-/*\r
- * clearcutcommand.cpp\r
- * Mothur\r
- *\r
- * Created by westcott on 5/11/10.\r
- * Copyright 2010 Schloss Lab. All rights reserved.\r
- *\r
- */\r
-\r
-#include "clearcutcommand.h"\r
-\r
-/**************************************************************************************/\r
-ClearcutCommand::ClearcutCommand(string option) { \r
- try {\r
- abort = false;\r
- \r
- //allow user to run help\r
- if(option == "help") { help(); abort = true; }\r
- \r
- else {\r
- //valid paramters for this command\r
- string Array[] = {"fasta","phylip","version","verbose","quiet","seed","norandom","shuffle","neighbor","expblen",\r
- "expdist","ntrees","matrixout","stdout","kimura","jukes","protein","DNA","stdin","outputdir","inputdir"};\r
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));\r
- \r
- OptionParser parser(option);\r
- map<string,string> parameters = parser.getParameters();\r
- \r
- ValidParameters validParameter;\r
- map<string, string>::iterator it;\r
- \r
- //check to make sure all parameters are valid for command\r
- for (it = parameters.begin(); it != parameters.end(); it++) { \r
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }\r
- }\r
- \r
- //if the user changes the input directory command factory will send this info to us in the output parameter \r
- string inputDir = validParameter.validFile(parameters, "inputdir", false); \r
- if (inputDir == "not found"){ inputDir = ""; }\r
- else {\r
- string path;\r
- it = parameters.find("fasta");\r
- //user has given a template file\r
- if(it != parameters.end()){ \r
- path = hasPath(it->second);\r
- //if the user has not given a path then, add inputdir. else leave path alone.\r
- if (path == "") { parameters["fasta"] = inputDir + it->second; }\r
- }\r
- \r
- it = parameters.find("phylip");\r
- //user has given a template file\r
- if(it != parameters.end()){ \r
- path = hasPath(it->second);\r
- //if the user has not given a path then, add inputdir. else leave path alone.\r
- if (path == "") { parameters["phylip"] = inputDir + it->second; }\r
- }\r
- }\r
-\r
- //check for required parameters\r
- fastafile = validParameter.validFile(parameters, "fasta", true);\r
- if (fastafile == "not open") { fastafile = ""; abort = true; }\r
- else if (fastafile == "not found") { fastafile = ""; } \r
- else { inputFile = fastafile; }\r
- \r
- phylipfile = validParameter.validFile(parameters, "phylip", true);\r
- if (phylipfile == "not open") { phylipfile = ""; abort = true; }\r
- else if (phylipfile == "not found") { phylipfile = ""; }\r
- else { inputFile = phylipfile; }\r
- \r
- if ((phylipfile == "") && (fastafile == "")) { m->mothurOut("You must provide either a phylip formatted distance matrix or an aligned fasta file."); m->mothurOutEndLine(); abort=true; }\r
- if ((phylipfile != "") && (fastafile != "")) { m->mothurOut("You must provide either a phylip formatted distance matrix or an aligned fasta file, not BOTH."); m->mothurOutEndLine(); abort=true; }\r
-\r
- \r
- //if the user changes the output directory command factory will send this info to us in the output parameter \r
- outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }\r
- \r
- string temp;\r
- temp = validParameter.validFile(parameters, "version", false); if (temp == "not found"){ temp = "F"; }\r
- version = isTrue(temp);\r
- \r
- temp = validParameter.validFile(parameters, "verbose", false); if (temp == "not found"){ temp = "F"; }\r
- verbose = isTrue(temp); \r
- \r
- temp = validParameter.validFile(parameters, "quiet", false); if (temp == "not found"){ temp = "F"; }\r
- quiet = isTrue(temp); \r
- \r
- seed = validParameter.validFile(parameters, "seed", false); if (seed == "not found"){ seed = "*"; }\r
- \r
- temp = validParameter.validFile(parameters, "norandom", false); if (temp == "not found"){ temp = "F"; }\r
- norandom = isTrue(temp); \r
- \r
- temp = validParameter.validFile(parameters, "shuffle", false); if (temp == "not found"){ temp = "F"; }\r
- shuffle = isTrue(temp); \r
- \r
- temp = validParameter.validFile(parameters, "neighbor", false); if (temp == "not found"){ temp = "F"; }\r
- neighbor = isTrue(temp); \r
- \r
- temp = validParameter.validFile(parameters, "stdin", false); if (temp == "not found"){ temp = "F"; }\r
- stdinWanted = isTrue(temp); \r
- \r
- temp = validParameter.validFile(parameters, "DNA", false); if (temp == "not found"){ temp = "F"; }\r
- DNA = isTrue(temp);\r
- \r
- temp = validParameter.validFile(parameters, "protein", false); if (temp == "not found"){ temp = "F"; }\r
- protein = isTrue(temp);\r
- \r
- temp = validParameter.validFile(parameters, "jukes", false); if (temp == "not found"){ temp = "F"; }\r
- jukes = isTrue(temp);\r
- \r
- temp = validParameter.validFile(parameters, "kimura", false); if (temp == "not found"){ temp = "F"; }\r
- kimura = isTrue(temp);\r
- \r
- temp = validParameter.validFile(parameters, "stdout", false); if (temp == "not found"){ temp = "F"; }\r
- stdoutWanted = isTrue(temp); \r
- \r
- matrixout = validParameter.validFile(parameters, "matrixout", false); if (matrixout == "not found"){ matrixout = ""; }\r
- \r
- ntrees = validParameter.validFile(parameters, "ntrees", false); if (ntrees == "not found"){ ntrees = "1"; }\r
- \r
- temp = validParameter.validFile(parameters, "expblen", false); if (temp == "not found"){ temp = "F"; }\r
- expblen = isTrue(temp);\r
- \r
- temp = validParameter.validFile(parameters, "expdist", false); if (temp == "not found"){ temp = "F"; }\r
- expdist = isTrue(temp);\r
- \r
- if ((fastafile != "") && ((!DNA) && (!protein))) { m->mothurOut("You must specify the type of sequences you are using: DNA or protein"); m->mothurOutEndLine(); abort=true; }\r
- }\r
-\r
- }\r
- catch(exception& e) {\r
- m->errorOut(e, "ClearcutCommand", "ClearcutCommand");\r
- exit(1);\r
- }\r
-}\r
-//**********************************************************************************************************************\r
-\r
-void ClearcutCommand::help(){\r
- try {\r
- m->mothurOut("The clearcut command interfaces mothur with the clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.\n");\r
- m->mothurOut("For more information about clearcut refer to http://bioinformatics.hungry.com/clearcut/ \n");\r
- m->mothurOut("The clearcut executable must be in a folder called clearcut in the same folder as your mothur executable, similar to mothur's requirements for using blast. \n");\r
- m->mothurOut("The clearcut command parameters are phylip, fasta, version, verbose, quiet, seed, norandom, shuffle, neighbor, expblen, expdist, ntrees, matrixout, stdoutWanted, kimura, jukes, protein, DNA, stdinWanted. \n");\r
- m->mothurOut("The phylip parameter allows you to enter your phylip formatted distance matrix. \n");\r
- m->mothurOut("The fasta parameter allows you to enter your aligned fasta file, if you enter a fastafile you specify if the sequences are DNA or protein using the DNA or protein parameters. \n");\r
- \r
- m->mothurOut("The version parameter prints out the version of clearcut you are using, default=F. \n");\r
- m->mothurOut("The verbose parameter prints out more output from clearcut, default=F. \n");\r
- m->mothurOut("The quiet parameter turns on silent operation mode, default=F. \n");\r
- m->mothurOut("The seed parameter allows you to explicitly set the PRNG seed to a specific value. \n");\r
- m->mothurOut("The norandom parameter allows you to attempt joins deterministically, default=F. \n");\r
- m->mothurOut("The shuffle parameter allows you to randomly shuffle the distance matrix, default=F. \n");\r
- m->mothurOut("The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=F. \n");\r
- \r
- m->mothurOut("The stdinWanted parameter reads input from STDIN, default=F. \n");\r
- m->mothurOut("The DNA parameter allows you to indicate your fasta file contains DNA sequences, default=F. \n");\r
- m->mothurOut("The protein parameter allows you to indicate your fasta file contains protein sequences, default=F. \n");\r
- \r
- m->mothurOut("The stdoutWanted parameter outputs your tree to STDOUT, default=F. \n");\r
- m->mothurOut("The matrixout parameter allows you to specify a filename to output a distance matrix to. \n");\r
- m->mothurOut("The ntrees parameter allows you to specify the number of output trees, default=1. \n");\r
- m->mothurOut("The expblen parameter allows you to use exponential notation for branch lengths, default=F. \n");\r
- m->mothurOut("The expdist parameter allows you to use exponential notation for distance outputs, default=F. \n");\r
-\r
- m->mothurOut("The clearcut command should be in the following format: \n");\r
- m->mothurOut("clearcut(phylip=yourDistanceFile) \n");\r
- m->mothurOut("Example: clearcut(phylip=abrecovery.phylip.dist) \n"); \r
- \r
- }\r
- catch(exception& e) {\r
- m->errorOut(e, "ClearcutCommand", "help");\r
- exit(1);\r
- }\r
-}\r
-\r
-/**************************************************************************************/\r
-int ClearcutCommand::execute() { \r
- try {\r
- \r
- if (abort == true) { return 0; }\r
- \r
- //prepare filename\r
- string outputName = outputDir + getRootName(getSimpleName(inputFile)) + "tre";\r
- \r
- //get location of clearcut\r
- GlobalData* globaldata = GlobalData::getInstance();\r
- string path = globaldata->argv;\r
- path = path.substr(0, (path.find_last_of('m')));\r
- \r
- string clearcutCommand = "";\r
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
- clearcutCommand = path + "clearcut/clearcut ";\r
- #else\r
- clearcutCommand = path + "clearcut\\clearcut ";\r
- #endif\r
- \r
- //you gave us a distance matrix\r
- if (phylipfile != "") { clearcutCommand += "--distance "; }\r
- \r
- //you gave us a fastafile\r
- if (fastafile != "") { clearcutCommand += "--alignment "; }\r
- \r
- if (version) { clearcutCommand += "--version "; }\r
- if (verbose) { clearcutCommand += "--verbose "; }\r
- if (quiet) { clearcutCommand += "--quiet "; }\r
- if (seed != "*") { clearcutCommand += "--seed=" + seed + " "; }\r
- if (norandom) { clearcutCommand += "--norandom "; }\r
- if (shuffle) { clearcutCommand += "--shuffle "; }\r
- if (neighbor) { clearcutCommand += "--neighbor "; }\r
- \r
- if (stdinWanted) { clearcutCommand += "--stdin "; }\r
- else{ \r
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
- clearcutCommand += "--in=" + inputFile + " "; }\r
- #else\r
- clearcutCommand += "--in=\"" + inputFile + "\" "; }\r
- #endif\r
- if (stdoutWanted) { clearcutCommand += "--stdout "; }\r
- else{ \r
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
- clearcutCommand += "--out=" + outputName + " "; }\r
- #else\r
- clearcutCommand += "--out=\"" + outputName + "\" "; }\r
- #endif\r
- \r
- if (DNA) { clearcutCommand += "--DNA "; }\r
- if (protein) { clearcutCommand += "--protein "; }\r
- if (jukes) { clearcutCommand += "--jukes "; }\r
- if (kimura) { clearcutCommand += "--kimura "; }\r
- if (matrixout != "") { clearcutCommand += "--matrixout=" + matrixout + " "; }\r
- if (ntrees != "1") { clearcutCommand += "--ntrees=" + ntrees + " "; }\r
- if (expblen) { clearcutCommand += "--expblen "; }\r
- if (expdist) { clearcutCommand += "--expdist "; }\r
- \r
- //run clearcut\r
- system(clearcutCommand.c_str());\r
- \r
- if (!stdoutWanted) { \r
- m->mothurOutEndLine();\r
- m->mothurOut("Output File Names: "); m->mothurOutEndLine();\r
- m->mothurOut(outputName); m->mothurOutEndLine(); \r
- m->mothurOutEndLine();\r
- }\r
-\r
- return 0;\r
- }\r
- catch(exception& e) {\r
- m->errorOut(e, "ClearcutCommand", "execute");\r
- exit(1);\r
- }\r
-}\r
-/**************************************************************************************/\r
-\r
-\r
-\r
-\r
+/*
+ * clearcutcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 5/11/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "clearcutcommand.h"
+
+/**************************************************************************************/
+ClearcutCommand::ClearcutCommand(string option) {
+ try {
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta","phylip","version","verbose","quiet","seed","norandom","shuffle","neighbor","expblen",
+ "expdist","ntrees","matrixout","stdout","kimura","jukes","protein","DNA","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("phylip");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["phylip"] = inputDir + it->second; }
+ }
+ }
+
+ //check for required parameters
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { fastafile = ""; abort = true; }
+ else if (fastafile == "not found") { fastafile = ""; }
+ else { inputFile = fastafile; }
+
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not open") { phylipfile = ""; abort = true; }
+ else if (phylipfile == "not found") { phylipfile = ""; }
+ else { inputFile = phylipfile; }
+
+ if ((phylipfile == "") && (fastafile == "")) { m->mothurOut("You must provide either a phylip formatted distance matrix or an aligned fasta file."); m->mothurOutEndLine(); abort=true; }
+ if ((phylipfile != "") && (fastafile != "")) { m->mothurOut("You must provide either a phylip formatted distance matrix or an aligned fasta file, not BOTH."); m->mothurOutEndLine(); abort=true; }
+
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ string temp;
+ temp = validParameter.validFile(parameters, "version", false); if (temp == "not found"){ temp = "F"; }
+ version = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "verbose", false); if (temp == "not found"){ temp = "F"; }
+ verbose = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "quiet", false); if (temp == "not found"){ temp = "F"; }
+ quiet = isTrue(temp);
+
+ seed = validParameter.validFile(parameters, "seed", false); if (seed == "not found"){ seed = "*"; }
+
+ temp = validParameter.validFile(parameters, "norandom", false); if (temp == "not found"){ temp = "F"; }
+ norandom = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "shuffle", false); if (temp == "not found"){ temp = "F"; }
+ shuffle = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "neighbor", false); if (temp == "not found"){ temp = "F"; }
+ neighbor = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "DNA", false); if (temp == "not found"){ temp = "F"; }
+ DNA = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "protein", false); if (temp == "not found"){ temp = "F"; }
+ protein = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "jukes", false); if (temp == "not found"){ temp = "F"; }
+ jukes = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "kimura", false); if (temp == "not found"){ temp = "F"; }
+ kimura = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "stdout", false); if (temp == "not found"){ temp = "F"; }
+ stdoutWanted = isTrue(temp);
+
+ matrixout = validParameter.validFile(parameters, "matrixout", false); if (matrixout == "not found"){ matrixout = ""; }
