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Efficient Algorithms for Comparing, Storing, and Sharing
EFFICIENT ALGORITHMS FOR COMPARING, STORING, AND SHARING LARGE COLLECTIONS OF EVOLUTIONARY TREES A Dissertation by SUZANNE JUDE MATTHEWS Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY May 2012 Major Subject: Computer Science EFFICIENT ALGORITHMS FOR COMPARING, STORING, AND SHARING LARGE COLLECTIONS OF EVOLUTIONARY TREES A Dissertation by SUZANNE JUDE MATTHEWS Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, Tiffani L. Williams Committee Members, Nancy M. Amato Jennifer L. Welch James B. Woolley Head of Department, Hank W. Walker May 2012 Major Subject: Computer Science iii ABSTRACT Efficient Algorithms for Comparing, Storing, and Sharing Large Collections of Evolutionary Trees. (May 2012) Suzanne Jude Matthews, B.S.; M.S., Rensselaer Polytechnic Institute Chair of Advisory Committee: Dr. Tiffani L. Williams Evolutionary relationships between a group of organisms are commonly summarized in a phylogenetic (or evolutionary) tree. The goal of phylogenetic inference is to infer the best tree structure that represents the relationships between a group of organisms, given a set of observations (e.g. molecular sequences). However, popular heuristics for inferring phylogenies output tens to hundreds of thousands of equally weighted candidate trees. Biologists summarize these trees into a single structure called the consensus tree. The central assumption is that the information discarded has less value than the information retained. But, what if this assumption is not true? In this dissertation, we demonstrate the value of retaining and studying tree collections. -
Opinnäytetyö Ohjeet
Lappeenrannan–Lahden teknillinen yliopisto LUT School of Engineering Science Tietotekniikan koulutusohjelma Kandidaatintyö Mikko Mustonen PARHAITEN OPETUSKÄYTTÖÖN SOVELTUVAN VERSIONHALLINTAJÄRJESTELMÄN LÖYTÄMINEN Työn tarkastaja: Tutkijaopettaja Uolevi Nikula Työn ohjaaja: Tutkijaopettaja Uolevi Nikula TIIVISTELMÄ LUT-yliopisto School of Engineering Science Tietotekniikan koulutusohjelma Mikko Mustonen Parhaiten opetuskäyttöön soveltuvan versionhallintajärjestelmän löytäminen Kandidaatintyö 2019 31 sivua, 8 kuvaa, 2 taulukkoa Työn tarkastajat: Tutkijaopettaja Uolevi Nikula Hakusanat: versionhallinta, versionhallintajärjestelmä, Git, GitLab, SVN, Subversion, oppimateriaali Keywords: version control, version control system, Git, GitLab, SVN, Subversion, learning material LUT-yliopistossa on tietotekniikan opetuksessa käytetty Apache Subversionia versionhallintaan. Subversionin käyttö kuitenkin johtaa ylimääräisiin ylläpitotoimiin LUTin tietohallinnolle. Lisäksi Subversionin julkaisun jälkeen on tullut uusia versionhallintajärjestelmiä ja tässä työssä tutkitaankin, olisiko Subversion syytä vaihtaa johonkin toiseen versionhallintajärjestelmään opetuskäytössä. Työn tavoitteena on löytää opetuskäyttöön parhaiten soveltuva versionhallintajärjestelmä ja tuottaa sille opetusmateriaalia. Työssä havaittiin, että Git on suosituin versionhallintajärjestelmä ja se on myös suhteellisen helppo käyttää. Lisäksi GitLab on tutkimuksen mukaan Suomen yliopistoissa käytetyin ja ominaisuuksiltaan ja hinnaltaan sopivin Gitin web-käyttöliittymä. Näille tehtiin -
This Book Doesn't Tell You How to Write Faster Code, Or How to Write Code with Fewer Memory Leaks, Or Even How to Debug Code at All
Practical Development Environments By Matthew B. Doar ............................................... Publisher: O'Reilly Pub Date: September 2005 ISBN: 0-596-00796-5 Pages: 328 Table of Contents | Index This book doesn't tell you how to write faster code, or how to write code with fewer memory leaks, or even how to debug code at all. What it does tell you is how to build your product in better ways, how to keep track of the code that you write, and how to track the bugs in your code. Plus some more things you'll wish you had known before starting a project. Practical Development Environments is a guide, a collection of advice about real development environments for small to medium-sized projects and groups. Each of the chapters considers a different kind of tool - tools for tracking versions of files, build tools, testing tools, bug-tracking tools, tools for creating documentation, and tools for creating packaged releases. Each chapter discusses what you should look for in that kind of tool and what to avoid, and also describes some good ideas, bad ideas, and annoying experiences for each area. Specific instances of each type of tool are described in enough detail so that you can decide which ones you want to investigate further. Developers want to write code, not maintain makefiles. Writers want to write content instead of manage templates. IT provides machines, but doesn't have time to maintain all the different tools. Managers want the product to move smoothly from development to release, and are interested in tools to help this happen more often. -
Documentation for Fisheye 2.8 Documentation for Fisheye 2.8 2
