From: westcott Date: Wed, 5 Jan 2011 13:42:03 +0000 (+0000) Subject: changed filename of pcacommand to pcoacommand X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=4956d362c5bc6a47cf7a6290258f0e763e3a406e changed filename of pcacommand to pcoacommand --- diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 1e52e09..e7e8183 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -157,7 +157,7 @@ A7E9B91212D37EC400DA6239 /* parselistscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */; }; A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78312D37EC400DA6239 /* parsimony.cpp */; }; A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */; }; - A7E9B91512D37EC400DA6239 /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78712D37EC400DA6239 /* pcacommand.cpp */; }; + A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */; }; A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */; }; A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */; }; A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */; }; @@ -296,7 +296,7 @@ /* End PBXCopyFilesBuildPhase section */ /* Begin PBXFileReference section */ - 8DD76FB20486AB0100D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; }; + 8DD76FB20486AB0100D96B5E /* Mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Mothur; sourceTree = BUILT_PRODUCTS_DIR; }; A70332B512D3A13400761E33 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = ""; }; A7E9B64F12D37EC300DA6239 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = ""; }; A7E9B65012D37EC300DA6239 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = ""; }; @@ -610,8 +610,8 @@ A7E9B78412D37EC400DA6239 /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = ""; }; A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.cpp; sourceTree = ""; }; A7E9B78612D37EC400DA6239 /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = ""; }; - A7E9B78712D37EC400DA6239 /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = ""; }; - A7E9B78812D37EC400DA6239 /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = ""; }; + A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcoacommand.cpp; sourceTree = ""; }; + A7E9B78812D37EC400DA6239 /* pcoacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcoacommand.h; sourceTree = ""; }; A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversity.cpp; sourceTree = ""; }; A7E9B78A12D37EC400DA6239 /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = ""; }; A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversitycommand.cpp; sourceTree = ""; }; @@ -983,7 +983,7 @@ 1AB674ADFE9D54B511CA2CBB /* Products */ = { isa = PBXGroup; children = ( - 8DD76FB20486AB0100D96B5E /* mothur */, + 8DD76FB20486AB0100D96B5E /* Mothur */, ); name = Products; sourceTree = ""; @@ -1110,8 +1110,8 @@ A7E9B78212D37EC400DA6239 /* parselistscommand.h */, A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */, A7E9B78612D37EC400DA6239 /* parsimonycommand.h */, - A7E9B78712D37EC400DA6239 /* pcacommand.cpp */, - A7E9B78812D37EC400DA6239 /* pcacommand.h */, + A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */, + A7E9B78812D37EC400DA6239 /* pcoacommand.h */, A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */, A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */, A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */, @@ -1537,9 +1537,9 @@ /* End PBXGroup section */ /* Begin PBXNativeTarget section */ - 8DD76FA90486AB0100D96B5E /* mothur */ = { + 8DD76FA90486AB0100D96B5E /* Mothur */ = { isa = PBXNativeTarget; - buildConfigurationList = 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "mothur" */; + buildConfigurationList = 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */; buildPhases = ( 8DD76FAB0486AB0100D96B5E /* Sources */, 8DD76FAD0486AB0100D96B5E /* Frameworks */, @@ -1549,10 +1549,10 @@ ); dependencies = ( ); - name = mothur; + name = Mothur; productInstallPath = "$(HOME)/bin"; productName = mothur; - productReference = 8DD76FB20486AB0100D96B5E /* mothur */; + productReference = 8DD76FB20486AB0100D96B5E /* Mothur */; productType = "com.apple.product-type.tool"; }; /* End PBXNativeTarget section */ @@ -1574,7 +1574,7 @@ projectDirPath = ""; projectRoot = ""; targets = ( - 8DD76FA90486AB0100D96B5E /* mothur */, + 8DD76FA90486AB0100D96B5E /* Mothur */, ); }; /* End PBXProject section */ @@ -1732,7 +1732,7 @@ A7E9B91212D37EC400DA6239 /* parselistscommand.cpp in Sources */, A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */, A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */, - A7E9B91512D37EC400DA6239 /* pcacommand.cpp in Sources */, + A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */, A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */, A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */, A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */, @@ -1872,7 +1872,7 @@ GCC_MODEL_TUNING = G5; GCC_OPTIMIZATION_LEVEL = 0; INSTALL_PATH = /usr/local/bin; - PRODUCT_NAME = mothur; + PRODUCT_NAME = Mothur; }; name = Debug; }; @@ -1885,7 +1885,7 @@ GCC_MODEL_TUNING = G5; GCC_WARN_UNUSED_VALUE = YES; INSTALL_PATH = ./; - PRODUCT_NAME = mothur; + PRODUCT_NAME = Mothur; }; name = Release; }; @@ -1956,7 +1956,7 @@ /* End XCBuildConfiguration section */ /* Begin XCConfigurationList section */ - 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = { + 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */ = { isa = XCConfigurationList; buildConfigurations = ( 1DEB928608733DD80010E9CD /* Debug */, diff --git a/pcacommand.cpp b/pcacommand.cpp deleted file mode 100644 index ee0a546..0000000 --- a/pcacommand.cpp +++ /dev/null @@ -1,607 +0,0 @@ - -/* - * pcacommand.cpp - * Mothur - * - * Created by westcott on 1/4/10. - * Copyright 2010 Schloss Lab. All rights reserved. - * - */ - -#include "pcacommand.h" - -//********************************************************************************************************************** -vector PCACommand::getValidParameters(){ - try { - string Array[] = {"phylip", "outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "PCACommand", "getValidParameters"); - exit(1); - } -} -//********************************************************************************************************************** -PCACommand::PCACommand(){ - try { - abort = true; - //initialize outputTypes - vector tempOutNames; - outputTypes["pcoa"] = tempOutNames; - outputTypes["loadings"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "PCACommand", "PCACommand"); - exit(1); - } -} -//********************************************************************************************************************** -vector PCACommand::getRequiredParameters(){ - try { - string Array[] = {"phylip"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "PCACommand", "getRequiredParameters"); - exit(1); - } -} -//********************************************************************************************************************** -vector PCACommand::getRequiredFiles(){ - try { - vector myArray; - return myArray; - } - catch(exception& e) { - m->errorOut(e, "PCACommand", "getRequiredFiles"); - exit(1); - } -} -//********************************************************************************************************************** - -PCACommand::PCACommand(string option) { - try { - abort = false; - - //allow user to run help - if(option == "help") { help(); abort = true; } - - else { - //valid paramters for this command - string Array[] = {"phylip","outputdir", "inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - - OptionParser parser(option); - map parameters = parser. getParameters(); - - ValidParameters validParameter; - map::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("phylip"); - //user has given a template file - if(it != parameters.end()){ - path = m->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; } - } - } - - //initialize outputTypes - vector tempOutNames; - outputTypes["pcoa"] = tempOutNames; - outputTypes["loadings"] = tempOutNames; - - //required parameters - phylipfile = validParameter.validFile(parameters, "phylip", true); - if (phylipfile == "not open") { abort = true; } - else if (phylipfile == "not found") { phylipfile = ""; abort = true; } - else { filename = phylipfile; } - - //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 = ""; - outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it - } - - //error