+
+ ntrees = validParameter.validFile(parameters, "ntrees", false); if (ntrees == "not found"){ ntrees = "1"; }
+
+ temp = validParameter.validFile(parameters, "expblen", false); if (temp == "not found"){ temp = "F"; }
+ expblen = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "expdist", false); if (temp == "not found"){ temp = "F"; }
+ expdist = isTrue(temp);
+
+ if ((fastafile != "") && ((!DNA) && (!protein))) { m->mothurOut("You must specify the type of sequences you are using: DNA or protein"); m->mothurOutEndLine(); abort=true; }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "ClearcutCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void ClearcutCommand::help(){
+ try {
+ m->mothurOut("The clearcut command interfaces mothur with the clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.\n");
+ m->mothurOut("For more information about clearcut refer to http://bioinformatics.hungry.com/clearcut/ \n");
+ m->mothurOut("The clearcut executable must be in a folder called clearcut in the same folder as your mothur executable, similar to mothur's requirements for using blast. \n");
+ m->mothurOut("The clearcut command parameters are phylip, fasta, version, verbose, quiet, seed, norandom, shuffle, neighbor, expblen, expdist, ntrees, matrixout, stdout, kimura, jukes, protein, DNA. \n");
+ m->mothurOut("The phylip parameter allows you to enter your phylip formatted distance matrix. \n");
+ m->mothurOut("The fasta parameter allows you to enter your aligned fasta file, if you enter a fastafile you specify if the sequences are DNA or protein using the DNA or protein parameters. \n");
+
+ m->mothurOut("The version parameter prints out the version of clearcut you are using, default=F. \n");
+ m->mothurOut("The verbose parameter prints out more output from clearcut, default=F. \n");
+ m->mothurOut("The quiet parameter turns on silent operation mode, default=F. \n");
+ m->mothurOut("The seed parameter allows you to explicitly set the PRNG seed to a specific value. \n");
+ m->mothurOut("The norandom parameter allows you to attempt joins deterministically, default=F. \n");
+ m->mothurOut("The shuffle parameter allows you to randomly shuffle the distance matrix, default=F. \n");
+ m->mothurOut("The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=F. \n");
+
+ m->mothurOut("The DNA parameter allows you to indicate your fasta file contains DNA sequences, default=F. \n");
+ m->mothurOut("The protein parameter allows you to indicate your fasta file contains protein sequences, default=F. \n");
+
+ m->mothurOut("The stdout parameter outputs your tree to STDOUT, default=F. \n");
+ m->mothurOut("The matrixout parameter allows you to specify a filename to output a distance matrix to. \n");
+ m->mothurOut("The ntrees parameter allows you to specify the number of output trees, default=1. \n");
+ m->mothurOut("The expblen parameter allows you to use exponential notation for branch lengths, default=F. \n");
+ m->mothurOut("The expdist parameter allows you to use exponential notation for distance outputs, default=F. \n");
+
+ m->mothurOut("The clearcut command should be in the following format: \n");
+ m->mothurOut("clearcut(phylip=yourDistanceFile) \n");
+ m->mothurOut("Example: clearcut(phylip=abrecovery.phylip.dist) \n");
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "help");
+ exit(1);
+ }
+}
+
+/**************************************************************************************/
+int ClearcutCommand::execute() {
+ try {
+
+ if (abort == true) { return 0; }
+
+ //prepare filename
+ string outputName = outputDir + getRootName(getSimpleName(inputFile)) + "tre";
+
+ //get location of clearcut
+ GlobalData* globaldata = GlobalData::getInstance();
+ string path = globaldata->argv;
+ path = path.substr(0, (path.find_last_of('m')));
+
+ string clearcutCommand = "";
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ clearcutCommand = path + "clearcut/clearcut ";
+ #else
+ clearcutCommand = path + "clearcut\\clearcut ";
+ #endif
+
+ //you gave us a distance matrix
+ if (phylipfile != "") { clearcutCommand += "--distance "; }
+
+ //you gave us a fastafile
+ if (fastafile != "") { clearcutCommand += "--alignment "; }
+
+ if (version) { clearcutCommand += "--version "; }
+ if (verbose) { clearcutCommand += "--verbose "; }
+ if (quiet) { clearcutCommand += "--quiet "; }
+ if (seed != "*") { clearcutCommand += "--seed=" + seed + " "; }
+ if (norandom) { clearcutCommand += "--norandom "; }
+ if (shuffle) { clearcutCommand += "--shuffle "; }
+ if (neighbor) { clearcutCommand += "--neighbor "; }
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ clearcutCommand += "--in=" + inputFile + " ";
+ #else
+ clearcutCommand += "--in=\"" + inputFile + "\" ";
+ #endif
+
+ if (stdoutWanted) { clearcutCommand += "--stdout "; }
+ else{
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ clearcutCommand += "--out=" + outputName + " "; }
+ #else
+ clearcutCommand += "--out=\"" + outputName + "\" "; }
+ #endif
+
+ if (DNA) { clearcutCommand += "--DNA "; }
+ if (protein) { clearcutCommand += "--protein "; }
+ if (jukes) { clearcutCommand += "--jukes "; }
+ if (kimura) { clearcutCommand += "--kimura "; }
+ if (matrixout != "") { clearcutCommand += "--matrixout=" + matrixout + " "; }
+ if (ntrees != "1") { clearcutCommand += "--ntrees=" + ntrees + " "; }
+ if (expblen) { clearcutCommand += "--expblen "; }
+ if (expdist) { clearcutCommand += "--expdist "; }
+
+ //run clearcut
+ system(clearcutCommand.c_str());
+
+ if (!stdoutWanted) {
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputName); m->mothurOutEndLine();
+ if (matrixout != "") { m->mothurOut(matrixout); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "execute");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+
+
+
+
-###################################################\r
-#\r
-# Makefile for mothur\r
-# Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]\r
-# Created: April 16, 2010\r
-#\r
-###################################################\r
-\r
-#\r
-# Macros\r
-#\r
-\r
-CC = g++\r
-CC_OPTIONS = -O3\r
-\r
-# if you do not want to use the readline library set to no, default yes.\r
-# make sure you have the library installed\r
-\r
-USEREADLINE ?= yes\r
-\r
-ifeq ($(strip $(USEREADLINE)),yes)\r
- CC_OPTIONS += -DUSE_READLINE\r
- LNK_OPTIONS += \\r
- -lreadline\\r
- -lncurses\\r
- -L../readline-6.0\r
-endif\r
-\r
+###################################################
+#
+# Makefile for mothur
+# Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]
+# Created: April 16, 2010
+#
+###################################################
+
+#
+# Macros
+#
+
+CC = g++
+CC_OPTIONS = -O3
+
+# if you do not want to use the readline library set to no, default yes.
+# make sure you have the library installed
+
+USEREADLINE ?= yes
+
+ifeq ($(strip $(USEREADLINE)),yes)
+ CC_OPTIONS += -DUSE_READLINE
+ LNK_OPTIONS += \
+ -lreadline\
+ -lncurses\
+ -L../readline-6.0
+endif
+
USEMPI ?= no
-\r
-\r
-ifeq ($(strip $(USEMPI)),yes)\r
- CC_OPTIONS += -DUSE_MPI\r
-endif\r
-\r
-#\r
-# INCLUDE directories for mothur\r
-#\r
+
+
+ifeq ($(strip $(USEMPI)),yes)
+ CC_OPTIONS += -DUSE_MPI
+endif
+
+#
+# INCLUDE directories for mothur
+#
INCLUDE = -I.
-\r
-#\r
-# Build mothur\r
-#\r
-\r
-mothur : \\r
- ./sharedutilities.o\\r
- ./treegroupscommand.o\\r
- ./bootstrapsharedcommand.o\\r
- ./matrixoutputcommand.o\\r
- ./getoturepcommand.o\\r
- ./screenseqscommand.o\\r
- ./chimera.o\\r
- ./decalc.o\\r
- ./readotucommand.o\\r
- ./readdistcommand.o\\r
- ./commandfactory.o\\r
- ./alignment.o\\r
- ./alignmentcell.o\\r
- ./gotohoverlap.o\\r
- ./overlap.o\\r
- ./needlemanoverlap.o\\r
- ./blastalign.o\\r
- ./noalign.o\\r
- ./suffixdb.o\\r
- ./suffixnodes.o\\r
- ./suffixtree.o\\r
- ./blastdb.o\\r
- ./nast.o\\r
- ./nastreport.o\\r
- ./boneh.o\\r
- ./efron.o\\r
- ./solow.o\\r
- ./unifracweightedcommand.o\\r
- ./weighted.o\\r
- ./unweighted.o\\r
- ./unifracunweightedcommand.o\\r
- ./getsabundcommand.o\\r
- ./getrabundcommand.o\\r
- ./bellerophon.o\\r
- ./pintail.o\\r
- ./sharedanderbergs.o\\r
- ./venncommand.o\\r
- ./venn.o\\r
- ./fullmatrix.o\\r
- ./heatmap.o\\r
- ./heatmapcommand.o\\r
- ./libshuffcommand.o\\r
- ./nocommands.o\\r
- ./sharedbraycurtis.o\\r
- ./sharedkulczynski.o\\r
- ./sharedlennon.o\\r
- ./sharedkulczynskicody.o\\r
- ./sharedmorisitahorn.o\\r
- ./sharedochiai.o\\r
- ./readcolumn.o\\r
- ./readotu.o\\r
- ./readphylip.o\\r
- ./consensuscommand.o\\r
- ./heatmapsimcommand.o\\r
- ./heatmapsim.o\\r
- ./optionparser.o\\r
- ./filterseqscommand.o\\r
- ./goodscoverage.o\\r
- ./sequencedb.o\\r
- ./sharedjackknife.o\\r
- ./sharedmarczewski.o\\r
- ./aligncommand.o\\r
- ./treemap.o\\r
- ./parsimonycommand.o\\r
- ./parsimony.o\\r
- ./seqsummarycommand.o\\r
- ./chimeraccodecommand.o\\r
- ./chimerabellerophoncommand.o\\r
- ./chimeracheckcommand.o\\r
- ./chimeraslayercommand.o\\r
- ./chimerapintailcommand.o\\r
- ./chimeraseqscommand.o\\r
- ./sharedlistvector.o\\r
- ./tree.o\\r
- ./readtree.o\\r
- ./sharedsobscollectsummary.o\\r
- ./deconvolutecommand.o\\r
- ./listseqscommand.o\\r
- ./getseqscommand.o\\r
- ./removeseqscommand.o\\r
- ./systemcommand.o\\r
- ./binsequencecommand.o\\r
- ./distancecommand.o\\r
- ./ace.o\\r
- ./averagelinkage.o\\r
- ./bootstrap.o\\r
- ./calculator.o\\r
- ./chao1.o\\r
- ./cluster.o\\r
- ./clustercommand.o\\r
- ./collect.o\\r
- ./collectcommand.o\\r
- ./collectsharedcommand.o\\r
- ./commandoptionparser.o\\r
- ./completelinkage.o\\r
- ./database.o\\r
- ./engine.o\\r
- ./fastamap.o\\r
- ./fileoutput.o\\r
- ./globaldata.o\\r
- ./groupmap.o\\r
+
+#
+# Build mothur
+#
+
+mothur : \
+ ./sharedutilities.o\
+ ./treegroupscommand.o\
+ ./bootstrapsharedcommand.o\
+ ./matrixoutputcommand.o\
+ ./getoturepcommand.o\
+ ./screenseqscommand.o\
+ ./chimera.o\
+ ./decalc.o\
+ ./readotucommand.o\
+ ./readdistcommand.o\
+ ./commandfactory.o\
+ ./alignment.o\
+ ./alignmentcell.o\
+ ./gotohoverlap.o\
+ ./overlap.o\
+ ./needlemanoverlap.o\
+ ./blastalign.o\
+ ./noalign.o\
+ ./suffixdb.o\
+ ./suffixnodes.o\
+ ./suffixtree.o\
+ ./blastdb.o\
+ ./nast.o\
+ ./nastreport.o\
+ ./boneh.o\
+ ./efron.o\
+ ./solow.o\
+ ./unifracweightedcommand.o\
+ ./weighted.o\
+ ./unweighted.o\
+ ./unifracunweightedcommand.o\
+ ./getsabundcommand.o\
+ ./getrabundcommand.o\
+ ./bellerophon.o\
+ ./pintail.o\
+ ./sharedanderbergs.o\
+ ./venncommand.o\
+ ./venn.o\
+ ./fullmatrix.o\
+ ./heatmap.o\
+ ./heatmapcommand.o\
+ ./libshuffcommand.o\
+ ./nocommands.o\
+ ./sharedbraycurtis.o\
+ ./sharedkulczynski.o\
+ ./sharedlennon.o\
+ ./sharedkulczynskicody.o\
+ ./sharedmorisitahorn.o\
+ ./sharedochiai.o\
+ ./readcolumn.o\
+ ./readotu.o\
+ ./readphylip.o\
+ ./consensuscommand.o\
+ ./heatmapsimcommand.o\
+ ./heatmapsim.o\
+ ./optionparser.o\
+ ./filterseqscommand.o\
+ ./goodscoverage.o\
+ ./sequencedb.o\
+ ./sharedjackknife.o\
+ ./sharedmarczewski.o\
+ ./aligncommand.o\
+ ./treemap.o\
+ ./parsimonycommand.o\
+ ./parsimony.o\
+ ./seqsummarycommand.o\
+ ./chimeraccodecommand.o\
+ ./chimerabellerophoncommand.o\
+ ./chimeracheckcommand.o\
+ ./chimeraslayercommand.o\
+ ./chimerapintailcommand.o\
+ ./chimeraseqscommand.o\
+ ./sharedlistvector.o\
+ ./tree.o\
+ ./readtree.o\
+ ./sharedsobscollectsummary.o\
+ ./deconvolutecommand.o\
+ ./listseqscommand.o\
+ ./getseqscommand.o\
+ ./removeseqscommand.o\
+ ./systemcommand.o\
+ ./binsequencecommand.o\
+ ./distancecommand.o\
+ ./ace.o\
+ ./averagelinkage.o\
+ ./bootstrap.o\
+ ./calculator.o\
+ ./chao1.o\
+ ./cluster.o\
+ ./clustercommand.o\
+ ./collect.o\
+ ./collectcommand.o\
+ ./collectsharedcommand.o\
+ ./commandoptionparser.o\
+ ./completelinkage.o\
+ ./database.o\
+ ./engine.o\
+ ./fastamap.o\
+ ./fileoutput.o\
+ ./globaldata.o\
+ ./groupmap.o\
./helpcommand.o\
./makegroupcommand.o\
./chopseqscommand.o\
./clearcutcommand.o\
- ./catchallcommand.o\\r
- ./inputdata.o\\r
- ./jackknife.o\\r
- ./kmer.o\\r
- ./kmerdb.o\\r
- ./listvector.o\\r
- ./mothur.o\\r
- ./nameassignment.o\\r
- ./npshannon.o\\r
- ./ordervector.o\\r
- ./progress.o\\r
- ./quitcommand.o\\r
- ./rabundvector.o\\r
- ./rarecalc.o\\r
- ./raredisplay.o\\r
- ./rarefact.o\\r
- ./rarefactcommand.o\\r
- ./rarefactsharedcommand.o\\r
- ./sabundvector.o\\r
- ./sequence.o\\r
- ./shannon.o\\r
- ./sharedace.o\\r
- ./sharedchao1.o\\r
- ./sharedcommand.o\\r
- ./sharedjabund.o\\r
- ./sharedjclass.o\\r
- ./sharedjest.o\\r
- ./sharedordervector.o\\r
- ./sharedrabundvector.o\\r
- ./sharedsabundvector.o\\r
- ./sharedsobs.o\\r
- ./sharedsorabund.o\\r
- ./sharedsorclass.o\\r
- ./sharedsorest.o\\r
- ./sharedthetan.o\\r
- ./sharedthetayc.o\\r
- ./simpson.o\\r
- ./singlelinkage.o\\r
- ./sparsematrix.o\\r
- ./summarycommand.o\\r
- ./summarysharedcommand.o\\r
- ./uvest.o\\r
- ./validcalculator.o\\r
- ./validparameter.o\\r
- ./treenode.o\\r
- ./readtreecommand.o\\r
- ./reversecommand.o\\r
- ./trimseqscommand.o\\r
- ./slibshuff.o\\r
- ./libshuff.o\\r
- ./dlibshuff.o\\r
- ./mergefilecommand.o\\r
- ./coverage.o\\r
- ./whittaker.o\\r
- ./preclustercommand.o\\r
- ./otuhierarchycommand.o\\r
- ./setdircommand.o\\r
- ./getgroupcommand.o\\r
- ./getlabelcommand.o\\r
- ./secondarystructurecommand.o\\r
- ./mothurout.o\\r
- ./parselistscommand.o\\r
- ./readblast.o\\r
- ./chimeracheckrdp.o\\r
- ./hclustercommand.o\\r
- ./hcluster.o\\r
- ./getlistcountcommand.o\\r
- ./readcluster.o\\r
- ./ccode.o\\r
- ./taxonomyequalizer.o\\r
- ./phylotypecommand.o\\r
- ./classifyseqscommand.o\\r
- ./parsesffcommand.o\\r
- ./classify.o\\r
+ ./catchallcommand.o\
+ ./splitabundcommand.o\
+ ./inputdata.o\
+ ./jackknife.o\
+ ./kmer.o\
+ ./kmerdb.o\
+ ./listvector.o\
+ ./mothur.o\
+ ./nameassignment.o\
+ ./npshannon.o\
+ ./ordervector.o\
+ ./progress.o\
+ ./quitcommand.o\
+ ./rabundvector.o\
+ ./rarecalc.o\
+ ./raredisplay.o\
+ ./rarefact.o\
+ ./rarefactcommand.o\
+ ./rarefactsharedcommand.o\
+ ./sabundvector.o\
+ ./sequence.o\
+ ./shannon.o\
+ ./sharedace.o\
+ ./sharedchao1.o\
+ ./sharedcommand.o\
+ ./sharedjabund.o\
+ ./sharedjclass.o\
+ ./sharedjest.o\
+ ./sharedordervector.o\
+ ./sharedrabundvector.o\
+ ./sharedsabundvector.o\
+ ./sharedsobs.o\
+ ./sharedsorabund.o\
+ ./sharedsorclass.o\
+ ./sharedsorest.o\
+ ./sharedthetan.o\
+ ./sharedthetayc.o\
+ ./simpson.o\
+ ./singlelinkage.o\
+ ./sparsematrix.o\
+ ./summarycommand.o\
+ ./summarysharedcommand.o\
+ ./uvest.o\
+ ./validcalculator.o\
+ ./validparameter.o\
+ ./treenode.o\
+ ./readtreecommand.o\
+ ./reversecommand.o\
+ ./trimseqscommand.o\
+ ./slibshuff.o\
+ ./libshuff.o\
+ ./dlibshuff.o\
+ ./mergefilecommand.o\
+ ./coverage.o\
+ ./whittaker.o\
+ ./preclustercommand.o\
+ ./otuhierarchycommand.o\
+ ./setdircommand.o\
+ ./getgroupcommand.o\
+ ./getlabelcommand.o\
+ ./secondarystructurecommand.o\
+ ./mothurout.o\
+ ./parselistscommand.o\
+ ./readblast.o\
