From f230fb6e52e16dace3680d5a7ebe1dae59033ec6 Mon Sep 17 00:00:00 2001 From: pschloss Date: Thu, 4 Jun 2009 17:33:37 +0000 Subject: [PATCH] remove some files --- Mothur.xcodeproj/project.pbxproj | 20 ++++----- readnexus.cpp | 72 -------------------------------- readnexus.h | 29 ------------- readseqs.cpp | 40 ------------------ readseqsphylip.h | 32 -------------- 5 files changed, 10 insertions(+), 183 deletions(-) delete mode 100644 readnexus.cpp delete mode 100644 readnexus.h delete mode 100644 readseqs.cpp delete mode 100644 readseqsphylip.h diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index fea328d..8d362b6 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -184,8 +184,8 @@ 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = matrixoutputcommand.cpp; sourceTree = SOURCE_ROOT; }; 370B88050F8A4EE4005AB382 /* getoturepcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getoturepcommand.h; sourceTree = SOURCE_ROOT; }; 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getoturepcommand.cpp; sourceTree = SOURCE_ROOT; }; - 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = screenseqscommand.cpp; sourceTree = ""; }; - 371B30B30FD7EE67000414CA /* screenseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = screenseqscommand.h; sourceTree = ""; }; + 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = screenseqscommand.cpp; sourceTree = SOURCE_ROOT; }; + 371B30B30FD7EE67000414CA /* screenseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = screenseqscommand.h; sourceTree = SOURCE_ROOT; }; 372E126E0F26365B0095CF7E /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = SOURCE_ROOT; }; 372E126F0F26365B0095CF7E /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = SOURCE_ROOT; }; 372E12940F263D5A0095CF7E /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = SOURCE_ROOT; }; @@ -231,10 +231,10 @@ 374610820F40652400460C57 /* unweighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unweighted.cpp; sourceTree = SOURCE_ROOT; }; 3746109B0F40657600460C57 /* unifracunweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracunweightedcommand.h; sourceTree = SOURCE_ROOT; }; 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracunweightedcommand.cpp; sourceTree = SOURCE_ROOT; }; - 3749271B0FD58C840031C06B /* getsabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsabundcommand.h; sourceTree = ""; }; - 3749271C0FD58C840031C06B /* getsabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsabundcommand.cpp; sourceTree = ""; }; - 3749273D0FD5956B0031C06B /* getrabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrabundcommand.h; sourceTree = ""; }; - 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrabundcommand.cpp; sourceTree = ""; }; + 3749271B0FD58C840031C06B /* getsabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsabundcommand.h; sourceTree = SOURCE_ROOT; }; + 3749271C0FD58C840031C06B /* getsabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsabundcommand.cpp; sourceTree = SOURCE_ROOT; }; + 3749273D0FD5956B0031C06B /* getrabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrabundcommand.h; sourceTree = SOURCE_ROOT; }; + 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrabundcommand.cpp; sourceTree = SOURCE_ROOT; }; 37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = SOURCE_ROOT; }; 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; 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All rights reserved. - * - */ - -#include "readnexus.h" -#include -#include - -/*******************************************************************************/ -ReadNexus::ReadNexus(string file) : ReadSeqs(file) { - try { - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ReadTree class function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -} -/*******************************************************************************/ -ReadNexus::~ReadNexus(){ -// for(int i = 0; i < sequencedb.getNumSeqs(); i++) -// delete sequencedb.get(i); -} -/*******************************************************************************/ -void ReadNexus::read() { - string temp; - string name; - string sequence; - for(int i = 0; i < 5; i++) - filehandle >> temp; - - int numSeqs = atoi(temp.substr(temp.find_first_of("=")+1, temp.length() - temp.find_first_of("=") - 1).c_str()); - - for(int i = 0; i < 9; i++) - filehandle >> temp; - - int count = 0; - bool firstDone = false; - while(!filehandle.eof()){ - filehandle >> name; - filehandle >> sequence; - if(name.compare(";") != 0) { - if(!firstDone) { - Sequence newSeq(name, sequence); - sequencedb.add(newSeq); - } - else - sequencedb.set(count, sequencedb.get(count).getUnaligned() + sequence); - - count++; - if(count == numSeqs) { - if(!firstDone) - firstDone = true; - count = 0; - } - } - } - filehandle.close(); -} - -/*********************************************************************************/ -SequenceDB* ReadNexus::getDB() { - return &sequencedb; -} diff --git a/readnexus.h b/readnexus.h deleted file mode 100644 index 7a0efba..0000000 --- a/readnexus.h +++ /dev/null @@ -1,29 +0,0 @@ -#ifndef READNEXUS_H -#define READNEXUS_H - -/* - * readnuxus.h - * Mothur - * - * Created by Thomas Ryabin on 4/22/09. - * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved. - * - */ - -#include "readseqs.h" -#include "globaldata.hpp" -#include "sequencedb.h" -#include "mothur.h" - -/**********************************************************************************/ - -class ReadNexus : public ReadSeqs { - - public: - ReadNexus(string); - ~ReadNexus(); - void read(); - SequenceDB* getDB(); -}; - -#endif \ No newline at end of file diff --git a/readseqs.cpp b/readseqs.cpp deleted file mode 100644 index 5e0826f..0000000 --- a/readseqs.cpp +++ /dev/null @@ -1,40 +0,0 @@ -/* - * readseqs.cpp - * Mothur - * - * Created by Thomas Ryabin on 5/11/09. - * Copyright 2009Schloss Lab UMASS Amherst. All rights reserved. - * - */ - -#include "readseqs.h" - -/*******************************************************************************/ -ReadSeqs::ReadSeqs(string file) { - try { - openInputFile(file, filehandle); - seqFile = file; - globaldata = GlobalData::getInstance(); - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ReadSeqs class Function ReadSeqs. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ReadSeqs class function ReadSeqs. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -} -/*******************************************************************************/ -ReadSeqs::~ReadSeqs(){ - //for(int i = 0; i < sequencedb.getNumSeqs(); i++) - //delete sequencedb.get(i); -} -/*******************************************************************************/ -void ReadSeqs::read() { -} - -/*********************************************************************************/ -SequenceDB* ReadSeqs::getDB() { - return &sequencedb; -} diff --git a/readseqsphylip.h b/readseqsphylip.h deleted file mode 100644 index ae2693b..0000000 --- a/readseqsphylip.h +++ /dev/null @@ -1,32 +0,0 @@ -#ifndef READPHYLIP_H -#define READPHYLIP_H - -/* - * readphylip.h - * Mothur - * - * Created by Thomas Ryabin on 4/24/09. - * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved. - * - */ - -#include "readseqs.h" -#include "globaldata.hpp" -#include "sequencedb.h" -#include "mothur.h" - -/**********************************************************************************/ - -class ReadPhylip : public ReadSeqs { - - public: - ReadPhylip(string); - ~ReadPhylip(); - void read(); - SequenceDB* getDB(); - - private: - bool isSeq(string); -}; - -#endif \ No newline at end of file -- 2.39.5