Documentation for FishEye 2.8 Documentation for FishEye 2.8 2 Contents Getting started . 8 Supported platforms . 8 End of Support Announcements for FishEye . 12 End of Support Announcement for IBM ClearCase . 14 End of Support Announcement for Internally Managed Repositories . 14 Installing FishEye on Windows . 16 Running FishEye as a Windows service . 19 Installing FishEye on Linux and Mac . 23 Starting to use FishEye . 26 Configuring JIRA Integration in the Setup Wizard . 31 Using FishEye . 38 Using the FishEye Screens . 39 Browsing through a repository . 41 Searching FishEye . 44 Viewing a File . 49 Viewing File Content . 50 Using Side by Side Diff View . 51 Viewing a File History . 53 Viewing the Changelog . 54 FishEye Charts . 56 Using Favourites in FishEye . 61 Changeset Discussions . 64 Viewing the commit graph for a repository . 64 Viewing People's Statistics . 68 Using smart commits . 70 Changing your User Profile . 75 Re-setting your password . 79 Antglob Reference Guide . 80 Date Expressions Reference Guide . 81 EyeQL Reference Guide . 82 Administering FishEye . 88 Managing your repositories . 89 Adding an External Repository . 91 CVS . 92 Git . 93 Mercurial . 96 Perforce . 98 Subversion . 101 SVN fisheye.access . 105 SVN tag and branch structure . 106 Adding an Internal Repository . 114 Enabling Repository Management in FishEye . 115 Creating Git Repositories . 117 Forking Git Repositories . 119 Deleting a Git Repository . 122 Setting up a Repository Client . 122 CVS Client . 122 Git Client . 122 Mercurial Client . 122 Perforce Client . 123 Subversion Client . 124 Native Subversion Client . 124 SVNkit Client . 126 Re-indexing your Repository . 126 Repository Options . 128 Authentication . 130 Created by Atlassian in 2012. -
Tortoisecvs User's Guide Version 1.8.0
TortoiseCVS User's Guide Version 1.8.0 Ben Campbell Martin Crawford Hartmut Honisch Francis Irving Torsten Martinsen Ian Dees Copyright © 2001 - 2004 TortoiseCVS Table of Contents 1. Getting Started What is CVS? What is TortoiseCVS? Where to Begin? 2. Basic Usage of TortoiseCVS Sandboxes Checking out a Module Windows Explorer and TortoiseCVS Total Commander and TortoiseCVS Updating your Sandbox Committing your Changes to the Repository Resolving Conflicts Adding Files and Directories to the Repository 3. Advanced Usage of TortoiseCVS Creating a New Repository or Module Watch, Edit and Unedit Tagging and Labeling Reverting to an Older Version of a File Branching And Merging Creating a Branch Selecting a Branch to Work On Merging from a Branch Going Back to the Head Branch Binary and Unicode Detection File Revision History History Dialog Revision Graph Dialog Web Log Making a Patch File 4. Customizing TortoiseCVS Overlay Icons Selecting a Different Set of Overlay Icons Changing how the Overlay Icons Work 5. Command Reference for TortoiseCVS Installing TortoiseCVS Obtaining a Working Copy: CVS Checkout... Getting Other People's Changes: CVS Update CVS Update Special... Making Your Changes Available to Others: CVS Commit... Adding New Files: CVS Add and CVS Add Contents... Discarding Obsolete Files: CVS Remove Finding Out What Has Changed: CVS Diff... Making a Snapshot: CVS Tag... Lines of Development: CVS Branch... CVS Merge... CVS Make New Module Watching And Locking Finding Out Who to Blame: CVS Annotate Showing More Information: CVS Explorer Columns Keyboard Shortcuts How Web Log Autodetects the Server URL 6. Dialog Reference for TortoiseCVS Add Dialog Checkout Dialog Update Special Dialog Commit Dialog Branch Dialog Make New Module Dialog Progress Dialog Tag Dialog Preferences Dialog Merge Dialog History Dialog Revision Graph Dialog About Dialog 7. -
1 Finalbuilder Server
FinalBuilder Server © 2012 VSoft Technologies 2 FinalBuilder Server Table of Contents Foreword 0 Part I FinalBuilder Server 5 1 FinalB.u..i.l.d..e..r. .S..e..r.v..e..r. .O...v..e..r.v..i.e..w................................................................................................ 5 2 Installa..t.i.o..n............................................................................................................................. 5 Requirements .......................................................................................................................................................... 6 Installing FinalB..u...i.l.d..e..r.. .S..e...r.v..e...r. ................................................................................................................................ 6 Post Installati.o..n.. .C...o..n...f.i.g..u...r.a..t..i.o..n.. ........................................................................................................................... 10 Configuration. .a..n..d... .M...a..i.n..t..e..n..a..n...c..e.. ......................................................................................................................... 14 3 Gettin..g.. .S..t.a..r.t.e..d..................................................................................................................... 17 Logging In .......................................................................................................................................................... 18 Creating New . .U..s..e...r.s... ............................................................................................................................................ -
Windows and CVS Suite