+ ./chimeracheckrdp.o\
+ ./hclustercommand.o\
+ ./hcluster.o\
+ ./getlistcountcommand.o\
+ ./readcluster.o\
+ ./ccode.o\
+ ./taxonomyequalizer.o\
+ ./phylotypecommand.o\
+ ./classifyseqscommand.o\
+ ./parsesffcommand.o\
+ ./classify.o\
./phylotree.o\
./phylodiversity.o\
- ./phylodiversitycommand.o\\r
+ ./phylodiversitycommand.o\
./bayesian.o\
- ./phylosummary.o\\r
- ./alignmentdb.o\\r
- ./knn.o\\r
- ./distancedb.o\\r
- ./chimeraslayer.o\\r
- ./slayer.o\\r
- ./pcacommand.o\\r
- ./formatcolumn.o\\r
- ./formatphylip.o\\r
- ./mgclustercommand.o\\r
- ./getsharedotucommand.o\\r
- ./maligner.o\\r
- ./chimerarealigner.o\\r
- ./bergerparker.o\\r
- ./bstick.o\\r
- ./sharedkstest.o\\r
- ./qstat.o\\r
- ./shen.o\\r
- ./logsd.o\\r
+ ./phylosummary.o\
+ ./alignmentdb.o\
+ ./knn.o\
+ ./distancedb.o\
+ ./chimeraslayer.o\
+ ./slayer.o\
+ ./pcacommand.o\
+ ./formatcolumn.o\
+ ./formatphylip.o\
+ ./mgclustercommand.o\
+ ./getsharedotucommand.o\
+ ./maligner.o\
+ ./chimerarealigner.o\
+ ./bergerparker.o\
+ ./bstick.o\
+ ./sharedkstest.o\
+ ./qstat.o\
+ ./shen.o\
+ ./logsd.o\
./geom.o\
- ./setlogfilecommand.o\r
- $(CC) $(LNK_OPTIONS) \\r
- ./sharedutilities.o\\r
- ./treegroupscommand.o\\r
- ./bootstrapsharedcommand.o\\r
- ./matrixoutputcommand.o\\r
- ./getoturepcommand.o\\r
- ./screenseqscommand.o\\r
- ./chimera.o\\r
- ./decalc.o\\r
- ./readotucommand.o\\r
- ./readdistcommand.o\\r
- ./commandfactory.o\\r
- ./alignment.o\\r
- ./alignmentcell.o\\r
- ./gotohoverlap.o\\r
- ./overlap.o\\r
- ./needlemanoverlap.o\\r
- ./blastalign.o\\r
- ./noalign.o\\r
- ./suffixdb.o\\r
- ./suffixnodes.o\\r
- ./suffixtree.o\\r
- ./blastdb.o\\r
- ./nast.o\\r
- ./nastreport.o\\r
- ./boneh.o\\r
- ./efron.o\\r
- ./solow.o\\r
- ./unifracweightedcommand.o\\r
- ./weighted.o\\r
- ./unweighted.o\\r
- ./unifracunweightedcommand.o\\r
- ./getsabundcommand.o\\r
- ./getrabundcommand.o\\r
- ./bellerophon.o\\r
- ./pintail.o\\r
- ./sharedanderbergs.o\\r
- ./venncommand.o\\r
- ./venn.o\\r
- ./fullmatrix.o\\r
- ./heatmap.o\\r
- ./heatmapcommand.o\\r
- ./libshuffcommand.o\\r
- ./nocommands.o\\r
- ./sharedbraycurtis.o\\r
- ./sharedkulczynski.o\\r
- ./sharedlennon.o\\r
- ./sharedkulczynskicody.o\\r
- ./sharedmorisitahorn.o\\r
- ./sharedochiai.o\\r
- ./readcolumn.o\\r
- ./readotu.o\\r
- ./readphylip.o\\r
- ./consensuscommand.o\\r
- ./heatmapsimcommand.o\\r
- ./heatmapsim.o\\r
- ./optionparser.o\\r
- ./filterseqscommand.o\\r
- ./goodscoverage.o\\r
- ./sequencedb.o\\r
- ./sharedjackknife.o\\r
- ./sharedmarczewski.o\\r
- ./aligncommand.o\\r
- ./treemap.o\\r
- ./parsimonycommand.o\\r
- ./parsimony.o\\r
- ./seqsummarycommand.o\\r
- ./chimeraccodecommand.o\\r
- ./chimerabellerophoncommand.o\\r
- ./chimeracheckcommand.o\\r
- ./chimeraslayercommand.o\\r
- ./chimerapintailcommand.o\\r
- ./chimeraseqscommand.o\\r
- ./sharedlistvector.o\\r
- ./tree.o\\r
- ./readtree.o\\r
- ./sharedsobscollectsummary.o\\r
- ./deconvolutecommand.o\\r
- ./listseqscommand.o\\r
- ./getseqscommand.o\\r
- ./removeseqscommand.o\\r
- ./systemcommand.o\\r
- ./binsequencecommand.o\\r
- ./distancecommand.o\\r
- ./ace.o\\r
- ./averagelinkage.o\\r
- ./bootstrap.o\\r
- ./calculator.o\\r
- ./chao1.o\\r
- ./cluster.o\\r
- ./clustercommand.o\\r
- ./collect.o\\r
- ./collectcommand.o\\r
- ./collectsharedcommand.o\\r
- ./commandoptionparser.o\\r
- ./completelinkage.o\\r
- ./database.o\\r
- ./engine.o\\r
- ./fastamap.o\\r
- ./fileoutput.o\\r
- ./globaldata.o\\r
- ./groupmap.o\\r
+ ./setlogfilecommand.o
+ $(CC) $(LNK_OPTIONS) \
+ ./sharedutilities.o\
+ ./treegroupscommand.o\
+ ./bootstrapsharedcommand.o\
+ ./matrixoutputcommand.o\
+ ./getoturepcommand.o\
+ ./screenseqscommand.o\
+ ./chimera.o\
+ ./decalc.o\
+ ./readotucommand.o\
+ ./readdistcommand.o\
+ ./commandfactory.o\
+ ./alignment.o\
+ ./alignmentcell.o\
+ ./gotohoverlap.o\
+ ./overlap.o\
+ ./needlemanoverlap.o\
+ ./blastalign.o\
+ ./noalign.o\
+ ./suffixdb.o\
+ ./suffixnodes.o\
+ ./suffixtree.o\
+ ./blastdb.o\
+ ./nast.o\
+ ./nastreport.o\
+ ./boneh.o\
+ ./efron.o\
+ ./solow.o\
+ ./unifracweightedcommand.o\
+ ./weighted.o\
+ ./unweighted.o\
+ ./unifracunweightedcommand.o\
+ ./getsabundcommand.o\
+ ./getrabundcommand.o\
+ ./bellerophon.o\
+ ./pintail.o\
+ ./sharedanderbergs.o\
+ ./venncommand.o\
+ ./venn.o\
+ ./fullmatrix.o\
+ ./heatmap.o\
+ ./heatmapcommand.o\
+ ./libshuffcommand.o\
+ ./nocommands.o\
+ ./sharedbraycurtis.o\
+ ./sharedkulczynski.o\
+ ./sharedlennon.o\
+ ./sharedkulczynskicody.o\
+ ./sharedmorisitahorn.o\
+ ./sharedochiai.o\
+ ./readcolumn.o\
+ ./readotu.o\
+ ./readphylip.o\
+ ./consensuscommand.o\
+ ./heatmapsimcommand.o\
+ ./heatmapsim.o\
+ ./optionparser.o\
+ ./filterseqscommand.o\
+ ./goodscoverage.o\
+ ./sequencedb.o\
+ ./sharedjackknife.o\
+ ./sharedmarczewski.o\
+ ./aligncommand.o\
+ ./treemap.o\
+ ./parsimonycommand.o\
+ ./parsimony.o\
+ ./seqsummarycommand.o\
+ ./chimeraccodecommand.o\
+ ./chimerabellerophoncommand.o\
+ ./chimeracheckcommand.o\
+ ./chimeraslayercommand.o\
+ ./chimerapintailcommand.o\
+ ./chimeraseqscommand.o\
+ ./sharedlistvector.o\
+ ./tree.o\
+ ./readtree.o\
+ ./sharedsobscollectsummary.o\
+ ./deconvolutecommand.o\
+ ./listseqscommand.o\
+ ./getseqscommand.o\
+ ./removeseqscommand.o\
+ ./systemcommand.o\
+ ./binsequencecommand.o\
+ ./distancecommand.o\
+ ./ace.o\
+ ./averagelinkage.o\
+ ./bootstrap.o\
+ ./calculator.o\
+ ./chao1.o\
+ ./cluster.o\
+ ./clustercommand.o\
+ ./collect.o\
+ ./collectcommand.o\
+ ./collectsharedcommand.o\
+ ./commandoptionparser.o\
+ ./completelinkage.o\
+ ./database.o\
+ ./engine.o\
+ ./fastamap.o\
+ ./fileoutput.o\
+ ./globaldata.o\
+ ./groupmap.o\
./helpcommand.o\
./makegroupcommand.o\
./chopseqscommand.o\
./clearcutcommand.o\
- ./catchallcommand.o\\r
- ./inputdata.o\\r
- ./jackknife.o\\r
- ./kmer.o\\r
- ./kmerdb.o\\r
- ./listvector.o\\r
- ./mothur.o\\r
- ./nameassignment.o\\r
- ./npshannon.o\\r
- ./ordervector.o\\r
- ./progress.o\\r
- ./quitcommand.o\\r
- ./rabundvector.o\\r
- ./rarecalc.o\\r
- ./raredisplay.o\\r
- ./rarefact.o\\r
- ./rarefactcommand.o\\r
- ./rarefactsharedcommand.o\\r
- ./sabundvector.o\\r
- ./sequence.o\\r
- ./shannon.o\\r
- ./sharedace.o\\r
- ./sharedchao1.o\\r
- ./sharedcommand.o\\r
- ./sharedjabund.o\\r
- ./sharedjclass.o\\r
- ./sharedjest.o\\r
- ./sharedordervector.o\\r
- ./sharedrabundvector.o\\r
- ./sharedsabundvector.o\\r
- ./sharedsobs.o\\r
- ./sharedsorabund.o\\r
- ./sharedsorclass.o\\r
- ./sharedsorest.o\\r
- ./sharedthetan.o\\r
- ./sharedthetayc.o\\r
- ./simpson.o\\r
- ./singlelinkage.o\\r
- ./sparsematrix.o\\r
- ./summarycommand.o\\r
- ./summarysharedcommand.o\\r
- ./uvest.o\\r
- ./validcalculator.o\\r
- ./validparameter.o\\r
- ./treenode.o\\r
- ./readtreecommand.o\\r
- ./reversecommand.o\\r
- ./trimseqscommand.o\\r
- ./slibshuff.o\\r
- ./libshuff.o\\r
- ./dlibshuff.o\\r
- ./mergefilecommand.o\\r
- ./coverage.o\\r
- ./whittaker.o\\r
- ./preclustercommand.o\\r
- ./otuhierarchycommand.o\\r
- ./setdircommand.o\\r
- ./getgroupcommand.o\\r
- ./getlabelcommand.o\\r
- ./secondarystructurecommand.o\\r
- ./mothurout.o\\r
- ./parselistscommand.o\\r
- ./readblast.o\\r
- ./chimeracheckrdp.o\\r
- ./hclustercommand.o\\r
- ./hcluster.o\\r
- ./getlistcountcommand.o\\r
- ./readcluster.o\\r
- ./ccode.o\\r
- ./taxonomyequalizer.o\\r
- ./phylotypecommand.o\\r
- ./classifyseqscommand.o\\r
- ./parsesffcommand.o\\r
- ./classify.o\\r
+ ./catchallcommand.o\
+ ./splitabundcommand.o\
+ ./inputdata.o\
+ ./jackknife.o\
+ ./kmer.o\
+ ./kmerdb.o\
+ ./listvector.o\
+ ./mothur.o\
+ ./nameassignment.o\
+ ./npshannon.o\
+ ./ordervector.o\
+ ./progress.o\
+ ./quitcommand.o\
+ ./rabundvector.o\
+ ./rarecalc.o\
+ ./raredisplay.o\
+ ./rarefact.o\
+ ./rarefactcommand.o\
+ ./rarefactsharedcommand.o\
+ ./sabundvector.o\
+ ./sequence.o\
+ ./shannon.o\
+ ./sharedace.o\
+ ./sharedchao1.o\
+ ./sharedcommand.o\
+ ./sharedjabund.o\
+ ./sharedjclass.o\
+ ./sharedjest.o\
+ ./sharedordervector.o\
+ ./sharedrabundvector.o\
+ ./sharedsabundvector.o\
+ ./sharedsobs.o\
+ ./sharedsorabund.o\
+ ./sharedsorclass.o\
+ ./sharedsorest.o\
+ ./sharedthetan.o\
+ ./sharedthetayc.o\
+ ./simpson.o\
+ ./singlelinkage.o\
+ ./sparsematrix.o\
+ ./summarycommand.o\
+ ./summarysharedcommand.o\
+ ./uvest.o\
+ ./validcalculator.o\
+ ./validparameter.o\
+ ./treenode.o\
+ ./readtreecommand.o\
+ ./reversecommand.o\
+ ./trimseqscommand.o\
+ ./slibshuff.o\
+ ./libshuff.o\
+ ./dlibshuff.o\
+ ./mergefilecommand.o\
+ ./coverage.o\
+ ./whittaker.o\
+ ./preclustercommand.o\
+ ./otuhierarchycommand.o\
+ ./setdircommand.o\
+ ./getgroupcommand.o\
+ ./getlabelcommand.o\
+ ./secondarystructurecommand.o\
+ ./mothurout.o\
+ ./parselistscommand.o\
+ ./readblast.o\
+ ./chimeracheckrdp.o\
+ ./hclustercommand.o\
+ ./hcluster.o\
+ ./getlistcountcommand.o\
+ ./readcluster.o\
+ ./ccode.o\
+ ./taxonomyequalizer.o\
+ ./phylotypecommand.o\
+ ./classifyseqscommand.o\
+ ./parsesffcommand.o\
+ ./classify.o\
./phylotree.o\
./phylodiversity.o\
- ./phylodiversitycommand.o\\r
+ ./phylodiversitycommand.o\
./bayesian.o\
- ./phylosummary.o\\r
- ./alignmentdb.o\\r
- ./knn.o\\r
- ./distancedb.o\\r
- ./chimeraslayer.o\\r
- ./slayer.o\\r
- ./pcacommand.o\\r
- ./formatcolumn.o\\r
- ./formatphylip.o\\r
- ./mgclustercommand.o\\r
- ./getsharedotucommand.o\\r
- ./maligner.o\\r
- ./chimerarealigner.o\\r
- ./bergerparker.o\\r
- ./bstick.o\\r
- ./sharedkstest.o\\r
- ./qstat.o\\r
- ./shen.o\\r
- ./logsd.o\\r
+ ./phylosummary.o\
+ ./alignmentdb.o\
+ ./knn.o\
+ ./distancedb.o\
+ ./chimeraslayer.o\
+ ./slayer.o\
+ ./pcacommand.o\
+ ./formatcolumn.o\
+ ./formatphylip.o\
+ ./mgclustercommand.o\
+ ./getsharedotucommand.o\
+ ./maligner.o\
+ ./chimerarealigner.o\
+ ./bergerparker.o\
+ ./bstick.o\
+ ./sharedkstest.o\
+ ./qstat.o\
+ ./shen.o\
+ ./logsd.o\
./geom.o\
- ./setlogfilecommand.o\\r
- -o ../Release/mothur\r
-\r
-clean : \r
- rm \\r
- ./sharedutilities.o\\r
- ./treegroupscommand.o\\r
- ./bootstrapsharedcommand.o\\r
- ./matrixoutputcommand.o\\r
- ./getoturepcommand.o\\r
- ./screenseqscommand.o\\r
- ./chimera.o\\r
- ./decalc.o\\r
- ./readotucommand.o\\r
- ./readdistcommand.o\\r
- ./commandfactory.o\\r
- ./alignment.o\\r
- ./alignmentcell.o\\r
- ./gotohoverlap.o\\r
- ./overlap.o\\r
- ./needlemanoverlap.o\\r
- ./blastalign.o\\r
- ./noalign.o\\r
- ./suffixdb.o\\r
- ./suffixnodes.o\\r
- ./suffixtree.o\\r
- ./blastdb.o\\r
- ./nast.o\\r
- ./nastreport.o\\r
- ./boneh.o\\r
- ./efron.o\\r
- ./solow.o\\r
- ./unifracweightedcommand.o\\r
- ./weighted.o\\r
- ./unweighted.o\\r
- ./unifracunweightedcommand.o\\r
- ./getsabundcommand.o\\r
- ./getrabundcommand.o\\r
- ./bellerophon.o\\r
- ./pintail.o\\r
- ./sharedanderbergs.o\\r
- ./venncommand.o\\r
- ./venn.o\\r
- ./fullmatrix.o\\r
- ./heatmap.o\\r
- ./heatmapcommand.o\\r
- ./libshuffcommand.o\\r
- ./nocommands.o\\r
- ./sharedbraycurtis.o\\r
- ./sharedkulczynski.o\\r
- ./sharedlennon.o\\r
- ./sharedkulczynskicody.o\\r
- ./sharedmorisitahorn.o\\r
- ./sharedochiai.o\\r
- ./readcolumn.o\\r
- ./readotu.o\\r
- ./readphylip.o\\r
- ./consensuscommand.o\\r
- ./heatmapsimcommand.o\\r
- ./heatmapsim.o\\r
- ./optionparser.o\\r
- ./filterseqscommand.o\\r
- ./goodscoverage.o\\r
- ./sequencedb.o\\r
- ./sharedjackknife.o\\r
- ./sharedmarczewski.o\\r
- ./aligncommand.o\\r
- ./treemap.o\\r
- ./parsimonycommand.o\\r
- ./parsimony.o\\r
- ./seqsummarycommand.o\\r
- ./chimeraccodecommand.o\\r
- ./chimerabellerophoncommand.o\\r
- ./chimeracheckcommand.o\\r
- ./chimeraslayercommand.o\\r
- ./chimerapintailcommand.o\\r
- ./chimeraseqscommand.o\\r
- ./sharedlistvector.o\\r
- ./tree.o\\r
- ./readtree.o\\r
- ./sharedsobscollectsummary.o\\r
- ./deconvolutecommand.o\\r
- ./listseqscommand.o\\r
- ./getseqscommand.o\\r
- ./removeseqscommand.o\\r
- ./systemcommand.o\\r
- ./binsequencecommand.o\\r
- ./distancecommand.o\\r
- ./ace.o\\r
- ./averagelinkage.o\\r
- ./bootstrap.o\\r
- ./calculator.o\\r
- ./chao1.o\\r
- ./cluster.o\\r
- ./clustercommand.o\\r
- ./collect.o\\r
- ./collectcommand.o\\r
- ./collectsharedcommand.o\\r
- ./commandoptionparser.o\\r
- ./completelinkage.o\\r
- ./database.o\\r
- ./engine.o\\r
- ./fastamap.o\\r
- ./fileoutput.o\\r
- ./globaldata.o\\r
- ./groupmap.o\\r
+ ./setlogfilecommand.o\
+ -o ../Release/mothur
+
+clean :
+ rm \
+ ./sharedutilities.o\
+ ./treegroupscommand.o\
+ ./bootstrapsharedcommand.o\
+ ./matrixoutputcommand.o\
+ ./getoturepcommand.o\
+ ./screenseqscommand.o\
+ ./chimera.o\
+ ./decalc.o\
+ ./readotucommand.o\
+ ./readdistcommand.o\
+ ./commandfactory.o\
+ ./alignment.o\
+ ./alignmentcell.o\
+ ./gotohoverlap.o\
+ ./overlap.o\
+ ./needlemanoverlap.o\
+ ./blastalign.o\
+ ./noalign.o\
+ ./suffixdb.o\
+ ./suffixnodes.o\
+ ./suffixtree.o\
+ ./blastdb.o\
+ ./nast.o\
+ ./nastreport.o\
+ ./boneh.o\
+ ./efron.o\
+ ./solow.o\
+ ./unifracweightedcommand.o\
+ ./weighted.o\
+ ./unweighted.o\
+ ./unifracunweightedcommand.o\
+ ./getsabundcommand.o\
+ ./getrabundcommand.o\
+ ./bellerophon.o\
+ ./pintail.o\
+ ./sharedanderbergs.o\
+ ./venncommand.o\
+ ./venn.o\
+ ./fullmatrix.o\
+ ./heatmap.o\
+ ./heatmapcommand.o\
+ ./libshuffcommand.o\
+ ./nocommands.o\
+ ./sharedbraycurtis.o\
+ ./sharedkulczynski.o\
+ ./sharedlennon.o\
+ ./sharedkulczynskicody.o\
+ ./sharedmorisitahorn.o\
+ ./sharedochiai.o\
+ ./readcolumn.o\
+ ./readotu.o\
+ ./readphylip.o\
+ ./consensuscommand.o\
+ ./heatmapsimcommand.o\
+ ./heatmapsim.o\
+ ./optionparser.o\
+ ./filterseqscommand.o\
+ ./goodscoverage.o\
+ ./sequencedb.o\
+ ./sharedjackknife.o\
+ ./sharedmarczewski.o\
+ ./aligncommand.o\
+ ./treemap.o\
+ ./parsimonycommand.o\
+ ./parsimony.o\
+ ./seqsummarycommand.o\
+ ./chimeraccodecommand.o\
+ ./chimerabellerophoncommand.o\
+ ./chimeracheckcommand.o\
+ ./chimeraslayercommand.o\
+ ./chimerapintailcommand.o\
+ ./chimeraseqscommand.o\
+ ./sharedlistvector.o\
+ ./tree.o\
+ ./readtree.o\
+ ./sharedsobscollectsummary.o\
+ ./deconvolutecommand.o\
+ ./listseqscommand.o\
+ ./getseqscommand.o\
+ ./removeseqscommand.o\
+ ./systemcommand.o\
+ ./binsequencecommand.o\
+ ./distancecommand.o\
+ ./ace.o\
+ ./averagelinkage.o\
+ ./bootstrap.o\
+ ./calculator.o\
+ ./chao1.o\
+ ./cluster.o\
+ ./clustercommand.o\
+ ./collect.o\
+ ./collectcommand.o\
+ ./collectsharedcommand.o\
+ ./commandoptionparser.o\
+ ./completelinkage.o\
+ ./database.o\
+ ./engine.o\
+ ./fastamap.o\
+ ./fileoutput.o\
+ ./globaldata.o\
+ ./groupmap.o\
./helpcommand.o\
./makegroupcommand.o\
./chopseqscommand.o\
./clearcutcommand.o\
- ./catchallcommand.o\\r
- ./inputdata.o\\r
- ./jackknife.o\\r
- ./kmer.o\\r
- ./kmerdb.o\\r
- ./listvector.o\\r
- ./mothur.o\\r
- ./nameassignment.o\\r
- ./npshannon.o\\r
- ./ordervector.o\\r
- ./progress.o\\r
- ./quitcommand.o\\r
- ./rabundvector.o\\r
- ./rarecalc.o\\r
- ./raredisplay.o\\r
- ./rarefact.o\\r
- ./rarefactcommand.o\\r
- ./rarefactsharedcommand.o\\r
- ./sabundvector.o\\r
- ./sequence.o\\r
- ./shannon.o\\r
