400DA6239 /* uniqueseqscommand.cpp */,
 				A7E9B87B12D37EC400DA6239 /* venncommand.h */,
 				A7E9B87A12D37EC400DA6239 /* venncommand.cpp */,
 			);
@@ -3256,7 +3256,7 @@
 				481FB6431AC1B7EA0076CFF3 /* sharedordervector.cpp in Sources */,
 				4803D5AD211CA67F001C63B5 /* testsharedrabundvector.cpp in Sources */,
 				481FB5301AC1B5C80076CFF3 /* calcsparcc.cpp in Sources */,
-				481FB5B01AC1B7300076CFF3 /* deconvolutecommand.cpp in Sources */,
+				481FB5B01AC1B7300076CFF3 /* uniqueseqscommand.cpp in Sources */,
 				481FB6001AC1B7970076CFF3 /* renameseqscommand.cpp in Sources */,
 				481FB5921AC1B71B0076CFF3 /* anosimcommand.cpp in Sources */,
 				481FB6201AC1B7B30076CFF3 /* commandoptionparser.cpp in Sources */,
@@ -3582,7 +3582,7 @@
 				A7E9B8B512D37EC400DA6239 /* corraxescommand.cpp in Sources */,
 				A7E9B8B612D37EC400DA6239 /* coverage.cpp in Sources */,
 				A7E9B8B812D37EC400DA6239 /* decalc.cpp in Sources */,
-				A7E9B8B912D37EC400DA6239 /* deconvolutecommand.cpp in Sources */,
+				A7E9B8B912D37EC400DA6239 /* uniqueseqscommand.cpp in Sources */,
 				A7E9B8BA12D37EC400DA6239 /* degapseqscommand.cpp in Sources */,
 				F4A866BF265BE7EC0010479A /* aminoacid.cpp in Sources */,
 				4815BEB12289E13500677EE2 /* lnrarefaction.cpp in Sources */,

diff --git a/source/commandfactory.cpp b/source/commandfactory.cpp
@@ -20,7 +20,7 @@
 #include "quitcommand.h"
 #include "helpcommand.h"
 #include "commandfactory.hpp"
-#include "deconvolutecommand.h"
+#include "uniqueseqscommand.h"
 #include "parsimonycommand.h"
 #include "unifracunweightedcommand.h"
 #include "unifracweightedcommand.h"
@@ -438,7 +438,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         if ((commandName != "help") && (commandName != "system")) { checkForRedirects(optionString); }
 
 		if(commandName == "cluster")                    {	command = new ClusterCommand(optionString);					}
-		else if(commandName == "unique.seqs")			{	command = new DeconvoluteCommand(optionString);				}
+		else if(commandName == "unique.seqs")			{	command = new UniqueSeqsCommand(optionString);				}
 		else if(commandName == "parsimony")				{	command = new ParsimonyCommand(optionString);				}
 		else if(commandName == "help")					{	command = new HelpCommand(optionString);					}
 		else if(commandName == "quit")					{	command = new QuitCommand(optionString);					}
@@ -614,7 +614,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
             }
         }
 		if(commandName == "cluster")				{	pipecommand = new ClusterCommand(optionString);					}
-		else if(commandName == "unique.seqs")			{	pipecommand = new DeconvoluteCommand(optionString);				}
+		else if(commandName == "unique.seqs")			{	pipecommand = new UniqueSeqsCommand(optionString);				}
 		else if(commandName == "parsimony")				{	pipecommand = new ParsimonyCommand(optionString);				}
 		else if(commandName == "help")					{	pipecommand = new HelpCommand(optionString);					}
 		else if(commandName == "quit")					{	pipecommand = new QuitCommand(optionString);					}

diff --git a/source/commands/chimeraperseuscommand.cpp b/source/commands/chimeraperseuscommand.cpp
@@ -8,7 +8,7 @@
  */
 
