Expert C Programming: Deep C Secrets by Peter Van Der Linden
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T-Coffee Documentation Release Version 13.45.47.Aba98c5
T-Coffee Documentation Release Version_13.45.47.aba98c5 Cedric Notredame Aug 31, 2021 Contents 1 T-Coffee Installation 3 1.1 Installation................................................3 1.1.1 Unix/Linux Binaries......................................4 1.1.2 MacOS Binaries - Updated...................................4 1.1.3 Installation From Source/Binaries downloader (Mac OSX/Linux)...............4 1.2 Template based modes: PSI/TM-Coffee and Expresso.........................5 1.2.1 Why do I need BLAST with T-Coffee?.............................6 1.2.2 Using a BLAST local version on Unix.............................6 1.2.3 Using the EBI BLAST client..................................6 1.2.4 Using the NCBI BLAST client.................................7 1.2.5 Using another client.......................................7 1.3 Troubleshooting.............................................7 1.3.1 Third party packages......................................7 1.3.2 M-Coffee parameters......................................9 1.3.3 Structural modes (using PDB)................................. 10 1.3.4 R-Coffee associated packages................................. 10 2 Quick Start Regressive Algorithm 11 2.1 Introduction............................................... 11 2.2 Installation from source......................................... 12 2.3 Examples................................................. 12 2.3.1 Fast and accurate........................................ 12 2.3.2 Slower and more accurate.................................... 12 2.3.3 Very Fast........................................... -
Modern Compiler Implementation in Java. Second Edition
Team-Fly Modern Compiler Implementation in Java, Second Edition by Andrew W. ISBN:052182060x Appel and Jens Palsberg Cambridge University Press © 2002 (501 pages) This textbook describes all phases of a compiler, and thorough coverage of current techniques in code generation and register allocation, and the compilation of functional and object-oriented languages. Table of Contents Modern Compiler Implementation in Java, Second Edition Preface Part One - Fundamentals of Compilation Ch apt - Introduction er 1 Ch apt - Lexical Analysis er 2 Ch apt - Parsing er 3 Ch apt - Abstract Syntax er 4 Ch apt - Semantic Analysis er 5 Ch apt - Activation Records er 6 Ch apt - Translation to Intermediate Code er 7 Ch apt - Basic Blocks and Traces er 8 Ch apt - Instruction Selection er 9 Ch apt - Liveness Analysis er 10 Ch apt - Register Allocation er 11 Ch apt - Putting It All Together er 12 Part Two - Advanced Topics Ch apt - Garbage Collection er 13 Ch apt - Object-Oriented Languages er 14 Ch apt - Functional Programming Languages er 15 Ch apt - Polymorphic Types er 16 Ch apt - Dataflow Analysis er 17 Ch apt - Loop Optimizations er 18 Ch apt - Static Single-Assignment Form er 19 Ch apt - Pipelining and Scheduling er 20 Ch apt - The Memory Hierarchy er 21 Ap pe ndi - MiniJava Language Reference Manual x A Bibliography Index List of Figures List of Tables List of Examples Team-Fly Team-Fly Back Cover This textbook describes all phases of a compiler: lexical analysis, parsing, abstract syntax, semantic actions, intermediate representations, instruction selection via tree matching, dataflow analysis, graph-coloring register allocation, and runtime systems. -
Practical C Programming, 3Rd Edition
Practical C Programming, 3rd Edition By Steve Oualline 3rd Edition August 1997 ISBN: 1-56592-306-5 This new edition of "Practical C Programming" teaches users not only the mechanics or programming, but also how to create programs that are easy to read, maintain, and debug. It features more extensive examples and an introduction to graphical development environments. Programs conform to ANSI C. 0 TEAM FLY PRESENTS Table of Contents Preface How This Book is Organized Chapter by Chapter Notes on the Third Edition Font Conventions Obtaining Source Code Comments and Questions Acknowledgments Acknowledgments to the Third Edition I. Basics 1. What Is C? How Programming Works Brief History of C How C Works How to Learn C 2. Basics of Program Writing Programs from Conception to Execution Creating a Real Program Creating a Program Using a Command-Line Compiler Creating a Program Using an Integrated Development Environment Getting Help on UNIX Getting Help in an Integrated Development Environment IDE Cookbooks Programming Exercises 3. Style Common Coding Practices Coding Religion Indentation and Code Format Clarity Simplicity Summary 4. Basic Declarations and Expressions Elements of a Program Basic Program Structure Simple Expressions Variables and Storage 1 TEAM FLY PRESENTS Variable Declarations Integers Assignment Statements printf Function Floating Point Floating Point Versus Integer Divide Characters Answers Programming Exercises 5. Arrays, Qualifiers, and Reading Numbers Arrays Strings Reading Strings Multidimensional Arrays Reading Numbers Initializing Variables Types of Integers Types of Floats Constant Declarations Hexadecimal and Octal Constants Operators for Performing Shortcuts Side Effects ++x or x++ More Side-Effect Problems Answers Programming Exercises 6. -
Modern Programming Languages CS508 Virtual University of Pakistan