- ./sharedace.o\\r
- ./sharedchao1.o\\r
- ./sharedcommand.o\\r
- ./sharedjabund.o\\r
- ./sharedjclass.o\\r
- ./sharedjest.o\\r
- ./sharedordervector.o\\r
- ./sharedrabundvector.o\\r
- ./sharedsabundvector.o\\r
- ./sharedsobs.o\\r
- ./sharedsorabund.o\\r
- ./sharedsorclass.o\\r
- ./sharedsorest.o\\r
- ./sharedthetan.o\\r
- ./sharedthetayc.o\\r
- ./simpson.o\\r
- ./singlelinkage.o\\r
- ./sparsematrix.o\\r
- ./summarycommand.o\\r
- ./summarysharedcommand.o\\r
- ./uvest.o\\r
- ./validcalculator.o\\r
- ./validparameter.o\\r
- ./treenode.o\\r
- ./readtreecommand.o\\r
- ./reversecommand.o\\r
- ./trimseqscommand.o\\r
- ./slibshuff.o\\r
- ./libshuff.o\\r
- ./dlibshuff.o\\r
- ./mergefilecommand.o\\r
- ./coverage.o\\r
- ./whittaker.o\\r
- ./preclustercommand.o\\r
- ./otuhierarchycommand.o\\r
- ./setdircommand.o\\r
- ./getgroupcommand.o\\r
- ./getlabelcommand.o\\r
- ./secondarystructurecommand.o\\r
- ./mothurout.o\\r
- ./parselistscommand.o\\r
- ./readblast.o\\r
- ./chimeracheckrdp.o\\r
- ./hclustercommand.o\\r
- ./hcluster.o\\r
- ./getlistcountcommand.o\\r
- ./readcluster.o\\r
- ./ccode.o\\r
- ./taxonomyequalizer.o\\r
- ./phylotypecommand.o\\r
- ./classifyseqscommand.o\\r
- ./parsesffcommand.o\\r
- ./classify.o\\r
+ ./catchallcommand.o\
+ ./splitabundcommand.o\
+ ./inputdata.o\
+ ./jackknife.o\
+ ./kmer.o\
+ ./kmerdb.o\
+ ./listvector.o\
+ ./mothur.o\
+ ./nameassignment.o\
+ ./npshannon.o\
+ ./ordervector.o\
+ ./progress.o\
+ ./quitcommand.o\
+ ./rabundvector.o\
+ ./rarecalc.o\
+ ./raredisplay.o\
+ ./rarefact.o\
+ ./rarefactcommand.o\
+ ./rarefactsharedcommand.o\
+ ./sabundvector.o\
+ ./sequence.o\
+ ./shannon.o\
+ ./sharedace.o\
+ ./sharedchao1.o\
+ ./sharedcommand.o\
+ ./sharedjabund.o\
+ ./sharedjclass.o\
+ ./sharedjest.o\
+ ./sharedordervector.o\
+ ./sharedrabundvector.o\
+ ./sharedsabundvector.o\
+ ./sharedsobs.o\
+ ./sharedsorabund.o\
+ ./sharedsorclass.o\
+ ./sharedsorest.o\
+ ./sharedthetan.o\
+ ./sharedthetayc.o\
+ ./simpson.o\
+ ./singlelinkage.o\
+ ./sparsematrix.o\
+ ./summarycommand.o\
+ ./summarysharedcommand.o\
+ ./uvest.o\
+ ./validcalculator.o\
+ ./validparameter.o\
+ ./treenode.o\
+ ./readtreecommand.o\
+ ./reversecommand.o\
+ ./trimseqscommand.o\
+ ./slibshuff.o\
+ ./libshuff.o\
+ ./dlibshuff.o\
+ ./mergefilecommand.o\
+ ./coverage.o\
+ ./whittaker.o\
+ ./preclustercommand.o\
+ ./otuhierarchycommand.o\
+ ./setdircommand.o\
+ ./getgroupcommand.o\
+ ./getlabelcommand.o\
+ ./secondarystructurecommand.o\
+ ./mothurout.o\
+ ./parselistscommand.o\
+ ./readblast.o\
+ ./chimeracheckrdp.o\
+ ./hclustercommand.o\
+ ./hcluster.o\
+ ./getlistcountcommand.o\
+ ./readcluster.o\
+ ./ccode.o\
+ ./taxonomyequalizer.o\
+ ./phylotypecommand.o\
+ ./classifyseqscommand.o\
+ ./parsesffcommand.o\
+ ./classify.o\
./phylotree.o\
./phylodiversity.o\
- ./phylodiversitycommand.o\\r
+ ./phylodiversitycommand.o\
./bayesian.o\
- ./phylosummary.o\\r
- ./alignmentdb.o\\r
- ./knn.o\\r
- ./distancedb.o\\r
- ./chimeraslayer.o\\r
- ./slayer.o\\r
- ./pcacommand.o\\r
- ./formatcolumn.o\\r
- ./formatphylip.o\\r
- ./mgclustercommand.o\\r
- ./getsharedotucommand.o\\r
- ./maligner.o\\r
- ./chimerarealigner.o\\r
- ./bergerparker.o\\r
- ./bstick.o\\r
- ./sharedkstest.o\\r
- ./qstat.o\\r
- ./shen.o\\r
- ./logsd.o\\r
+ ./phylosummary.o\
+ ./alignmentdb.o\
+ ./knn.o\
+ ./distancedb.o\
+ ./chimeraslayer.o\
+ ./slayer.o\
+ ./pcacommand.o\
+ ./formatcolumn.o\
+ ./formatphylip.o\
+ ./mgclustercommand.o\
+ ./getsharedotucommand.o\
+ ./maligner.o\
+ ./chimerarealigner.o\
+ ./bergerparker.o\
+ ./bstick.o\
+ ./sharedkstest.o\
+ ./qstat.o\
+ ./shen.o\
+ ./logsd.o\
./geom.o\
- ./setlogfilecommand.o\\r
- mothur\r
-\r
-install : mothur\r
- #cp mothur ../Release/mothur\r
-\r
-#\r
-# Build the parts of mothur\r
-#\r
-\r
-\r
-# Item # 1 -- sharedutilities --\r
-./sharedutilities.o : sharedutilities.cpp\r
- $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o\r
-\r
-\r
-# Item # 2 -- treegroupscommand --\r
-./treegroupscommand.o : treegroupscommand.cpp\r
- $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o\r
-\r
-\r
-# Item # 3 -- bootstrapsharedcommand --\r
-./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp\r
- $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o\r
-\r
-\r
-# Item # 4 -- matrixoutputcommand --\r
-./matrixoutputcommand.o : matrixoutputcommand.cpp\r
- $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o\r
-\r
-\r
-# Item # 5 -- getoturepcommand --\r
-./getoturepcommand.o : getoturepcommand.cpp\r
- $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o\r
-\r
-\r
-# Item # 6 -- screenseqscommand --\r
-./screenseqscommand.o : screenseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o\r
-\r
-\r
-# Item # 7 -- chimera --\r
-./chimera.o : chimera.cpp\r
- $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o\r
-\r
-\r
-# Item # 8 -- decalc --\r
-./decalc.o : decalc.cpp\r
- $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o\r
-\r
-\r
-# Item # 9 -- readotucommand --\r
-./readotucommand.o : readotucommand.cpp\r
- $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o\r
-\r
-\r
-# Item # 10 -- readdistcommand --\r
-./readdistcommand.o : readdistcommand.cpp\r
- $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o\r
-\r
-\r
-# Item # 11 -- commandfactory --\r
-./commandfactory.o : commandfactory.cpp\r
- $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o\r
-\r
-\r
-# Item # 12 -- alignment --\r
-./alignment.o : alignment.cpp\r
- $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o\r
-\r
-\r
-# Item # 13 -- alignmentcell --\r
-./alignmentcell.o : alignmentcell.cpp\r
- $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o\r
-\r
-\r
-# Item # 14 -- gotohoverlap --\r
-./gotohoverlap.o : gotohoverlap.cpp\r
- $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o\r
-\r
-\r
-# Item # 15 -- overlap --\r
-./overlap.o : overlap.cpp\r
- $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o\r
-\r
-\r
-# Item # 16 -- needlemanoverlap --\r
-./needlemanoverlap.o : needlemanoverlap.cpp\r
- $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o\r
-\r
-\r
-# Item # 17 -- blastalign --\r
-./blastalign.o : blastalign.cpp\r
- $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o\r
-\r
-\r
-# Item # 18 -- noalign --\r
-./noalign.o : noalign.cpp\r
- $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o\r
-\r
-\r
-# Item # 19 -- suffixdb --\r
-./suffixdb.o : suffixdb.cpp\r
- $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o\r
-\r
-\r
-# Item # 20 -- suffixnodes --\r
-./suffixnodes.o : suffixnodes.cpp\r
- $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o\r
-\r
-\r
-# Item # 21 -- suffixtree --\r
-./suffixtree.o : suffixtree.cpp\r
- $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o\r
-\r
-\r
-# Item # 22 -- blastdb --\r
-./blastdb.o : blastdb.cpp\r
- $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o\r
-\r
-\r
-# Item # 23 -- nast --\r
-./nast.o : nast.cpp\r
- $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o\r
-\r
-\r
-# Item # 24 -- nastreport --\r
-./nastreport.o : nastreport.cpp\r
- $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o\r
-\r
-\r
-# Item # 25 -- boneh --\r
-./boneh.o : boneh.cpp\r
- $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o\r
-\r
-\r
-# Item # 26 -- efron --\r
-./efron.o : efron.cpp\r
- $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o\r
-\r
-\r
-# Item # 27 -- solow --\r
-./solow.o : solow.cpp\r
- $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o\r
-\r
-\r
-# Item # 28 -- unifracweightedcommand --\r
-./unifracweightedcommand.o : unifracweightedcommand.cpp\r
- $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o\r
-\r
-\r
-# Item # 29 -- weighted --\r
-./weighted.o : weighted.cpp\r
- $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o\r
-\r
-\r
-# Item # 30 -- unweighted --\r
-./unweighted.o : unweighted.cpp\r
- $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o\r
-\r
-\r
-# Item # 31 -- unifracunweightedcommand --\r
-./unifracunweightedcommand.o : unifracunweightedcommand.cpp\r
- $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o\r
-\r
-\r
-# Item # 32 -- getsabundcommand --\r
-./getsabundcommand.o : getsabundcommand.cpp\r
- $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o\r
-\r
-\r
-# Item # 33 -- getrabundcommand --\r
-./getrabundcommand.o : getrabundcommand.cpp\r
- $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o\r
-\r
-\r
-# Item # 34 -- bellerophon --\r
-./bellerophon.o : bellerophon.cpp\r
- $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o\r
-\r
-\r
-# Item # 35 -- pintail --\r
-./pintail.o : pintail.cpp\r
- $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o\r
-\r
-\r
-# Item # 36 -- sharedanderbergs --\r
-./sharedanderbergs.o : sharedanderbergs.cpp\r
- $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o\r
-\r
-\r
-# Item # 37 -- venncommand --\r
-./venncommand.o : venncommand.cpp\r
- $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o\r
-\r
-\r
-# Item # 38 -- venn --\r
-./venn.o : venn.cpp\r
- $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o\r
-\r
-\r
-# Item # 39 -- fullmatrix --\r
-./fullmatrix.o : fullmatrix.cpp\r
- $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o\r
-\r
-\r
-# Item # 40 -- heatmap --\r
-./heatmap.o : heatmap.cpp\r
- $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o\r
-\r
-\r
-# Item # 41 -- heatmapcommand --\r
-./heatmapcommand.o : heatmapcommand.cpp\r
- $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o\r
-\r
-\r
-# Item # 42 -- libshuffcommand --\r
-./libshuffcommand.o : libshuffcommand.cpp\r
- $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o\r
-\r
-\r
-# Item # 43 -- nocommands --\r
-./nocommands.o : nocommands.cpp\r
- $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o\r
-\r
-\r
-# Item # 44 -- sharedbraycurtis --\r
-./sharedbraycurtis.o : sharedbraycurtis.cpp\r
- $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o\r
-\r
-\r
-# Item # 45 -- sharedkulczynski --\r
-./sharedkulczynski.o : sharedkulczynski.cpp\r
- $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o\r
-\r
-\r
-# Item # 46 -- sharedlennon --\r
-./sharedlennon.o : sharedlennon.cpp\r
- $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o\r
-\r
-\r
-# Item # 47 -- sharedkulczynskicody --\r
-./sharedkulczynskicody.o : sharedkulczynskicody.cpp\r
- $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o\r
-\r
-\r
-# Item # 48 -- sharedmorisitahorn --\r
-./sharedmorisitahorn.o : sharedmorisitahorn.cpp\r
- $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o\r
-\r
-\r
-# Item # 49 -- sharedochiai --\r
-./sharedochiai.o : sharedochiai.cpp\r
- $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o\r
-\r
-\r
-# Item # 50 -- readcolumn --\r
-./readcolumn.o : readcolumn.cpp\r
- $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o\r
-\r
-\r
-# Item # 51 -- readotu --\r
-./readotu.o : readotu.cpp\r
- $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o\r
-\r
-\r
-# Item # 52 -- readphylip --\r
-./readphylip.o : readphylip.cpp\r
- $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o\r
-\r
-\r
-# Item # 53 -- consensuscommand --\r
-./consensuscommand.o : consensuscommand.cpp\r
- $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o\r
-\r
-\r
-# Item # 54 -- heatmapsimcommand --\r
-./heatmapsimcommand.o : heatmapsimcommand.cpp\r
- $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o\r
-\r
-\r
-# Item # 55 -- heatmapsim --\r
-./heatmapsim.o : heatmapsim.cpp\r
- $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o\r
-\r
-\r
-# Item # 56 -- optionparser --\r
-./optionparser.o : optionparser.cpp\r
- $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o\r
-\r
-\r
-# Item # 57 -- filterseqscommand --\r
-./filterseqscommand.o : filterseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o\r
-\r
-\r
-# Item # 58 -- goodscoverage --\r
-./goodscoverage.o : goodscoverage.cpp\r
- $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o\r
-\r
-\r
-# Item # 59 -- sequencedb --\r
-./sequencedb.o : sequencedb.cpp\r
- $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o\r
-\r
-\r
-# Item # 60 -- sharedjackknife --\r
-./sharedjackknife.o : sharedjackknife.cpp\r
- $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o\r
-\r
-\r
-# Item # 61 -- sharedmarczewski --\r
-./sharedmarczewski.o : sharedmarczewski.cpp\r
- $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o\r
-\r
-\r
-# Item # 62 -- aligncommand --\r
-./aligncommand.o : aligncommand.cpp\r
- $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o\r
-\r
-\r
-# Item # 63 -- treemap --\r
-./treemap.o : treemap.cpp\r
- $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o\r
-\r
-\r
-# Item # 64 -- parsimonycommand --\r
-./parsimonycommand.o : parsimonycommand.cpp\r
- $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o\r
-\r
-\r
-# Item # 65 -- parsimony --\r
-./parsimony.o : parsimony.cpp\r
- $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o\r
-\r
-\r
-# Item # 66 -- seqsummarycommand --\r
-./seqsummarycommand.o : seqsummarycommand.cpp\r
- $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o\r
-\r
-\r
-# Item # 67 -- chimeraseqscommand --\r
-./chimeraseqscommand.o : chimeraseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o\r
-\r
-\r
-# Item # 68 -- sharedlistvector --\r
-./sharedlistvector.o : sharedlistvector.cpp\r
- $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o\r
-\r
-\r
-# Item # 69 -- tree --\r
-./tree.o : tree.cpp\r
- $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o\r
-\r
-\r
-# Item # 70 -- readtree --\r
-./readtree.o : readtree.cpp\r
- $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o\r
-\r
-\r
-# Item # 71 -- sharedsobscollectsummary --\r
-./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp\r
- $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o\r
-\r
-\r
-# Item # 72 -- deconvolutecommand --\r
-./deconvolutecommand.o : deconvolutecommand.cpp\r
- $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o\r
-\r
-\r
-# Item # 73 -- listseqscommand --\r
-./listseqscommand.o : listseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o\r
-\r
-\r
-# Item # 74 -- getseqscommand --\r
-./getseqscommand.o : getseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o\r
-\r
-\r
-# Item # 75 -- removeseqscommand --\r
-./removeseqscommand.o : removeseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o\r
-\r
-\r
-# Item # 76 -- systemcommand --\r
-./systemcommand.o : systemcommand.cpp\r
- $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o\r
-\r
-\r
-# Item # 77 -- binsequencecommand --\r
-./binsequencecommand.o : binsequencecommand.cpp\r
- $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o\r
-\r
-\r
-# Item # 78 -- distancecommand --\r
-./distancecommand.o : distancecommand.cpp\r