checking on files - if (phylipfile == "") { m->mothurOut("You must provide a distance file before running the pca command."); m->mothurOutEndLine(); abort = true; } - } - - } - catch(exception& e) { - m->errorOut(e, "PCACommand", "PCACommand"); - exit(1); - } -} -//********************************************************************************************************************** -void PCACommand::help(){ - try { - - m->mothurOut("The pca command..."); m->mothurOutEndLine(); - } - catch(exception& e) { - m->errorOut(e, "PCACommand", "help"); - exit(1); - } -} -//********************************************************************************************************************** -PCACommand::~PCACommand(){} -//********************************************************************************************************************** -int PCACommand::execute(){ - try { - - if (abort == true) { return 0; } - - cout.setf(ios::fixed, ios::floatfield); - cout.setf(ios::showpoint); - cerr.setf(ios::fixed, ios::floatfield); - cerr.setf(ios::showpoint); - - vector names; - vector > D; - - fbase = outputDir + m->getRootName(m->getSimpleName(filename)); - - read(filename, names, D); - - if (m->control_pressed) { return 0; } - - double offset = 0.0000; - vector d; - vector e; - vector > G = D; - vector > copy_G; - //int rank = D.size(); - - m->mothurOut("\nProcessing...\n"); - - for(int count=0;count<2;count++){ - recenter(offset, D, G); if (m->control_pressed) { return 0; } - tred2(G, d, e); if (m->control_pressed) { return 0; } - qtli(d, e, G); if (m->control_pressed) { return 0; } - offset = d[d.size()-1]; - if(offset > 0.0) break; - } - - if (m->control_pressed) { return 0; } - - output(fbase, names, G, d); - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } - - 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, "PCACommand", "execute"); - exit(1); - } -} -/*********************************************************************************************************************************/ - -inline double SIGN(const double a, const double b) -{ - return b>=0 ? (a>=0 ? a:-a) : (a>=0 ? -a:a); -} - -/*********************************************************************************************************************************/ - -void PCACommand::get_comment(istream& f, char begin, char end){ - try { - char d=f.get(); - while(d != end){ d = f.get(); } - d = f.peek(); - } - catch(exception& e) { - m->errorOut(e, "PCACommand", "get_comment"); - exit(1); - } -} - -/*********************************************************************************************************************************/ - -int PCACommand::read_phylip(istream& f, int square_m, vector& name_list, vector >& d){ - try { - // int count1=0; - // int count2=0; - - int rank; - f >> rank; - - name_list.resize(rank); - d.resize(rank); - if(square_m == 1){ - for(int i=0;i> name_list[i]; - // cout << i << "\t" << name_list[i] << endl; - for(int j=0;jcontrol_pressed) { return 0; } - - f >> d[i][j]; - if (d[i][j] == -0.0000) - d[i][j] = 0.0000; - } - } - } - else if(square_m == 2){ - for(int i=0;i> name_list[0]; - for(int i=1;i> name_list[i]; - d[i][i]=0.0000; - for(int j=0;jcontrol_pressed) { return 0; } - f >> d[i][j]; - if (d[i][j] == -0.0000) - d[i][j] = 0.0000; - d[j][i]=d[i][j]; - } - } - } - - return 0; - } - catch(exception& e) { - m->errorOut(e, "PCACommand", "read_phylip"); - exit(1); - } - -} - -/*********************************************************************************************************************************/ - -void PCACommand::read(string fname, vector& names, vector >& D){ - try { - ifstream f; - m->openInputFile(fname, f); - - //check whether matrix is square - char d; - int q = 1; - int numSeqs; - string name; - - f >> numSeqs >> name; - - while((d=f.get()) != EOF){ - - //is d a number meaning its square - if(isalnum(d)){ - q = 1; - break; - } - - //is d a line return meaning its lower triangle - if(d == '\n'){ - q = 2; - break; - } - } - f.close(); - - //reopen to get back to beginning - m->openInputFile(fname, f); - read_phylip(f, q, names, D); - } - catch(exception& e) { - m->errorOut(e, "PCACommand", "read"); - exit(1); - } -} - -/*********************************************************************************************************************************/ - -double PCACommand::pythag(double a, double b) { return(pow(a*a+b*b,0.5)); } - -/*********************************************************************************************************************************/ - -void PCACommand::matrix_mult(vector > first, vector > second, vector >& product){ - try { - int first_rows = first.size(); - int first_cols = first[0].size(); - int second_cols = second[0].size(); - - product.resize(first_rows); - for(int i=0;ierrorOut(e, "PCACommand", "matrix_mult"); - exit(1); - } - -} - -/*********************************************************************************************************************************/ - -void PCACommand::recenter(double offset, vector > D, vector >& G){ - try { - int rank = D.size(); - - vector > A(rank); - vector > C(rank); - for(int i=0;ierrorOut(e, "PCACommand", "recenter"); - exit(1); - } - -} - -/*********************************************************************************************************************************/ - -// This function is taken from Numerical Recipes in C++ by Press et al., 2nd edition, pg. 479 - -void PCACommand::tred2(vector >& a, vector& d, vector& e){ - try { - double scale, hh, h, g, f; - - int n = a.size(); - - d.resize(n); - e.resize(n); - - for(int i=n-1;i>0;i--){ - int l=i-1; - h = scale = 0.0000; - if(l>0){ - for(int k=0;k= 0.0 ? -sqrt(h) : sqrt(h)); - e[i] = scale * g; - h -= f * g; - a[i][l] = f - g; - f = 0.0; - for(int j=0;jerrorOut(e, "PCACommand", "tred2"); - exit(1); - } - -} - -/*********************************************************************************************************************************/ - -// This function is taken from Numerical Recipes in C++ by Press et al., 2nd edition, pg. 479 - -void PCACommand::qtli(vector& d, vector& e, vector >& z) { - try { - int m, i, iter; - double s, r, p, g, f, dd, c, b; - - int n = d.size(); - for(int i=1;i<=n;i++){ - e[i-1] = e[i]; - } - e[n-1] = 0.0000; - - for(int l=0;l=l;i--){ - f = s * e[i]; - b = c * e[i]; - e[i+1] = (r=pythag(f,g)); - if(r==0.0){ - d[i+1] -= p; - e[m] = 0.0000; - break; - } - s = f / r; - c = g / r; - g = d[i+1] - p; - r = (d[i] - g) * s + 2.0 * c * b; - d[i+1] = g + ( p = s * r); - g = c * r - b; - for(int k=0;k= l) continue; - d[l] -= p; - e[l] = g; - e[m] = 0.0; - } - } while (m != l); - } - - int k; - for(int i=0;i= p){ - p=d[k=j]; - } - } - if(k!=i){ - d[k]=d[i]; - d[i]=p; - for(int j=0;jerrorOut(e, "PCACommand", "qtli"); - exit(1); - } -} - -/*********************************************************************************************************************************/ - -void PCACommand::output(string fnameRoot, vector name_list, vector > G, vector d) { - try { - int rank = name_list.size(); - double dsum = 0.0000; - for(int i=0;i= 0) { G[i][j] *= pow(d[j],0.5); } - else { G[i][j] = 0.00000; } - } - } - - ofstream pcaData((fnameRoot+"pcoa").c_str(), ios::trunc); - pcaData.setf(ios::fixed, ios::floatfield); - pcaData.setf(ios::showpoint); - outputNames.push_back(fnameRoot+"pcoa"); - outputTypes["pcoa"].push_back(fnameRoot+"pcoa"); - - ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc); - pcaLoadings.setf(ios::fixed, ios::floatfield); - pcaLoadings.setf(ios::showpoint); - outputNames.push_back(fnameRoot+"pcoa.loadings"); - outputTypes["loadings"].push_back(fnameRoot+"pcoa.loadings"); - - pcaLoadings << "axis\tloading\n"; - for(int i=0;ierrorOut(e, "PCACommand", "output"); - exit(1); - } -} - -/*********************************************************************************************************************************/ - diff --git a/pcacommand.h b/pcacommand.h deleted file mode 100644 index 22f288a..0000000 --- a/pcacommand.h +++ /dev/null @@ -1,53 +0,0 @@ -#ifndef PCACOMMAND_H -#define PCACOMMAND_H - -/* - * pcacommand.h - * Mothur - * - * Created by westcott on 1/4/10. - * Copyright 2010 Schloss Lab. All rights reserved. - * - */ - -#include "command.hpp" - - -/*****************************************************************/ -class PCACommand : public Command { - -public: - PCACommand(string); - PCACommand(); - ~PCACommand(); - vector getRequiredParameters(); - vector getValidParameters(); - vector getRequiredFiles(); - map > getOutputFiles() { return outputTypes; } - int execute(); - void help(); - -private: - - bool abort; - string phylipfile, columnfile, namefile, format, filename, fbase, outputDir; - float cutoff, precision; - vector outputNames; - map > outputTypes; - - void get_comment(istream&, char, char); - int read_phylip(istream&, int, vector&, vector >&); - void read(string, vector&, vector >&); - double pythag(double, double); - void matrix_mult(vector >, vector >, vector >&); - void recenter(double, vector >, vector >&); - void tred2(vector >&, vector&, vector&); - void qtli(vector&, vector&, vector >&); - void output(string, vector, vector >, vector); - -}; - -/*****************************************************************/ - -#endif - diff --git a/pcoacommand.cpp b/pcoacommand.cpp new file mode 100644 index 0000000..ee0a546 --- /dev/null +++ b/pcoacommand.cpp @@ -0,0 +1,607 @@ + +/* + * pcacommand.cpp + * Mothur + * + * Created by westcott on 1/4/10. + * Copyright 2010 Schloss Lab. All rights reserved. + * + */ + +#include "pcacommand.h" + +//********************************************************************************************************************** +vector PCACommand::getValidParameters(){ + try { + string Array[] = {"phylip", "outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "PCACommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +PCACommand::PCACommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["pcoa"] = tempOutNames; + outputTypes["loadings"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "PCACommand", "PCACommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector PCACommand::getRequiredParameters(){ + try { + string Array[] = {"phylip"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "PCACommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector PCACommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "PCACommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** + +PCACommand::PCACommand(string option) { + try { + abort = false; + + //allow user to run help + if(option == "help") { help(); abort = true; } + + else { + //valid paramters for this command + string Array[] = {"phylip","outputdir", "inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + OptionParser parser(option); + map parameters = parser. getParameters(); + + ValidParameters validParameter; + map::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("phylip"); + //user has given a template file + if(it != parameters.end()){ + path = m->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; } + } + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["pcoa"] = tempOutNames; + outputTypes["loadings"] = tempOutNames; + + //required parameters + phylipfile = validParameter.validFile(parameters, "phylip", true); + if (phylipfile == "not open") { abort = true; } + else if (phylipfile == "not found") { phylipfile = ""; abort = true; } + else { filename = phylipfile; } + + //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 = ""; + outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it + } + + //error checking on files + if (phylipfile == "") { m->mothurOut("You must provide a distance file before running the pca command."); m->mothurOutEndLine(); abort = true; } + } + + } + catch(exception& e) { + m->errorOut(e, "PCACommand", "PCACommand"); + exit(1); + } +} +//********************************************************************************************************************** +void PCACommand::help(){ + try { + + m->mothurOut("The pca command..."); m->mothurOutEndLine(); + } + catch(exception& e) { + m->errorOut(e, "PCACommand", "help"); + exit(1); + } +} +//********************************************************************************************************************** +PCACommand::~PCACommand(){} +//********************************************************************************************************************** +int PCACommand::execute(){ + try { + + if (abort == true) { return 0; } + + cout.setf(ios::fixed, ios::floatfield); + cout.setf(ios::showpoint); + cerr.setf(ios::fixed, ios::floatfield); + cerr.setf(ios::showpoint); + + vector names; + vector > D; + + fbase = outputDir + m->getRootName(m->getSimpleName(filename)); + + read(filename, names, D); + + if (m->control_pressed) { return 0; } + + double offset = 0.0000; + vector d; + vector e; + vector > G = D; + vector > copy_G; + //int rank = D.size(); + + m->mothurOut("\nProcessing...