Windows and CVS Suite INSTALL GUIDE 2009 Build 7799 April 2021 March Hare Software Ltd INSTALL GUIDE 2009 Build 7799 April 2021 Legal Notices Legal Notices There are various product or company names used herein that are the trademarks, service marks, or trade names of their respective owners, and March Hare Software Limited makes no claim of ownership to, nor intends to imply an endorsement of, such products or companies by their usage. This document and all information contained herein are the property of March Hare Software Limited, and may not be reproduced, disclosed, revealed, or used in any way without prior written consent of March Hare Software Limited. This document and the information contained herein are subject to confidentiality agreement, violation of which will subject the violator to all remedies and penalties provided by the law. LIMITED WARRANTY. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, March Hare Software Limited AND ITS SUPPLIERS DISCLAIM ALL WARRANTIES AND CONDITIONS, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, IMPLIED WARRANTIES OR CONDITIONS OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT, WITH REGARD TO THIS DOCUMENT, AND ANY ADVICE OR RECOMMENDATION CONTAINED IN THIS DOCUMENT. NO OTHER WARRANTIES. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL March Hare Software Limited OR ITS SUPPLIERS BE LIABLE FOR ANY SPECIAL, INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES WHATSOEVER (INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF BUSINESS PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION, OR ANY OTHER PECUNIARY LOSS) ARISING OUT OF THE USE OF OR INABILITY TO USE THE FOLLOWING DOCUMENTATION INCLUDING ANY RECOMMENDATION OR ADVICE THERIN, EVEN IF March Hare Software Limtied HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. -
Getting Started W Ith CVS
Getting Started W ith CVS An Oracle White Paper February 2005 Getting Started W ith CVS Introduction....................................................................................................... 3 W HAT IS CVS.................................................................................................. 3 terminology........................................................................................................ 3 CVS Step by step............................................................................................... 4 Downloading and Installing CVS............................................................... 4 Creating a Repository................................................................................... 5 Creating a CVS Connection........................................................................ 5 Configuring the Repository......................................................................... 6 Importing a Module...................................................................................... 7 Checking Out a Module............................................................................... 9 Adding Files................................................................................................... 9 Updating Files (Common)......................................................................... 10 Editing Files................................................................................................. 11 Deleting Files.............................................................................................. -
Perforce and CVS
Comparison: Perforce and CVS Perforce& CVS Overview This document compares Perforce (version 2009.1) with CVS (CVSNT version 2.5.04.3510). Rather than compare every available feature in the two products, it focuses on their most significant differences, such as performance, atomic transactions, and distributed development. Executive Summary Attribute CVS Perforce Branching and CVS offers branching, but requires manual Perforce branching automatically tracks the merging tracking of merge history. history of all branching operations. Distributed No performance solutions for remote The Perforce Proxy offers a caching solution development development are available. for remote users, with minimal administrative overhead, and at no extra cost. Atomic transactions Doesn’t have an atomic change mechanism Natively supported as changelists, enabling and cannot group changes to related files. users to track file versions associated with a feature addition or issue resolution. Scalability and Metadata is appended and maintained in the Centralized metadata records all user and performance content of each versioned file. file activity. Deployed in 10,000+ user environments. Defect tracking Not part of CVS; need to use a separate Perforce provides a basic defect tracking defect tracking solution. system called jobs, and integrates with leading third-party defect tracking systems. Integration with Integrations are available via the open source Many third-party tools are designed related tools community. specifically to work with Perforce. Support Available at additional cost from a third party. Relied upon by over 350,000 users. 1 Branching and Merging branches automatically. This enables a variety of development scenarios, such as client- CVS branching doesn’t keep a history of specific versions, experimental branches, operations, such as integrations between files personal or task branches, and the classic or branches. -
Bill Laboon Friendly Introduction Version Control: a Brief History