Modern Programming Languages (CS508) VU Modern Programming Languages CS508 Virtual University of Pakistan Leaders in Education Technology 1 © Copyright Virtual University of Pakistan Modern Programming Languages (CS508) VU TABLE of CONTENTS Course Objectives...........................................................................................................................4 Introduction and Historical Background (Lecture 1-8)..............................................................5 Language Evaluation Criterion.....................................................................................................6 Language Evaluation Criterion...................................................................................................15 An Introduction to SNOBOL (Lecture 9-12).............................................................................32 Ada Programming Language: An Introduction (Lecture 13-17).............................................45 LISP Programming Language: An Introduction (Lecture 18-21)...........................................63 PROLOG - Programming in Logic (Lecture 22-26) .................................................................77 Java Programming Language (Lecture 27-30)..........................................................................92 C# Programming Language (Lecture 31-34) ...........................................................................111 PHP – Personal Home Page PHP: Hypertext Preprocessor (Lecture 35-37)........................129 Modern Programming Languages-JavaScript -
About ILE C/C++ Compiler Reference
IBM i 7.3 Programming IBM Rational Development Studio for i ILE C/C++ Compiler Reference IBM SC09-4816-07 Note Before using this information and the product it supports, read the information in “Notices” on page 121. This edition applies to IBM® Rational® Development Studio for i (product number 5770-WDS) and to all subsequent releases and modifications until otherwise indicated in new editions. This version does not run on all reduced instruction set computer (RISC) models nor does it run on CISC models. This document may contain references to Licensed Internal Code. Licensed Internal Code is Machine Code and is licensed to you under the terms of the IBM License Agreement for Machine Code. © Copyright International Business Machines Corporation 1993, 2015. US Government Users Restricted Rights – Use, duplication or disclosure restricted by GSA ADP Schedule Contract with IBM Corp. Contents ILE C/C++ Compiler Reference............................................................................... 1 What is new for IBM i 7.3.............................................................................................................................3 PDF file for ILE C/C++ Compiler Reference.................................................................................................5 About ILE C/C++ Compiler Reference......................................................................................................... 7 Prerequisite and Related Information.................................................................................................. -
Emerging Technologies Multi/Parallel Processing
Emerging Technologies Multi/Parallel Processing Mary C. Kulas New Computing Structures Strategic Relations Group December 1987 For Internal Use Only Copyright @ 1987 by Digital Equipment Corporation. Printed in U.S.A. The information contained herein is confidential and proprietary. It is the property of Digital Equipment Corporation and shall not be reproduced or' copied in whole or in part without written permission. This is an unpublished work protected under the Federal copyright laws. The following are trademarks of Digital Equipment Corporation, Maynard, MA 01754. DECpage LN03 This report was produced by Educational Services with DECpage and the LN03 laser printer. Contents Acknowledgments. 1 Abstract. .. 3 Executive Summary. .. 5 I. Analysis . .. 7 A. The Players . .. 9 1. Number and Status . .. 9 2. Funding. .. 10 3. Strategic Alliances. .. 11 4. Sales. .. 13 a. Revenue/Units Installed . .. 13 h. European Sales. .. 14 B. The Product. .. 15 1. CPUs. .. 15 2. Chip . .. 15 3. Bus. .. 15 4. Vector Processing . .. 16 5. Operating System . .. 16 6. Languages. .. 17 7. Third-Party Applications . .. 18 8. Pricing. .. 18 C. ~BM and Other Major Computer Companies. .. 19 D. Why Success? Why Failure? . .. 21 E. Future Directions. .. 25 II. Company/Product Profiles. .. 27 A. Multi/Parallel Processors . .. 29 1. Alliant . .. 31 2. Astronautics. .. 35 3. Concurrent . .. 37 4. Cydrome. .. 41 5. Eastman Kodak. .. 45 6. Elxsi . .. 47 Contents iii 7. Encore ............... 51 8. Flexible . ... 55 9. Floating Point Systems - M64line ................... 59 10. International Parallel ........................... 61 11. Loral .................................... 63 12. Masscomp ................................. 65 13. Meiko .................................... 67 14. Multiflow. ~ ................................ 69 15. Sequent................................... 71 B. Massively Parallel . 75 1. Ametek.................................... 77 2. Bolt Beranek & Newman Advanced Computers ........... -
Easyaccess: Enhanced SQL Command Line Interpreter for Astronomical Surveys