 #include "chimeraperseuscommand.h"
-#include "deconvolutecommand.h"
+#include "uniqueseqscommand.h"
 #include "sequence.hpp"
 #include "counttable.h"
 #include "sequencecountparser.h"
@@ -550,7 +550,7 @@ string ChimeraPerseusCommand::getCountFile(string& inputFile){
 		m->mothurOut("Running command: unique.seqs(" + inputString + ")\n");
 		current->setMothurCalling(true);
 
-		Command* uniqueCommand = new DeconvoluteCommand(inputString);
+		Command* uniqueCommand = new UniqueSeqsCommand(inputString);
 		uniqueCommand->execute();
 
 		map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();

diff --git a/source/commands/chimeraslayercommand.cpp b/source/commands/chimeraslayercommand.cpp
@@ -8,7 +8,7 @@
  */
 
 #include "chimeraslayercommand.h"
-#include "deconvolutecommand.h"
+#include "uniqueseqscommand.h"
 #include "sequenceparser.h"
 #include "counttable.h"
 #include "removeseqscommand.h"
@@ -635,7 +635,7 @@ string ChimeraSlayerCommand::getCountFile(string& inputFile){
 		m->mothurOut("Running command: unique.seqs(" + inputString + ")\n");
 		current->setMothurCalling(true);
 
-		Command* uniqueCommand = new DeconvoluteCommand(inputString);
+		Command* uniqueCommand = new UniqueSeqsCommand(inputString);
 		uniqueCommand->execute();
 
 		map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();

diff --git a/source/commands/chimerauchimecommand.cpp b/source/commands/chimerauchimecommand.cpp
@@ -8,7 +8,7 @@
  */
 
 #include "chimerauchimecommand.h"
-#include "deconvolutecommand.h"
+#include "uniqueseqscommand.h"
 #include "sequence.hpp"
 #include "systemcommand.h"
 #include "removeseqscommand.h"
@@ -1094,7 +1094,7 @@ string ChimeraUchimeCommand::getCountFile(string& inputFile){
 		m->mothurOut("Running command: unique.seqs(" + inputString + ")\n");
 		current->setMothurCalling(true);
 
-		Command* uniqueCommand = new DeconvoluteCommand(inputString);
+		Command* uniqueCommand = new UniqueSeqsCommand(inputString);
 		uniqueCommand->execute();
 
 		map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();

diff --git a/source/commands/chimeravsearchcommand.cpp b/source/commands/chimeravsearchcommand.cpp
@@ -7,7 +7,7 @@
 //
 
 #include "chimeravsearchcommand.h"
-#include "deconvolutecommand.h"
+#include "uniqueseqscommand.h"
 #include "sequence.hpp"
 #include "systemcommand.h"
 #include "degapseqscommand.h"
@@ -931,7 +931,7 @@ string ChimeraVsearchCommand::getCountFile(string& inputFile){
         m->mothurOut("Running command: unique.seqs(" + inputString + ")\n");
         current->setMothurCalling(true);
 
-        Command* uniqueCommand = new DeconvoluteCommand(inputString);
+        Command* uniqueCommand = new UniqueSeqsCommand(inputString);
         uniqueCommand->execute();
 
         map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();

diff --git a/source/commands/clusterfitcommand.cpp b/source/commands/clusterfitcommand.cpp
@@ -1136,7 +1136,7 @@ void ClusterFitCommand::createReferenceNameCount() {
             string options = "fasta=" + reffastafile + ", format=count";
             m->mothurOut("/******************************************/\n");
             m->mothurOut("Running command: unique.seqs(" + options + ")\n");
-            Command* deconvoluteCommand = new DeconvoluteCommand(options);
+            Command* deconvoluteCommand = new UniqueSeqsCommand(options);
 
             deconvoluteCommand->execute();
             map<string, vector<string> > filenames = deconvoluteCommand->getOutputFiles();

diff --git a/source/commands/clusterfitcommand.hpp b/source/commands/clusterfitcommand.hpp
@@ -19,7 +19,7 @@
 #include "distancecommand.h"
 #include "aligncommand.h"
 #include "filterseqscommand.h"
-#include "deconvolutecommand.h"
+#include "uniqueseqscommand.h"
 #include "listseqscommand.h"
 #include "getdistscommand.h"
 #include "getseqscommand.h"