- $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o\r
-\r
-\r
-# Item # 79 -- ace --\r
-./ace.o : ace.cpp\r
- $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o\r
-\r
-\r
-# Item # 80 -- averagelinkage --\r
-./averagelinkage.o : averagelinkage.cpp\r
- $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o\r
-\r
-\r
-# Item # 81 -- bootstrap --\r
-./bootstrap.o : bootstrap.cpp\r
- $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o\r
-\r
-\r
-# Item # 82 -- calculator --\r
-./calculator.o : calculator.cpp\r
- $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o\r
-\r
-\r
-# Item # 83 -- chao1 --\r
-./chao1.o : chao1.cpp\r
- $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o\r
-\r
-\r
-# Item # 84 -- cluster --\r
-./cluster.o : cluster.cpp\r
- $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o\r
-\r
-\r
-# Item # 85 -- clustercommand --\r
-./clustercommand.o : clustercommand.cpp\r
- $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o\r
-\r
-\r
-# Item # 86 -- collect --\r
-./collect.o : collect.cpp\r
- $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o\r
-\r
-\r
-# Item # 87 -- collectcommand --\r
-./collectcommand.o : collectcommand.cpp\r
- $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o\r
-\r
-\r
-# Item # 88 -- collectsharedcommand --\r
-./collectsharedcommand.o : collectsharedcommand.cpp\r
- $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o\r
-\r
-\r
-# Item # 89 -- commandoptionparser --\r
-./commandoptionparser.o : commandoptionparser.cpp\r
- $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o\r
-\r
-\r
-# Item # 90 -- completelinkage --\r
-./completelinkage.o : completelinkage.cpp\r
- $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o\r
-\r
-\r
-# Item # 91 -- database --\r
-./database.o : database.cpp\r
- $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o\r
-\r
-\r
-# Item # 92 -- engine --\r
-./engine.o : engine.cpp\r
- $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o\r
-\r
-\r
-# Item # 93 -- fastamap --\r
-./fastamap.o : fastamap.cpp\r
- $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o\r
-\r
-\r
-# Item # 94 -- fileoutput --\r
-./fileoutput.o : fileoutput.cpp\r
- $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o\r
-\r
-\r
-# Item # 95 -- globaldata --\r
-./globaldata.o : globaldata.cpp\r
- $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o\r
-\r
-\r
-# Item # 96 -- groupmap --\r
-./groupmap.o : groupmap.cpp\r
- $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o\r
-\r
-\r
-# Item # 97 -- helpcommand --\r
-./helpcommand.o : helpcommand.cpp\r
- $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o\r
-\r
-\r
-# Item # 98 -- inputdata --\r
-./inputdata.o : inputdata.cpp\r
- $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o\r
-\r
-\r
-# Item # 99 -- jackknife --\r
-./jackknife.o : jackknife.cpp\r
- $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o\r
-\r
-\r
-# Item # 100 -- kmer --\r
-./kmer.o : kmer.cpp\r
- $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o\r
-\r
-\r
-# Item # 101 -- kmerdb --\r
-./kmerdb.o : kmerdb.cpp\r
- $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o\r
-\r
-\r
-# Item # 102 -- listvector --\r
-./listvector.o : listvector.cpp\r
- $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o\r
-\r
-\r
-# Item # 103 -- mothur --\r
-./mothur.o : mothur.cpp\r
- $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o\r
-\r
-\r
-# Item # 104 -- nameassignment --\r
-./nameassignment.o : nameassignment.cpp\r
- $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o\r
-\r
-\r
-# Item # 105 -- npshannon --\r
-./npshannon.o : npshannon.cpp\r
- $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o\r
-\r
-\r
-# Item # 106 -- ordervector --\r
-./ordervector.o : ordervector.cpp\r
- $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o\r
-\r
-\r
-# Item # 107 -- progress --\r
-./progress.o : progress.cpp\r
- $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o\r
-\r
-\r
-# Item # 108 -- quitcommand --\r
-./quitcommand.o : quitcommand.cpp\r
- $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o\r
-\r
-\r
-# Item # 109 -- rabundvector --\r
-./rabundvector.o : rabundvector.cpp\r
- $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o\r
-\r
-\r
-# Item # 110 -- rarecalc --\r
-./rarecalc.o : rarecalc.cpp\r
- $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o\r
-\r
-\r
-# Item # 111 -- raredisplay --\r
-./raredisplay.o : raredisplay.cpp\r
- $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o\r
-\r
-\r
-# Item # 112 -- rarefact --\r
-./rarefact.o : rarefact.cpp\r
- $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o\r
-\r
-\r
-# Item # 113 -- rarefactcommand --\r
-./rarefactcommand.o : rarefactcommand.cpp\r
- $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o\r
-\r
-\r
-# Item # 114 -- rarefactsharedcommand --\r
-./rarefactsharedcommand.o : rarefactsharedcommand.cpp\r
- $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o\r
-\r
-\r
-# Item # 115 -- sabundvector --\r
-./sabundvector.o : sabundvector.cpp\r
- $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o\r
-\r
-\r
-# Item # 116 -- sequence --\r
-./sequence.o : sequence.cpp\r
- $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o\r
-\r
-\r
-# Item # 117 -- shannon --\r
-./shannon.o : shannon.cpp\r
- $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o\r
-\r
-\r
-# Item # 118 -- sharedace --\r
-./sharedace.o : sharedace.cpp\r
- $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o\r
-\r
-\r
-# Item # 119 -- sharedchao1 --\r
-./sharedchao1.o : sharedchao1.cpp\r
- $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o\r
-\r
-\r
-# Item # 120 -- sharedcommand --\r
-./sharedcommand.o : sharedcommand.cpp\r
- $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o\r
-\r
-\r
-# Item # 121 -- sharedjabund --\r
-./sharedjabund.o : sharedjabund.cpp\r
- $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o\r
-\r
-\r
-# Item # 122 -- sharedjclass --\r
-./sharedjclass.o : sharedjclass.cpp\r
- $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o\r
-\r
-\r
-# Item # 123 -- sharedjest --\r
-./sharedjest.o : sharedjest.cpp\r
- $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o\r
-\r
-\r
-# Item # 124 -- sharedordervector --\r
-./sharedordervector.o : sharedordervector.cpp\r
- $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o\r
-\r
-\r
-# Item # 125 -- sharedrabundvector --\r
-./sharedrabundvector.o : sharedrabundvector.cpp\r
- $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o\r
-\r
-\r
-# Item # 126 -- sharedsabundvector --\r
-./sharedsabundvector.o : sharedsabundvector.cpp\r
- $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o\r
-\r
-\r
-# Item # 127 -- sharedsobs --\r
-./sharedsobs.o : sharedsobs.cpp\r
- $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o\r
-\r
-\r
-# Item # 128 -- sharedsorabund --\r
-./sharedsorabund.o : sharedsorabund.cpp\r
- $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o\r
-\r
-\r
-# Item # 129 -- sharedsorclass --\r
-./sharedsorclass.o : sharedsorclass.cpp\r
- $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o\r
-\r
-\r
-# Item # 130 -- sharedsorest --\r
-./sharedsorest.o : sharedsorest.cpp\r
- $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o\r
-\r
-\r
-# Item # 131 -- sharedthetan --\r
-./sharedthetan.o : sharedthetan.cpp\r
- $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o\r
-\r
-\r
-# Item # 132 -- sharedthetayc --\r
-./sharedthetayc.o : sharedthetayc.cpp\r
- $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o\r
-\r
-\r
-# Item # 133 -- simpson --\r
-./simpson.o : simpson.cpp\r
- $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o\r
-\r
-\r
-# Item # 134 -- singlelinkage --\r
-./singlelinkage.o : singlelinkage.cpp\r
- $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o\r
-\r
-\r
-# Item # 135 -- sparsematrix --\r
-./sparsematrix.o : sparsematrix.cpp\r
- $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o\r
-\r
-\r
-# Item # 136 -- summarycommand --\r
-./summarycommand.o : summarycommand.cpp\r
- $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o\r
-\r
-\r
-# Item # 137 -- summarysharedcommand --\r
-./summarysharedcommand.o : summarysharedcommand.cpp\r
- $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o\r
-\r
-\r
-# Item # 138 -- uvest --\r
-./uvest.o : uvest.cpp\r
- $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o\r
-\r
-\r
-# Item # 139 -- validcalculator --\r
-./validcalculator.o : validcalculator.cpp\r
- $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o\r
-\r
-\r
-# Item # 140 -- validparameter --\r
-./validparameter.o : validparameter.cpp\r
- $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o\r
-\r
-\r
-# Item # 141 -- treenode --\r
-./treenode.o : treenode.cpp\r
- $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o\r
-\r
-\r
-# Item # 142 -- readtreecommand --\r
-./readtreecommand.o : readtreecommand.cpp\r
- $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o\r
-\r
-\r
-# Item # 143 -- reversecommand --\r
-./reversecommand.o : reversecommand.cpp\r
- $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o\r
-\r
-\r
-# Item # 144 -- trimseqscommand --\r
-./trimseqscommand.o : trimseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o\r
-\r
-\r
-# Item # 145 -- slibshuff --\r
-./slibshuff.o : slibshuff.cpp\r
- $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o\r
-\r
-\r
-# Item # 146 -- libshuff --\r
-./libshuff.o : libshuff.cpp\r
- $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o\r
-\r
-\r
-# Item # 147 -- dlibshuff --\r
-./dlibshuff.o : dlibshuff.cpp\r
- $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o\r
-\r
-\r
-# Item # 148 -- mergefilecommand --\r
-./mergefilecommand.o : mergefilecommand.cpp\r
- $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o\r
-\r
-\r
-# Item # 149 -- coverage --\r
-./coverage.o : coverage.cpp\r
- $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o\r
-\r
-\r
-# Item # 150 -- whittaker --\r
-./whittaker.o : whittaker.cpp\r
- $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o\r
-\r
-\r
-# Item # 151 -- preclustercommand --\r
-./preclustercommand.o : preclustercommand.cpp\r
- $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o\r
-\r
-\r
-# Item # 152 -- otuhierarchycommand --\r
-./otuhierarchycommand.o : otuhierarchycommand.cpp\r
- $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o\r
-\r
-\r
-# Item # 153 -- setdircommand --\r
-./setdircommand.o : setdircommand.cpp\r
- $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o\r
-\r
-\r
-# Item # 154 -- getgroupcommand --\r
-./getgroupcommand.o : getgroupcommand.cpp\r
- $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o\r
-\r
-\r
-# Item # 155 -- getlabelcommand --\r
-./getlabelcommand.o : getlabelcommand.cpp\r
- $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o\r
-\r
-\r
-# Item # 156 -- secondarystructurecommand --\r
-./secondarystructurecommand.o : secondarystructurecommand.cpp\r
- $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o\r
-\r
-\r
-# Item # 157 -- mothurout --\r
-./mothurout.o : mothurout.cpp\r
- $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o\r
-\r
-\r
-# Item # 158 -- parselistscommand --\r
-./parselistscommand.o : parselistscommand.cpp\r
- $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o\r
-\r
-\r
-# Item # 159 -- readblast --\r
-./readblast.o : readblast.cpp\r
- $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o\r
-\r
-\r
-# Item # 160 -- chimeracheckrdp --\r
-./chimeracheckrdp.o : chimeracheckrdp.cpp\r
- $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o\r
-\r
-\r
-# Item # 161 -- hclustercommand --\r
-./hclustercommand.o : hclustercommand.cpp\r
- $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o\r
-\r
-\r
-# Item # 162 -- hcluster --\r
-./hcluster.o : hcluster.cpp\r
- $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o\r
-\r
-\r
-# Item # 163 -- getlistcountcommand --\r
-./getlistcountcommand.o : getlistcountcommand.cpp\r
- $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o\r
-\r
-\r
-# Item # 164 -- readcluster --\r
-./readcluster.o : readcluster.cpp\r
- $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o\r
-\r
-\r
-# Item # 165 -- ccode --\r
-./ccode.o : ccode.cpp\r
- $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o\r
-\r
-\r
-# Item # 166 -- taxonomyequalizer --\r
-./taxonomyequalizer.o : taxonomyequalizer.cpp\r
- $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o\r
-\r
-\r
-# Item # 167 -- phylotypecommand --\r
-./phylotypecommand.o : phylotypecommand.cpp\r
- $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o\r
-\r
-\r
-# Item # 168 -- classifyseqscommand --\r
-./classifyseqscommand.o : classifyseqscommand.cpp\r
- $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o\r
-\r
-\r
-# Item # 169 -- classify --\r
-./classify.o : classify.cpp\r
- $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o\r
-\r
-\r
-# Item # 170 -- phylotree --\r
-./phylotree.o : phylotree.cpp\r
- $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o\r
-\r
-\r
-# Item # 171 -- bayesian --\r
-./bayesian.o : bayesian.cpp\r
- $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o\r
-\r
-\r
-# Item # 172 -- alignmentdb --\r
-./alignmentdb.o : alignmentdb.cpp\r
- $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o\r
-\r
-\r
-# Item # 173 -- knn --\r
-./knn.o : knn.cpp\r
- $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o\r
-\r
-\r
-# Item # 174 -- distancedb --\r
-./distancedb.o : distancedb.cpp\r
- $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o\r
-\r
-\r
-# Item # 175 -- chimeraslayer --\r
-./chimeraslayer.o : chimeraslayer.cpp\r
- $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o\r
-\r
-\r
-# Item # 176 -- slayer --\r
-./slayer.o : slayer.cpp\r
- $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o\r
-\r
-\r
-# Item # 177 -- pcacommand --\r
-./pcacommand.o : pcacommand.cpp\r
- $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o\r
-\r
-\r
-# Item # 178 -- formatcolumn --\r
-./formatcolumn.o : formatcolumn.cpp\r
- $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o\r
-\r
-\r
-# Item # 179 -- formatphylip --\r
-./formatphylip.o : formatphylip.cpp\r
- $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o\r
-\r
-\r
-# Item # 180 -- mgclustercommand --\r
-./mgclustercommand.o : mgclustercommand.cpp\r
- $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o\r
-\r
-\r
-# Item # 181 -- getsharedotucommand --\r
-./getsharedotucommand.o : getsharedotucommand.cpp\r
- $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o\r
-\r
-\r
-# Item # 182 -- maligner --\r
-./maligner.o : maligner.cpp\r
- $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o\r
-\r
-\r
