remove some files

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index fea328dcc8dc71daf7a5ff9bf86b668958baf0df..8d362b69205396a26faaf766b14bd6c4ef994bb3 100644 (file)
--- 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 = "<group>"; };
-               371B30B30FD7EE67000414CA /* screenseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = screenseqscommand.h; sourceTree = "<group>"; };
+               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 = "<group>"; };
-               3749271C0FD58C840031C06B /* getsabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsabundcommand.cpp; sourceTree = "<group>"; };
-               3749273D0FD5956B0031C06B /* getrabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrabundcommand.h; sourceTree = "<group>"; };
-               3749273E0FD5956B0031C06B /* getrabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrabundcommand.cpp; sourceTree = "<group>"; };
+               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; path = sharedanderbergs.cpp; sourceTree = SOURCE_ROOT; };
                37519A9F0F810D0200FED5E8 /* venncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venncommand.h; sourceTree = SOURCE_ROOT; };
@@ -292,10 +292,10 @@
                379294880F2E258500B9034A /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = SOURCE_ROOT; };
                379294890F2E258500B9034A /* parsimony.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimony.cpp; sourceTree = SOURCE_ROOT; };
                3792948D0F2E271100B9034A /* treecalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treecalculator.h; sourceTree = SOURCE_ROOT; };
-               3799A94C0FD6A58C00E33EDE /* distancedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancedb.cpp; sourceTree = "<group>"; };
-               3799A94D0FD6A58C00E33EDE /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; sourceTree = "<group>"; };
-               3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqsummarycommand.cpp; sourceTree = "<group>"; };
-               3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqsummarycommand.h; sourceTree = "<group>"; };
+               3799A94C0FD6A58C00E33EDE /* distancedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancedb.cpp; sourceTree = SOURCE_ROOT; };
+               3799A94D0FD6A58C00E33EDE /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; sourceTree = SOURCE_ROOT; };
+               3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqsummarycommand.cpp; sourceTree = SOURCE_ROOT; };
+               3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqsummarycommand.h; sourceTree = SOURCE_ROOT; };
                37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = SOURCE_ROOT; };
                37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = SOURCE_ROOT; };
                37AD4DB90F28E2FE00AA2D49 /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = SOURCE_ROOT; };

diff --git a/readnexus.cpp b/readnexus.cpp
deleted file mode 100644 (file)
index 5dffa42..0000000
--- a/readnexus.cpp
+++ /dev/null
@@ -1,72 +0,0 @@
-/*
- *  readnexusaln.cpp
- *  Mothur
- *
- *  Created by Thomas Ryabin on 4/22/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "readnexus.h"
-#include <iostream>
-#include <fstream>
-
-/*******************************************************************************/
-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 (file)
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 (file)
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 (file)
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