\n"); + + for(int count=0;count<2;count++){ + recenter(offset, D, G); if (m->control_pressed) { return 0; } + tred2(G, d, e); if (m->control_pressed) { return 0; } + qtli(d, e, G); if (m->control_pressed) { return 0; } + offset = d[d.size()-1]; + if(offset > 0.0) break; + } + + if (m->control_pressed) { return 0; } + + output(fbase, names, G, d); + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + + 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, "PCACommand", "execute"); + exit(1); + } +} +/*********************************************************************************************************************************/ + +inline double SIGN(const double a, const double b) +{ + return b>=0 ? (a>=0 ? a:-a) : (a>=0 ? -a:a); +} + +/*********************************************************************************************************************************/ + +void PCACommand::get_comment(istream& f, char begin, char end){ + try { + char d=f.get(); + while(d != end){ d = f.get(); } + d = f.peek(); + } + catch(exception& e) { + m->errorOut(e, "PCACommand", "get_comment"); + exit(1); + } +} + +/*********************************************************************************************************************************/ + +int PCACommand::read_phylip(istream& f, int square_m, vector& name_list, vector >& d){ + try { + // int count1=0; + // int count2=0; + + int rank; + f >> rank; + + name_list.resize(rank); + d.resize(rank); + if(square_m == 1){ + for(int i=0;i> name_list[i]; + // cout << i << "\t" << name_list[i] << endl; + for(int j=0;jcontrol_pressed) { return 0; } + + f >> d[i][j]; + if (d[i][j] == -0.0000) + d[i][j] = 0.0000; + } + } + } + else if(square_m == 2){ + for(int i=0;i> name_list[0]; + for(int i=1;i> name_list[i]; + d[i][i]=0.0000; + for(int j=0;jcontrol_pressed) { return 0; } + f >> d[i][j]; + if (d[i][j] == -0.0000) + d[i][j] = 0.0000; + d[j][i]=d[i][j]; + } + } + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "PCACommand", "read_phylip"); + exit(1); + } + +} + +/*********************************************************************************************************************************/ + +void PCACommand::read(string fname, vector& names, vector >& D){ + try { + ifstream f; + m->openInputFile(fname, f); + + //check whether matrix is square + char d; + int q = 1; + int numSeqs; + string name; + + f >> numSeqs >> name; + + while((d=f.get()) != EOF){ + + //is d a number meaning its square + if(isalnum(d)){ + q = 1; + break; + } + + //is d a line return meaning its lower triangle + if(d == '\n'){ + q = 2; + break; + } + } + f.close(); + + //reopen to get back to beginning + m->openInputFile(fname, f); + read_phylip(f, q, names, D); + } + catch(exception& e) { + m->errorOut(e, "PCACommand", "read"); + exit(1); + } +} + +/*********************************************************************************************************************************/ + +double PCACommand::pythag(double a, double b) { return(pow(a*a+b*b,0.5)); } + +/*********************************************************************************************************************************/ + +void PCACommand::matrix_mult(vector > first, vector > second, vector >& product){ + try { + int first_rows = first.size(); + int first_cols = first[0].size(); + int second_cols = second[0].size(); + + product.resize(first_rows); + for(int i=0;ierrorOut(e, "PCACommand", "matrix_mult"); + exit(1); + } + +} + +/*********************************************************************************************************************************/ + +void PCACommand::recenter(double offset, vector > D, vector >& G){ + try { + int rank = D.size(); + + vector > A(rank); + vector > C(rank); + for(int i=0;ierrorOut(e, "PCACommand", "recenter"); + exit(1); + } + +} + +/*********************************************************************************************************************************/ + +// This function is taken from Numerical Recipes in C++ by Press et al., 2nd edition, pg. 479 + +void PCACommand::tred2(vector >& a, vector& d, vector& e){ + try { + double scale, hh, h, g, f; + + int n = a.size(); + + d.resize(n); + e.resize(n); + + for(int i=n-1;i>0;i--){ + int l=i-1; + h = scale = 0.0000; + if(l>0){ + for(int k=0;k= 0.0 ? -sqrt(h) : sqrt(h)); + e[i] = scale * g; + h -= f * g; + a[i][l] = f - g; + f = 0.0; + for(int j=0;jerrorOut(e, "PCACommand", "tred2"); + exit(1); + } + +} + +/*********************************************************************************************************************************/ + +// This function is taken from Numerical Recipes in C++ by Press et al., 2nd edition, pg. 479 + +void PCACommand::qtli(vector& d, vector& e, vector >& z) { + try { + int m, i, iter; + double s, r, p, g, f, dd, c, b; + + int n = d.size(); + for(int i=1;i<=n;i++){ + e[i-1] = e[i]; + } + e[n-1] = 0.0000; + + for(int l=0;l=l;i--){ + f = s * e[i]; + b = c * e[i]; + e[i+1] = (r=pythag(f,g)); + if(r==0.0){ + d[i+1] -= p; + e[m] = 0.0000; + break; + } + s = f / r; + c = g / r; + g = d[i+1] - p; + r = (d[i] - g) * s + 2.0 * c * b; + d[i+1] = g + ( p = s * r); + g = c * r - b; + for(int k=0;k= l) continue; + d[l] -= p; + e[l] = g; + e[m] = 0.0; + } + } while (m != l); + } + + int k; + for(int i=0;i= p){ + p=d[k=j]; + } + } + if(k!=i){ + d[k]=d[i]; + d[i]=p; + for(int j=0;jerrorOut(e, "PCACommand", "qtli"); + exit(1); + } +} + +/*********************************************************************************************************************************/ + +void PCACommand::output(string fnameRoot, vector name_list, vector > G, vector d) { + try { + int rank = name_list.size(); + double dsum = 0.0000; + for(int i=0;i= 0) { G[i][j] *= pow(d[j],0.5); } + else { G[i][j] = 0.00000; } + } + } + + ofstream pcaData((fnameRoot+"pcoa").c_str(), ios::trunc); + pcaData.setf(ios::fixed, ios::floatfield); + pcaData.setf(ios::showpoint); + outputNames.push_back(fnameRoot+"pcoa"); + outputTypes["pcoa"].push_back(fnameRoot+"pcoa"); + + ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc); + pcaLoadings.setf(ios::fixed, ios::floatfield); + pcaLoadings.setf(ios::showpoint); + outputNames.push_back(fnameRoot+"pcoa.loadings"); + outputTypes["loadings"].push_back(fnameRoot+"pcoa.loadings"); + + pcaLoadings << "axis\tloading\n"; + for(int i=0;ierrorOut(e, "PCACommand", "output"); + exit(1); + } +} + +/*********************************************************************************************************************************/ + diff --git a/pcoacommand.h b/pcoacommand.h new file mode 100644 index 0000000..22f288a --- /dev/null +++ b/pcoacommand.h @@ -0,0 +1,53 @@ +#ifndef PCACOMMAND_H +#define PCACOMMAND_H + +/* + * pcacommand.h + * Mothur + * + * Created by westcott on 1/4/10. + * Copyright 2010 Schloss Lab. All rights reserved. + * + */ + +#include "command.hpp" + + +/*****************************************************************/ +class PCACommand : public Command { + +public: + PCACommand(string); + PCACommand(); + ~PCACommand(); + vector getRequiredParameters(); + vector getValidParameters(); + vector getRequiredFiles(); + map > getOutputFiles() { return outputTypes; } + int execute(); + void help(); + +private: + + bool abort; + string phylipfile, columnfile, namefile, format, filename, fbase, outputDir; + float cutoff, precision; + vector outputNames; + map > outputTypes; + + void get_comment(istream&, char, char); + int read_phylip(istream&, int, vector&, vector >&); + void read(string, vector&, vector >&); + double pythag(double, double); + void matrix_mult(vector >, vector >, vector >&); + void recenter(double, vector >, vector >&); + void tred2(vector >&, vector&, vector&); + void qtli(vector&, vector&, vector >&); + void output(string, vector, vector >, vector); + +}; + +/*****************************************************************/ + +#endif +