-# Item # 183 -- chimerarealigner --\r
-./chimerarealigner.o : chimerarealigner.cpp\r
- $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o\r
-\r
-\r
-# Item # 184 -- bergerparker --\r
-./bergerparker.o : bergerparker.cpp\r
- $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o\r
-\r
-\r
-# Item # 185 -- bstick --\r
-./bstick.o : bstick.cpp\r
- $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o\r
-\r
-\r
-# Item # 186 -- sharedkstest --\r
-./sharedkstest.o : sharedkstest.cpp\r
- $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o\r
-\r
-\r
-# Item # 187 -- qstat --\r
-./qstat.o : qstat.cpp\r
- $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o\r
-\r
-\r
-# Item # 188 -- shen --\r
-./shen.o : shen.cpp\r
- $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o\r
-\r
-\r
-# Item # 189 -- logsd --\r
-./logsd.o : logsd.cpp\r
- $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o\r
-\r
-\r
-# Item # 190 -- geom --\r
-./geom.o : geom.cpp\r
- $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o\r
-\r
-# Item # 191 -- parsesffcommand --\r
-./parsesffcommand.o : parsesffcommand.cpp\r
- $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o\r
-\r
-# Item # 192 -- chimeraccodecommand --\r
-./chimeraccodecommand.o : chimeraccodecommand.cpp\r
- $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o\r
-\r
-# Item # 193 -- chimeracheckcommand --\r
-./chimeracheckcommand.o : chimeracheckcommand.cpp\r
- $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o\r
-\r
-\r
-# Item # 194 -- chimeraslayercommand --\r
-./chimeraslayercommand.o : chimeraslayercommand.cpp\r
- $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o\r
-\r
-# Item # 195 -- chimerapintailcommand --\r
-./chimerapintailcommand.o : chimerapintailcommand.cpp\r
- $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o\r
-\r
-# Item # 196 -- chimerabellerophoncommand --\r
-./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp\r
- $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o\r
-
-# Item # 197 -- phylosummary --\r
-./phylosummary.o : phylosummary.cpp\r
- $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o\r
-
-# Item # 198 -- setlogfilecommand --\r
-./setlogfilecommand.o : setlogfilecommand.cpp\r
- $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o\r
-\r
-# Item # 199 -- phylodiversity --\r
-./phylodiversity.o : phylodiversity.cpp\r
- $(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o\r
-\r
-# Item # 200 -- phylodiversitycommand --\r
-./phylodiversitycommand.o : phylodiversitycommand.cpp\r
- $(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o\r
-\r
-# Item # 201 -- makegroupcommand --\r
-./makegroupcommand.o : makegroupcommand.cpp\r
- $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o\r
-
-# Item # 202 -- chopseqscommand --\r
-./chopseqscommand.o : chopseqscommand.cpp\r
+ ./setlogfilecommand.o\
+ mothur
+
+install : mothur
+ #cp mothur ../Release/mothur
+
+#
+# Build the parts of mothur
+#
+
+
+# Item # 1 -- sharedutilities --
+./sharedutilities.o : sharedutilities.cpp
+ $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o
+
+
+# Item # 2 -- treegroupscommand --
+./treegroupscommand.o : treegroupscommand.cpp
+ $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o
+
+
+# Item # 3 -- bootstrapsharedcommand --
+./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp
+ $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o
+
+
+# Item # 4 -- matrixoutputcommand --
+./matrixoutputcommand.o : matrixoutputcommand.cpp
+ $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o
+
+
+# Item # 5 -- getoturepcommand --
+./getoturepcommand.o : getoturepcommand.cpp
+ $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o
+
+
+# Item # 6 -- screenseqscommand --
+./screenseqscommand.o : screenseqscommand.cpp
+ $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o
+
+
+# Item # 7 -- chimera --
+./chimera.o : chimera.cpp
+ $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o
+
+
+# Item # 8 -- decalc --
+./decalc.o : decalc.cpp
+ $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o
+
+
+# Item # 9 -- readotucommand --
+./readotucommand.o : readotucommand.cpp
+ $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o
+
+
+# Item # 10 -- readdistcommand --
+./readdistcommand.o : readdistcommand.cpp
+ $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o
+
+
+# Item # 11 -- commandfactory --
+./commandfactory.o : commandfactory.cpp
+ $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o
+
+
+# Item # 12 -- alignment --
+./alignment.o : alignment.cpp
+ $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o
+
+
+# Item # 13 -- alignmentcell --
+./alignmentcell.o : alignmentcell.cpp
+ $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o
+
+
+# Item # 14 -- gotohoverlap --
+./gotohoverlap.o : gotohoverlap.cpp
+ $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o
+
+
+# Item # 15 -- overlap --
+./overlap.o : overlap.cpp
+ $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o
+
+
+# Item # 16 -- needlemanoverlap --
+./needlemanoverlap.o : needlemanoverlap.cpp
+ $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o
+
+
+# Item # 17 -- blastalign --
+./blastalign.o : blastalign.cpp
+ $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o
+
+
+# Item # 18 -- noalign --
+./noalign.o : noalign.cpp
+ $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o
+
+
+# Item # 19 -- suffixdb --
+./suffixdb.o : suffixdb.cpp
+ $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o
+
+
+# Item # 20 -- suffixnodes --
+./suffixnodes.o : suffixnodes.cpp
+ $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o
+
+
+# Item # 21 -- suffixtree --
+./suffixtree.o : suffixtree.cpp
+ $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o
+
+
+# Item # 22 -- blastdb --
+./blastdb.o : blastdb.cpp
+ $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o
+
+
+# Item # 23 -- nast --
+./nast.o : nast.cpp
+ $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o
+
+
+# Item # 24 -- nastreport --
+./nastreport.o : nastreport.cpp
+ $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o
+
+
+# Item # 25 -- boneh --
+./boneh.o : boneh.cpp
+ $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o
+
+
+# Item # 26 -- efron --
+./efron.o : efron.cpp
+ $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o
+
+
+# Item # 27 -- solow --
+./solow.o : solow.cpp
+ $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o
+
+
+# Item # 28 -- unifracweightedcommand --
+./unifracweightedcommand.o : unifracweightedcommand.cpp
+ $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o
+
+
+# Item # 29 -- weighted --
+./weighted.o : weighted.cpp
+ $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o
+
+
+# Item # 30 -- unweighted --
+./unweighted.o : unweighted.cpp
+ $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o
+
+
+# Item # 31 -- unifracunweightedcommand --
+./unifracunweightedcommand.o : unifracunweightedcommand.cpp
+ $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o
+
+
+# Item # 32 -- getsabundcommand --
+./getsabundcommand.o : getsabundcommand.cpp
+ $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o
+
+
+# Item # 33 -- getrabundcommand --
+./getrabundcommand.o : getrabundcommand.cpp
+ $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o
+
+
+# Item # 34 -- bellerophon --
+./bellerophon.o : bellerophon.cpp
+ $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o
+
+
+# Item # 35 -- pintail --
+./pintail.o : pintail.cpp
+ $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o
+
+
+# Item # 36 -- sharedanderbergs --
+./sharedanderbergs.o : sharedanderbergs.cpp
+ $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o
+
+
+# Item # 37 -- venncommand --
+./venncommand.o : venncommand.cpp
+ $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o
+
+
+# Item # 38 -- venn --
+./venn.o : venn.cpp
+ $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o
+
+
+# Item # 39 -- fullmatrix --
+./fullmatrix.o : fullmatrix.cpp
+ $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o
+
+
+# Item # 40 -- heatmap --
+./heatmap.o : heatmap.cpp
+ $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o
+
+
+# Item # 41 -- heatmapcommand --
+./heatmapcommand.o : heatmapcommand.cpp
+ $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o
+
+
+# Item # 42 -- libshuffcommand --
+./libshuffcommand.o : libshuffcommand.cpp
+ $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o
+
+
+# Item # 43 -- nocommands --
+./nocommands.o : nocommands.cpp
+ $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o
+
+
+# Item # 44 -- sharedbraycurtis --
+./sharedbraycurtis.o : sharedbraycurtis.cpp
+ $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o
+
+
+# Item # 45 -- sharedkulczynski --
+./sharedkulczynski.o : sharedkulczynski.cpp
+ $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o
+
+
+# Item # 46 -- sharedlennon --
+./sharedlennon.o : sharedlennon.cpp
+ $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o
+
+
+# Item # 47 -- sharedkulczynskicody --
+./sharedkulczynskicody.o : sharedkulczynskicody.cpp
+ $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o
+
+
+# Item # 48 -- sharedmorisitahorn --
+./sharedmorisitahorn.o : sharedmorisitahorn.cpp
+ $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o
+
+
+# Item # 49 -- sharedochiai --
+./sharedochiai.o : sharedochiai.cpp
+ $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o
+
+
+# Item # 50 -- readcolumn --
+./readcolumn.o : readcolumn.cpp
+ $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o
+
+
+# Item # 51 -- readotu --
+./readotu.o : readotu.cpp
+ $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o
+
+
+# Item # 52 -- readphylip --
+./readphylip.o : readphylip.cpp
+ $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o
+
+
+# Item # 53 -- consensuscommand --
+./consensuscommand.o : consensuscommand.cpp
+ $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o
+
+
+# Item # 54 -- heatmapsimcommand --
+./heatmapsimcommand.o : heatmapsimcommand.cpp
+ $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o
+
+
+# Item # 55 -- heatmapsim --
+./heatmapsim.o : heatmapsim.cpp
+ $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o
+
+
+# Item # 56 -- optionparser --
+./optionparser.o : optionparser.cpp
+ $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o
+
+
+# Item # 57 -- filterseqscommand --
+./filterseqscommand.o : filterseqscommand.cpp
+ $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o
+
+
+# Item # 58 -- goodscoverage --
+./goodscoverage.o : goodscoverage.cpp
+ $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o
+
+
+# Item # 59 -- sequencedb --
+./sequencedb.o : sequencedb.cpp
+ $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o
+
+
+# Item # 60 -- sharedjackknife --
+./sharedjackknife.o : sharedjackknife.cpp
+ $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o
+
+
+# Item # 61 -- sharedmarczewski --
+./sharedmarczewski.o : sharedmarczewski.cpp
+ $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o
+
+
+# Item # 62 -- aligncommand --
+./aligncommand.o : aligncommand.cpp
+ $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o
+
+
+# Item # 63 -- treemap --
+./treemap.o : treemap.cpp
+ $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o
+
+
+# Item # 64 -- parsimonycommand --
+./parsimonycommand.o : parsimonycommand.cpp
+ $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o
+
+
+# Item # 65 -- parsimony --
+./parsimony.o : parsimony.cpp
+ $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o
+
+
+# Item # 66 -- seqsummarycommand --
+./seqsummarycommand.o : seqsummarycommand.cpp
+ $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o
+
+
+# Item # 67 -- chimeraseqscommand --
+./chimeraseqscommand.o : chimeraseqscommand.cpp
+ $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o
+
+
+# Item # 68 -- sharedlistvector --
+./sharedlistvector.o : sharedlistvector.cpp
+ $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o
+
+
+# Item # 69 -- tree --
+./tree.o : tree.cpp
+ $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o
+
+
+# Item # 70 -- readtree --
+./readtree.o : readtree.cpp
+ $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o
+
+
+# Item # 71 -- sharedsobscollectsummary --
+./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp
+ $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o
+
+
+# Item # 72 -- deconvolutecommand --
+./deconvolutecommand.o : deconvolutecommand.cpp
+ $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o
+
+
+# Item # 73 -- listseqscommand --
+./listseqscommand.o : listseqscommand.cpp
+ $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o
+
+
+# Item # 74 -- getseqscommand --
+./getseqscommand.o : getseqscommand.cpp
+ $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o
+
+
+# Item # 75 -- removeseqscommand --
+./removeseqscommand.o : removeseqscommand.cpp
+ $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o
+
+
+# Item # 76 -- systemcommand --
+./systemcommand.o : systemcommand.cpp
+ $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o
+
+
+# Item # 77 -- binsequencecommand --
+./binsequencecommand.o : binsequencecommand.cpp
+ $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o
+
+
+# Item # 78 -- distancecommand --
+./distancecommand.o : distancecommand.cpp
+ $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o
+
+
+# Item # 79 -- ace --
+./ace.o : ace.cpp
+ $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o
+
+
+# Item # 80 -- averagelinkage --
+./averagelinkage.o : averagelinkage.cpp
+ $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o
+
+
+# Item # 81 -- bootstrap --
+./bootstrap.o : bootstrap.cpp
+ $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o
+
+
+# Item # 82 -- calculator --
+./calculator.o : calculator.cpp
+ $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o
+
+
+# Item # 83 -- chao1 --
+./chao1.o : chao1.cpp
+ $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o
+
+
+# Item # 84 -- cluster --
+./cluster.o : cluster.cpp
+ $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o
+
+
+# Item # 85 -- clustercommand --
+./clustercommand.o : clustercommand.cpp
+ $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o
+
+
+# Item # 86 -- collect --
+./collect.o : collect.cpp
+ $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o
+
+
+# Item # 87 -- collectcommand --
+./collectcommand.o : collectcommand.cpp
+ $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o
+
+
+# Item # 88 -- collectsharedcommand --
+./collectsharedcommand.o : collectsharedcommand.cpp
+ $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o
+
+
+# Item # 89 -- commandoptionparser --
+./commandoptionparser.o : commandoptionparser.cpp
+ $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o