Git and GitHub: A Bill Laboon Friendly Introduction Version Control: A Brief History ❖ In the old days, you could make a copy of your code at a certain point, and release it ❖ You could then continue working on your code, adding features, fixing bugs, etc. ❖ But this had several problems! VERSION 1 VERSION 2 Version Control: A Brief History ❖ Working with others was difficult - if you both modified the same file, it could be very difficult to fix! ❖ Reviewing changes from “Release n” to “Release n + 1” could be very time-consuming, if not impossible ❖ Modifying code locally meant that a crash could take out much of your work Version Control: A Brief History ❖ So now we have version control - a way to manage our source code in a regular way. ❖ We can tag releases without making a copy ❖ We can have numerous “save points” in case our modifications need to be unwound ❖ We can easily distribute our code across multiple machines ❖ We can easily merge work from different people to the same codebase Version Control ❖ There are many kinds of version control out there: ❖ BitKeeper, Perforce, Subversion, Visual SourceSafe, Mercurial, IBM ClearCase, AccuRev, AutoDesk Vault, Team Concert, Vesta, CVSNT, OpenCVS, Aegis, ArX, Darcs, Fossil, GNU Arch, BitKeeper, Code Co-Op, Plastic, StarTeam, MKS Integrity, Team Foundation Server, PVCS, DCVS, StarTeam, Veracity, Razor, Sun TeamWare, Code Co-Op, SVK, Fossil, Codeville, Bazaar…. ❖ But we will discuss git and its most popular repository hosting service, GitHub What is git? ❖ Developed by Linus Torvalds ❖ Strong support for distributed development ❖ Very fast ❖ Very efficient ❖ Very resistant against data corruption ❖ Makes branching and merging easy ❖ Can run over various protocols Git and GitHub ❖ git != GitHub ❖ git is the software itself - GitHub is just a place to store it, and some web-based tools to help with development. -
Altova Diffdog 2012 User & Reference Manual
User and Reference Manual Altova DiffDog 2012 User & Reference Manual All rights reserved. No parts of this work may be reproduced in any form or by any means - graphic, electronic, or mechanical, including photocopying, recording, taping, or information storage and retrieval systems - without the written permission of the publisher. Products that are referred to in this document may be either trademarks and/or registered trademarks of the respective owners. The publisher and the author make no claim to these trademarks. While every precaution has been taken in the preparation of this document, the publisher and the author assume no responsibility for errors or omissions, or for damages resulting from the use of information contained in this document or from the use of programs and source code that may accompany it. In no event shall the publisher and the author be liable for any loss of profit or any other commercial damage caused or alleged to have been caused directly or indirectly by this document. Published: 2012 © 2012 Altova GmbH Table of Contents 1 Welcome to DiffDog 2012 3 2 What's New in DiffDog 6 2.1 Version.............................................................................................................................. 2011 7 2.2 Version.............................................................................................................................. 2010 8 3 Introduction 10 3.1 Product............................................................................................................................. -
Jak Programować W Zespole I Się Nie Pozabijać
Jak programować w zespole i się nie pozabijać czyli strategia i praca z gałęziami w repozytoriach kodu Mercurial. Adam Kruszewski <[email protected]> www.tkomp.pl www.tkomp.pl www.tkomp.pl Ocena zespołu programistów w 5 minut Test Joela* 1. Czy stosujesz system kontroli wersji? 2. Czy możesz zbudować wersję w jednym kroku? 3. Czy stosujesz codzienne budowanie wersji? 4. Czy używasz system zarządzania błędami? 5. Czy usuwasz błędy zanim napiszesz nowy kod? 6. Czy masz harmonogram aktualizowany na bieżąco? 7. Czy masz specyfikację? 8. Czy programiści mają komfortowe warunki pracy? 9. Czy używasz najlepszych dostępnych narzędzi? 10. Czy masz testerów? 11. Czy kandydaci piszą programy podczas rozmowy kwalifikacyjnej? 12. Czy praktykujesz korytarzowe testy wygody użytkowania? * Joel Spolsky - http://polish.joelonsoftware.com/Articles/TheJoelTest.html www.tkomp.pl Czym tak naprawdę jest system kontroli wersji? int main (int argc, char **argv) { printf(„Witaj przygodo!\n”); } www.tkomp.pl Czym tak naprawdę jest system kontroli wersji? int main (int argc, char **argv) { printf(„Witaj przygodo!\n”); + return 0; } www.tkomp.pl Czym tak naprawdę jest system kontroli wersji? +#include <stdio.h> int main (int argc, char **argv) { printf(„Witaj przygodo!\n”); return 0; } www.tkomp.pl Czym tak naprawdę jest system kontroli wersji? int main (int argc, char **argv) { printf(„Witaj przygodo!\n”); return 0; } www.tkomp.pl Czym tak naprawdę jest system kontroli wersji? int main (int argc, char **argv) { printf(„Witaj przygodo!\n”); - return 0; + return -1; } www.tkomp.pl Czym tak naprawdę jest system kontroli wersji? +#include <stdio.h> int main (int argc, char **argv) { printf(„Witaj przygodo!\n”); - return 0; + return -1; } www.tkomp.pl Czym tak naprawdę jest system kontroli wersji? - Graf skierowany składający się z „łatek” - Przechowuje dodatkowe metadane, tj.