+
+
+# Item # 90 -- completelinkage --
+./completelinkage.o : completelinkage.cpp
+ $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o
+
+
+# Item # 91 -- database --
+./database.o : database.cpp
+ $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o
+
+
+# Item # 92 -- engine --
+./engine.o : engine.cpp
+ $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o
+
+
+# Item # 93 -- fastamap --
+./fastamap.o : fastamap.cpp
+ $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o
+
+
+# Item # 94 -- fileoutput --
+./fileoutput.o : fileoutput.cpp
+ $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o
+
+
+# Item # 95 -- globaldata --
+./globaldata.o : globaldata.cpp
+ $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o
+
+
+# Item # 96 -- groupmap --
+./groupmap.o : groupmap.cpp
+ $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o
+
+
+# Item # 97 -- helpcommand --
+./helpcommand.o : helpcommand.cpp
+ $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o
+
+
+# Item # 98 -- inputdata --
+./inputdata.o : inputdata.cpp
+ $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o
+
+
+# Item # 99 -- jackknife --
+./jackknife.o : jackknife.cpp
+ $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o
+
+
+# Item # 100 -- kmer --
+./kmer.o : kmer.cpp
+ $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o
+
+
+# Item # 101 -- kmerdb --
+./kmerdb.o : kmerdb.cpp
+ $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o
+
+
+# Item # 102 -- listvector --
+./listvector.o : listvector.cpp
+ $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o
+
+
+# Item # 103 -- mothur --
+./mothur.o : mothur.cpp
+ $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o
+
+
+# Item # 104 -- nameassignment --
+./nameassignment.o : nameassignment.cpp
+ $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o
+
+
+# Item # 105 -- npshannon --
+./npshannon.o : npshannon.cpp
+ $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o
+
+
+# Item # 106 -- ordervector --
+./ordervector.o : ordervector.cpp
+ $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o
+
+
+# Item # 107 -- progress --
+./progress.o : progress.cpp
+ $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o
+
+
+# Item # 108 -- quitcommand --
+./quitcommand.o : quitcommand.cpp
+ $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o
+
+
+# Item # 109 -- rabundvector --
+./rabundvector.o : rabundvector.cpp
+ $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o
+
+
+# Item # 110 -- rarecalc --
+./rarecalc.o : rarecalc.cpp
+ $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o
+
+
+# Item # 111 -- raredisplay --
+./raredisplay.o : raredisplay.cpp
+ $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o
+
+
+# Item # 112 -- rarefact --
+./rarefact.o : rarefact.cpp
+ $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o
+
+
+# Item # 113 -- rarefactcommand --
+./rarefactcommand.o : rarefactcommand.cpp
+ $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o
+
+
+# Item # 114 -- rarefactsharedcommand --
+./rarefactsharedcommand.o : rarefactsharedcommand.cpp
+ $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o
+
+
+# Item # 115 -- sabundvector --
+./sabundvector.o : sabundvector.cpp
+ $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o
+
+
+# Item # 116 -- sequence --
+./sequence.o : sequence.cpp
+ $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o
+
+
+# Item # 117 -- shannon --
+./shannon.o : shannon.cpp
+ $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o
+
+
+# Item # 118 -- sharedace --
+./sharedace.o : sharedace.cpp
+ $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o
+
+
+# Item # 119 -- sharedchao1 --
+./sharedchao1.o : sharedchao1.cpp
+ $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o
+
+
+# Item # 120 -- sharedcommand --
+./sharedcommand.o : sharedcommand.cpp
+ $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o
+
+
+# Item # 121 -- sharedjabund --
+./sharedjabund.o : sharedjabund.cpp
+ $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o
+
+
+# Item # 122 -- sharedjclass --
+./sharedjclass.o : sharedjclass.cpp
+ $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o
+
+
+# Item # 123 -- sharedjest --
+./sharedjest.o : sharedjest.cpp
+ $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o
+
+
+# Item # 124 -- sharedordervector --
+./sharedordervector.o : sharedordervector.cpp
+ $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o
+
+
+# Item # 125 -- sharedrabundvector --
+./sharedrabundvector.o : sharedrabundvector.cpp
+ $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o
+
+
+# Item # 126 -- sharedsabundvector --
+./sharedsabundvector.o : sharedsabundvector.cpp
+ $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o
+
+
+# Item # 127 -- sharedsobs --
+./sharedsobs.o : sharedsobs.cpp
+ $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o
+
+
+# Item # 128 -- sharedsorabund --
+./sharedsorabund.o : sharedsorabund.cpp
+ $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o
+
+
+# Item # 129 -- sharedsorclass --
+./sharedsorclass.o : sharedsorclass.cpp
+ $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o
+
+
+# Item # 130 -- sharedsorest --
+./sharedsorest.o : sharedsorest.cpp
+ $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o
+
+
+# Item # 131 -- sharedthetan --
+./sharedthetan.o : sharedthetan.cpp
+ $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o
+
+
+# Item # 132 -- sharedthetayc --
+./sharedthetayc.o : sharedthetayc.cpp
+ $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o
+
+
+# Item # 133 -- simpson --
+./simpson.o : simpson.cpp
+ $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o
+
+
+# Item # 134 -- singlelinkage --
+./singlelinkage.o : singlelinkage.cpp
+ $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o
+
+
+# Item # 135 -- sparsematrix --
+./sparsematrix.o : sparsematrix.cpp
+ $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o
+
+
+# Item # 136 -- summarycommand --
+./summarycommand.o : summarycommand.cpp
+ $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o
+
+
+# Item # 137 -- summarysharedcommand --
+./summarysharedcommand.o : summarysharedcommand.cpp
+ $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o
+
+
+# Item # 138 -- uvest --
+./uvest.o : uvest.cpp
+ $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o
+
+
+# Item # 139 -- validcalculator --
+./validcalculator.o : validcalculator.cpp
+ $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o
+
+
+# Item # 140 -- validparameter --
+./validparameter.o : validparameter.cpp
+ $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o
+
+
+# Item # 141 -- treenode --
+./treenode.o : treenode.cpp
+ $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o
+
+
+# Item # 142 -- readtreecommand --
+./readtreecommand.o : readtreecommand.cpp
+ $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o
+
+
+# Item # 143 -- reversecommand --
+./reversecommand.o : reversecommand.cpp
+ $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o
+
+
+# Item # 144 -- trimseqscommand --
+./trimseqscommand.o : trimseqscommand.cpp
+ $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o
+
+
+# Item # 145 -- slibshuff --
+./slibshuff.o : slibshuff.cpp
+ $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o
+
+
+# Item # 146 -- libshuff --
+./libshuff.o : libshuff.cpp
+ $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o
+
+
+# Item # 147 -- dlibshuff --
+./dlibshuff.o : dlibshuff.cpp
+ $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o
+
+
+# Item # 148 -- mergefilecommand --
+./mergefilecommand.o : mergefilecommand.cpp
+ $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o
+
+
+# Item # 149 -- coverage --
+./coverage.o : coverage.cpp
+ $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o
+
+
+# Item # 150 -- whittaker --
+./whittaker.o : whittaker.cpp
+ $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o
+
+
+# Item # 151 -- preclustercommand --
+./preclustercommand.o : preclustercommand.cpp
+ $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o
+
+
+# Item # 152 -- otuhierarchycommand --
+./otuhierarchycommand.o : otuhierarchycommand.cpp
+ $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o
+
+
+# Item # 153 -- setdircommand --
+./setdircommand.o : setdircommand.cpp
+ $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o
+
+
+# Item # 154 -- getgroupcommand --
+./getgroupcommand.o : getgroupcommand.cpp
+ $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o
+
+
+# Item # 155 -- getlabelcommand --
+./getlabelcommand.o : getlabelcommand.cpp
+ $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o
+
+
+# Item # 156 -- secondarystructurecommand --
+./secondarystructurecommand.o : secondarystructurecommand.cpp
+ $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o
+
+
+# Item # 157 -- mothurout --
+./mothurout.o : mothurout.cpp
+ $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o
+
+
+# Item # 158 -- parselistscommand --
+./parselistscommand.o : parselistscommand.cpp
+ $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o
+
+
+# Item # 159 -- readblast --
+./readblast.o : readblast.cpp
+ $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o
+
+
+# Item # 160 -- chimeracheckrdp --
+./chimeracheckrdp.o : chimeracheckrdp.cpp
+ $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o
+
+
+# Item # 161 -- hclustercommand --
+./hclustercommand.o : hclustercommand.cpp
+ $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o
+
+
+# Item # 162 -- hcluster --
+./hcluster.o : hcluster.cpp
+ $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o
+
+
+# Item # 163 -- getlistcountcommand --
+./getlistcountcommand.o : getlistcountcommand.cpp
+ $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o
+
+
+# Item # 164 -- readcluster --
+./readcluster.o : readcluster.cpp
+ $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o
+
+
+# Item # 165 -- ccode --
+./ccode.o : ccode.cpp
+ $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o
+
+
+# Item # 166 -- taxonomyequalizer --
+./taxonomyequalizer.o : taxonomyequalizer.cpp
+ $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o
+
+
+# Item # 167 -- phylotypecommand --
+./phylotypecommand.o : phylotypecommand.cpp
+ $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o
+
+
+# Item # 168 -- classifyseqscommand --
+./classifyseqscommand.o : classifyseqscommand.cpp
+ $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o
+
+
+# Item # 169 -- classify --
+./classify.o : classify.cpp
+ $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o
+
+
+# Item # 170 -- phylotree --
+./phylotree.o : phylotree.cpp
+ $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o
+
+
+# Item # 171 -- bayesian --
+./bayesian.o : bayesian.cpp
+ $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o
+
+
+# Item # 172 -- alignmentdb --
+./alignmentdb.o : alignmentdb.cpp
+ $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o
+
+
+# Item # 173 -- knn --
+./knn.o : knn.cpp
+ $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o
+
+
+# Item # 174 -- distancedb --
+./distancedb.o : distancedb.cpp
+ $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o
+
+
+# Item # 175 -- chimeraslayer --
+./chimeraslayer.o : chimeraslayer.cpp
+ $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o
+
+
+# Item # 176 -- slayer --
+./slayer.o : slayer.cpp
+ $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o
+
+
+# Item # 177 -- pcacommand --
+./pcacommand.o : pcacommand.cpp
+ $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o
+
+
+# Item # 178 -- formatcolumn --
+./formatcolumn.o : formatcolumn.cpp
+ $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o
+
+
+# Item # 179 -- formatphylip --
+./formatphylip.o : formatphylip.cpp
+ $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o
+
+
+# Item # 180 -- mgclustercommand --
+./mgclustercommand.o : mgclustercommand.cpp
+ $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o
+
+
+# Item # 181 -- getsharedotucommand --
+./getsharedotucommand.o : getsharedotucommand.cpp
+ $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o
+
+
+# Item # 182 -- maligner --
+./maligner.o : maligner.cpp
+ $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o
+
+
+# Item # 183 -- chimerarealigner --
+./chimerarealigner.o : chimerarealigner.cpp
+ $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o
+
+
+# Item # 184 -- bergerparker --
+./bergerparker.o : bergerparker.cpp
+ $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o
+
+
+# Item # 185 -- bstick --
+./bstick.o : bstick.cpp
+ $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o
+
+
+# Item # 186 -- sharedkstest --
+./sharedkstest.o : sharedkstest.cpp
+ $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o
+
+
+# Item # 187 -- qstat --
+./qstat.o : qstat.cpp
+ $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o
+
+
+# Item # 188 -- shen --
+./shen.o : shen.cpp
+ $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o
+
+
+# Item # 189 -- logsd --
+./logsd.o : logsd.cpp
+ $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o
+
+
+# Item # 190 -- geom --
+./geom.o : geom.cpp
+ $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o
+
+# Item # 191 -- parsesffcommand --
+./parsesffcommand.o : parsesffcommand.cpp
+ $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o
+
+# Item # 192 -- chimeraccodecommand --
+./chimeraccodecommand.o : chimeraccodecommand.cpp
+ $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o
+
+# Item # 193 -- chimeracheckcommand --
+./chimeracheckcommand.o : chimeracheckcommand.cpp
+ $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o
+
+
+# Item # 194 -- chimeraslayercommand --
+./chimeraslayercommand.o : chimeraslayercommand.cpp
+ $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o
+
+# Item # 195 -- chimerapintailcommand --
+./chimerapintailcommand.o : chimerapintailcommand.cpp
+ $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o
+
+# Item # 196 -- chimerabellerophoncommand --
+./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp
+ $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o
+
+# Item # 197 -- phylosummary --
+./phylosummary.o : phylosummary.cpp
+ $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o
+
+# Item # 198 -- setlogfilecommand --
+./setlogfilecommand.o : setlogfilecommand.cpp
+ $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o
+
+# Item # 199 -- phylodiversity --
+./phylodiversity.o : phylodiversity.cpp
+ $(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o
+
+# Item # 200 -- phylodiversitycommand --
+./phylodiversitycommand.o : phylodiversitycommand.cpp
+ $(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o
+
+# Item # 201 -- makegroupcommand --
+./makegroupcommand.o : makegroupcommand.cpp
+ $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o
+
+# Item # 202 -- chopseqscommand --
+./chopseqscommand.o : chopseqscommand.cpp
$(CC) $(CC_OPTIONS) chopseqscommand.cpp -c $(INCLUDE) -o ./chopseqscommand.o
-# Item # 203 -- clearcutcommand --\r
-./clearcutcommand.o : clearcutcommand.cpp\r
+# Item # 203 -- clearcutcommand --
+./clearcutcommand.o : clearcutcommand.cpp
$(CC) $(CC_OPTIONS) clearcutcommand.cpp -c $(INCLUDE) -o ./clearcutcommand.o
-# Item # 204 -- catchallcommand --\r
-./catchallcommand.o : catchallcommand.cpp\r
- $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o\r
-\r
-##### END RUN ####\r
+# Item # 204 -- catchallcommand --
+./catchallcommand.o : catchallcommand.cpp
+ $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o
+
+# Item # 205 -- catchallcommand --
+./splitabundcommand : splitabundcommand
+ $(CC) $(CC_OPTIONS) splitabundcommand -c $(INCLUDE) -o ./splitabundcommand
+
+##### END RUN ####
--- /dev/null
+/*
+ * splitabundcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 5/17/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "splitabundcommand.h"
+
+//**********************************************************************************************************************
+SplitAbundCommand::SplitAbundCommand(string option) {
+ try {
+ abort = false;
+ wroteRareList = false;
+ wroteAbundList = false;
+ allLines = 1;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"list","name","group","label","accnos","cutoff","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("list");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["list"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+
+ }
+
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ //check for required parameters
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+
+ //check for required parameters
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else {
+ groupMap = new GroupMap(groupfile);
+
+ int error = groupMap->readMap();
+ if (error == 1) { abort = true; }
+ }
+
+ //do you have all files needed
+ if ((listfile == "") && (namefile == "")) { m->mothurOut("You must either a listfile or a namefile for the split.abund command. "); m->mothurOutEndLine(); abort = true; }
+ if ((listfile != "") && (namefile != "")) { m->mothurOut("You must either a listfile or a namefile for the split.abund command, but NOT BOTH. "); m->mothurOutEndLine(); abort = true; }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; allLines = 1; }
+ else {
+ if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ string temp = validParameter.validFile(parameters, "accnos", false); if (temp == "not found") { temp = "F"; }
+ accnos = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, cutoff);
+
+ if (cutoff == 0) { m->mothurOut("You must provide a cutoff to qualify what is abundant for the split.abund command. "); m->mothurOutEndLine(); abort = true; }
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "SplitAbundCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void SplitAbundCommand::help(){
+ try {
+ m->mothurOut("The split.abund command reads a list or a names file splits the sequences into rare and abundant groups.. \n");
+ m->mothurOut("The split.abund command parameters are list, name, cutoff, group, label and accnos.\n");
+ m->mothurOut("The list or name parameter is required, and you must provide a cutoff value.\n");
+ m->mothurOut("The cutoff parameter is used to qualify what is abundant and rare.\n");
+ m->mothurOut("The group parameter allows you to parse a group file into rare and abundant groups.\n");
+ m->mothurOut("The label parameter is used to read specific labels in your listfile you want to use.\n");
+ m->mothurOut("The accnos parameter allows you to output a .rare.accnos and .abund.accnos files to use with the get.seqs and remove.seqs commands.\n");
+ m->mothurOut("The split.abund command should be used in the following format: split.abund(list=yourListFile, group=yourGroupFile, label=yourLabels, cutoff=yourCutoff).\n");
+ m->mothurOut("Example: split.abundt(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, cutoff=2).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "help");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SplitAbundCommand::~SplitAbundCommand(){
+ if (groupfile != "") { delete groupMap; }
+}
+//**********************************************************************************************************************
+int SplitAbundCommand::execute(){
+ try {
+
+ if (abort == true) { return 0; }
+
+ if (namefile != "") { split(); }
+ else {
+
+ //remove old files so you can append later....
+ string fileroot = outputDir + getRootName(getSimpleName(listfile));
+ remove((fileroot + "rare.list").c_str());
+ remove((fileroot + "abund.list").c_str());
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ input = new InputData(listfile, "list");
+ list = input->getListVector();
+ string lastLabel = list->getLabel();
+
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ split(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
+
+ if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+ list = input->getListVector(lastLabel); //get new list vector to process
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ split(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ }
+
+
+ lastLabel = list->getLabel();
+
+ delete list;
+ list = input->getListVector(); //get new list vector to process
+ }
+
+ if (m->control_pressed) { delete input; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+
+ }
+
+ if (m->control_pressed) { delete input; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (list != NULL) { delete list; }
+ list = input->getListVector(lastLabel); //get new list vector to process
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ split(list);
+
+ delete list;
+ }
+
+ delete input;
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ if (wroteAbundList) { outputNames.push_back(fileroot + "abund.list"); }
+ if (wroteRareList) { outputNames.push_back(fileroot + "rare.list"); }
+ }
+
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "execute");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::split(ListVector* thisList) {
+ try {
+
+ SAbundVector* sabund = new SAbundVector();
+ *sabund = thisList->getSAbundVector();
+
+ //find out how many bins are rare and how many are abundant so you can process the list vector one bin at a time
+ // and don't have to store the bins until you are done with the whole vector, this save alot of space.
+ int numRareBins = 0;
+ for (int i = 0; i <= sabund->getMaxRank(); i++) {
+ if (i > cutoff) { break; }
+ numRareBins += sabund->get(i);
+ }
+ int numAbundBins = thisList->getNumBins() - numRareBins;
+ delete sabund;
+
+ //setup output files
+ ofstream outListAbund;
+ ofstream outListRare;
+ ofstream outGroupRare;
+ ofstream outGroupAbund;
+ ofstream outAccnosRare;
+ ofstream outAccnosAbund;
+
+ string fileroot = outputDir + getRootName(getSimpleName(listfile));
+ if (numRareBins > 0) {
+ wroteRareList = true;
+ string listRareName = fileroot + "rare.list";
+ openOutputFileAppend(listRareName, outListRare);
+ outListRare << thisList->getLabel() << '\t' << numRareBins << '\t';
+
+ if (accnos) {
+ string accnosName = fileroot + thisList->getLabel() + ".rare.accnos";
+ openOutputFile(accnosName, outAccnosRare);
+ outputNames.push_back(accnosName);
+ }
+
+ if (groupfile != "") {
+ string groupFileName = outputDir + getRootName(getSimpleName(groupfile)) + thisList->getLabel() + ".rare.group";
+ openOutputFile(groupFileName, outGroupRare);
+ outputNames.push_back(groupFileName);
+ }
+ }
+
+ if (numAbundBins > 0) {
+ wroteAbundList = true;
+ string listAbundName = fileroot + "abund.list";
+ openOutputFileAppend(listAbundName, outListAbund);
+ outListAbund << thisList->getLabel() << '\t' << numAbundBins << '\t';
+
+ if (accnos) {
+ string accnosName = fileroot + thisList->getLabel() + ".abund.accnos";
+ openOutputFile(accnosName, outAccnosAbund);
+ outputNames.push_back(accnosName);
+ }
+
+ if (groupfile != "") {
+ string groupFileName = outputDir + getRootName(getSimpleName(groupfile)) + thisList->getLabel() + ".abund.group";
+ openOutputFile(groupFileName, outGroupAbund);
+ outputNames.push_back(groupFileName);
+ }
+ }
+
+ for (int i = 0; i < thisList->getNumBins(); i++) {
+ if (m->control_pressed) { break; }
+
+ string bin = list->get(i);
+
+ int size = getNumNames(bin);
+
+ if (size <= cutoff) { outListRare << bin << '\t'; }
+ else { outListAbund << bin << '\t'; }
+
+ if ((groupfile != "") || (accnos)) { //you need to parse the bin...
+ vector<string> names;
+ splitAtComma(bin, names); //parses bin into individual sequence names
+
+ //parse bin into list of sequences in each group
+ for (int j = 0; j < names.size(); j++) {
+
+ //write to accnos file
+ if (accnos) {
+ if (size <= cutoff) { outAccnosRare << names[j] << endl; }
+ else { outAccnosAbund << names[j] << endl; }
+ }
+
+ //write to groupfile
+ if (groupfile != "") {
+ string group = groupMap->getGroup(names[j]);
+
+ if (group == "not found") { //error in groupfile so close and remove output file and disregard groupfile
+ m->mothurOut(names[j] + " is not in your groupfile. disregarding groupfile."); m->mothurOutEndLine();
+ delete groupMap;
+ if (numAbundBins > 0) {
+ outGroupAbund.close();
+ remove((outputDir + getRootName(getSimpleName(groupfile)) + thisList->getLabel() + ".abund.group").c_str());
+ }
+ if (numRareBins > 0) {
+ outGroupRare.close();
+ remove((outputDir + getRootName(getSimpleName(groupfile)) + thisList->getLabel() + ".rare.group").c_str());
+ }
+ groupfile = "";
+ }else {
+ if (size <= cutoff) { outGroupRare << names[j] << '\t' << group << endl; }
+ else { outGroupAbund << names[j] << '\t' << group << endl; }
+ }
+ }
+
+ }//end for names
+ }//end if parse
+ }//end for list
+
+
+ //close files
+ if (numRareBins > 0) {
+ outListRare << endl;
+ outListRare.close();
+ if (accnos) { outAccnosRare.close(); }
+ if (groupfile != "") { outGroupRare.close(); }
+ }
+
+ if (numAbundBins > 0) {
+ outListAbund << endl;
+ outListAbund.close();
+ if (accnos) { outAccnosAbund.close(); }
+ if (groupfile != "") { outGroupAbund.close(); }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "split");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::split() { //namefile
+ try {
+ //setup output files
+ ofstream outNameAbund;
+ ofstream outNameRare;
+ ofstream outGroupRare;
+ ofstream outGroupAbund;
+ ofstream outAccnosRare;
+ ofstream outAccnosAbund;
+
+ bool wroteNameAbund = false;
+ bool wroteNameRare = false;
+ bool wroteGroupRare = false;
+ bool wroteGroupAbund = false;
+ bool wroteAccnosRare = false;
+ bool wroteAccnosAbund = false;
+
+ //prepare output files
+ string fileroot = outputDir + getRootName(getSimpleName(namefile));
+
+ string nameRareName = fileroot + "rare.names";
+ openOutputFile(nameRareName, outNameRare);
+ string nameAbundName = fileroot + "abund.names";
+ openOutputFile(nameAbundName, outNameAbund);
+
+ if (accnos) {
+ string accnosName = fileroot + "rare.accnos";
+ openOutputFile(accnosName, outAccnosRare);
+
+ accnosName = fileroot + "abund.accnos";
+ openOutputFile(accnosName, outAccnosAbund);
+ }
+
+ if (groupfile != "") {
+ string groupFileName = outputDir + getRootName(getSimpleName(groupfile)) + ".rare.group";
+ openOutputFile(groupFileName, outGroupRare);
+
+ groupFileName = outputDir + getRootName(getSimpleName(groupfile)) + ".abund.group";
+ openOutputFile(groupFileName, outGroupAbund);
+ }
+
+
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ string firstCol, secondCol;
+ in >> firstCol >> secondCol; gobble(in);
+
+ int size = getNumNames(secondCol);
+
+ if (size <= cutoff) { outNameRare << firstCol << '\t' << secondCol << endl; wroteNameRare = true; }
+ else { outNameAbund << firstCol << '\t' << secondCol << endl; wroteNameAbund = true; }
+
+
+ if ((groupfile != "") || (accnos)) { //you need to parse the bin...
+ vector<string> names;
+ splitAtComma(secondCol, names); //parses bin into individual sequence names
+
+ //parse bin into list of sequences in each group
+ for (int j = 0; j < names.size(); j++) {
+
+ //write to accnos file
+ if (accnos) {
+ if (size <= cutoff) { outAccnosRare << names[j] << endl; wroteAccnosRare = true; }
+ else { outAccnosAbund << names[j] << endl; wroteAccnosAbund = true; }
+ }
+
+ //write to groupfile
+ if (groupfile != "") {
+ string group = groupMap->getGroup(names[j]);
+
+ if (group == "not found") { //error in groupfile so close and remove output file and disregard groupfile
+ m->mothurOut(names[j] + " is not in your groupfile. disregarding groupfile."); m->mothurOutEndLine();
+ delete groupMap;
+
+ outGroupAbund.close();
+ remove((outputDir + getRootName(getSimpleName(groupfile)) + ".abund.group").c_str());
+ outGroupRare.close();
+ remove((outputDir + getRootName(getSimpleName(groupfile)) + ".rare.group").c_str());
+
+ groupfile = "";
+ wroteGroupRare = false;
+ wroteGroupAbund = false;
+ }else {
+ if (size <= cutoff) { outGroupRare << names[j] << '\t' << group << endl; wroteGroupRare = true; }
+ else { outGroupAbund << names[j] << '\t' << group << endl; wroteGroupAbund = true; }
+ }
+ }
+
+ }//end for names
+ }//end if parse
+ }//end while
+
+
+ //close files
+ in.close();
+ outNameRare.close();
+ outNameAbund.close();
+ if (!wroteNameRare) { remove((fileroot + "rare.names").c_str()); }
+ else { outputNames.push_back((fileroot + "rare.names")); }
+ if (!wroteNameAbund) { remove((fileroot + "abund.names").c_str()); }
+ else { outputNames.push_back((fileroot + "abund.names")); }
+
+ if (groupfile != "") {
+ outGroupRare.close(); outGroupAbund.close();
+ if (!wroteGroupRare) { remove((outputDir + getRootName(getSimpleName(groupfile)) + ".rare.group").c_str()); }
+ else { outputNames.push_back((outputDir + getRootName(getSimpleName(groupfile)) + ".rare.group")); }
+ if (!wroteGroupAbund) { remove((outputDir + getRootName(getSimpleName(groupfile)) + ".abund.group").c_str()); }
+ else { outputNames.push_back((outputDir + getRootName(getSimpleName(groupfile)) + ".abund.group")); }
+ }
+
+ if (accnos) {
+ outAccnosAbund.close(); outAccnosRare.close();
+ if (!wroteAccnosRare) { remove((fileroot + "rare.accnos").c_str()); }
+ else { outputNames.push_back((fileroot + "rare.accnos")); }
+ if (!wroteAccnosAbund) { remove((fileroot + "abund.accnos").c_str()); }
+ else { outputNames.push_back((fileroot + "abund.accnos")); }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "split");
+ exit(1);
+ }
+}
+
+/**********************************************************************************************************************/
+
+
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