easyaccess: Enhanced SQL command line interpreter for astronomical surveys Matias Carrasco Kind1, Alex Drlica-Wagner2, Audrey Koziol1, and Don Petravick1 1 National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign. 1205 W Clark St, Urbana, IL USA 61801 2 Fermi National Accelerator Laboratory, P. O. Box 500, DOI: 00.00000/joss.00000 Batavia,IL 60510, USA Software • Review Summary • Repository • Archive easyaccess is an enhanced command line interpreter and Python package created to Submitted: 00 January 0000 facilitate access to astronomical catalogs stored in SQL Databases. It provides a custom Published: 00 January 0000 interface with custom commands and was specifically designed to access data from the License Dark Energy Survey Oracle database, although it can easily be extended to another survey Authors of papers retain copyright or SQL database. The package was completely written in Python and support customized and release the work under a Cre- addition of commands and functionalities. Visit https://github.com/mgckind/easyaccess ative Commons Attribution 4.0 In- to view installation instructions, tutorials, and the Python source code for easyaccess. ternational License (CC-BY). The Dark Energy Survey The Dark Energy Survey (DES) (DES Collaboration 2005; DES Collaboration 2016) is an international, collaborative effort of over 500 scientists from 26 institutions in seven countries. The primary goals of DES are reveal the nature of the mysterious dark energy and dark matter by mapping hundreds of millions of galaxies, detecting thousands of supernovae, and finding patterns in the large-scale structure of the Universe. Survey operations began on on August 31, 2013 and will conclude in early 2019. -
Coffeescript Accelerated Javascript Development.Pdf
Download from Wow! eBook <www.wowebook.com> What readers are saying about CoffeeScript: Accelerated JavaScript Development It’s hard to imagine a new web application today that doesn’t make heavy use of JavaScript, but if you’re used to something like Ruby, it feels like a significant step down to deal with JavaScript, more of a chore than a joy. Enter CoffeeScript: a pre-compiler that removes all the unnecessary verbosity of JavaScript and simply makes it a pleasure to write and read. Go, go, Coffee! This book is a great introduction to the world of CoffeeScript. ➤ David Heinemeier Hansson Creator, Rails Just like CoffeeScript itself, Trevor gets straight to the point and shows you the benefits of CoffeeScript and how to write concise, clear CoffeeScript code. ➤ Scott Leberknight Chief Architect, Near Infinity Though CoffeeScript is a new language, you can already find it almost everywhere. This book will show you just how powerful and fun CoffeeScript can be. ➤ Stan Angeloff Managing Director, PSP WebTech Bulgaria Download from Wow! eBook <www.wowebook.com> This book helps readers become better JavaScripters in the process of learning CoffeeScript. What’s more, it’s a blast to read, especially if you are new to Coffee- Script and ready to learn. ➤ Brendan Eich Creator, JavaScript CoffeeScript may turn out to be one of the great innovations in web application development; since I first discovered it, I’ve never had to write a line of pure JavaScript. I hope the readers of this wonderful book will be able to say the same. ➤ Dr. Nic Williams CEO/Founder, Mocra CoffeeScript: Accelerated JavaScript Development is an excellent guide to Coffee- Script from one of the community’s most esteemed members. -
Pete's Unsung Contribution to IEEE Standard 754 for Binary Floating
File: 19July10 Pete’s Unsung Contribution to IEEE 754 Version dated July 10, 2010 8:21 am Pete’s Unsung Contribution to IEEE Standard 754 for Binary Floating-Point Prepared for the Conference to Celebrate Prof. G.W. “Pete” Stewart’s 70th Birthday July 19-20, 2010, at the University of Texas at Austin by Prof. W. Kahan Mathematics Dept. & Computer Science Dept. University of California @ Berkeley This is posted at <www.eecs.berkeley.edu/~wkahan/19July10.pdf> Prof. W. Kahan Page 1/18 File: 19July10 Pete’s Unsung Contribution to IEEE 754 Version dated July 10, 2010 8:21 am Pete’s Unsung Contribution to IEEE Standard 754 for Binary Floating-Point Abstract The near-universal portability, after recompilation, of numerical software for scientific, engineering, medical and entertaining computations owes a lot to the near-universal adoption of IEEE Standard 754 by computer arithmetic hardware starting in the 1980s. But in 1980, after forty months of dispute, the committee drafting this Standard was still unable to reach a consensus. The disagreement seemed irreconcilable. That was when Pete helped to close the divide. This is posted at <www.eecs.berkeley.edu/~wkahan/19July10.pdf> Prof. W. Kahan Page 2/18 File: 19July10 Pete’s Unsung Contribution to IEEE 754 Version dated July 10, 2010 8:21 am “Three Removes are as bad as a Fire.” Benjamin Franklin, Preface to Poor Richard’s Almanack (1758) My office has been moved twice since 1980, so now my notes for the events in question are buried in one of a few dozen full cartons,— I know not which. -
Cscope Security Update (RHSA-2009-1101)
cscope security update (RHSA-2009-1101) Original Release Date: June 16, 2009 Last Revised: June 16, 2009 Number: ASA-2009-236 Risk Level: None Advisory Version: 1.0 Advisory Status: Final 1. Overview: cscope is a mature, ncurses-based, C source-code tree browsing tool. Multiple buffer overflow flaws were found in cscope. An attacker could create a specially crafted source code file that could cause cscope to crash or, possibly, execute arbitrary code when browsed with cscope. The Common Vulnerabilities and Exposures project (cve.mitre.org) has assigned the names CVE-2004-2541, CVE-2006-4262, CVE-2009- 0148 and CVE-2009-1577 to these issues. Note: This advisory is specific to RHEL3 and RHEL4. No Avaya system products are vulnerable, as cscope is not installed by default. More information about these vulnerabilities can be found in the security advisory issued by RedHat Linux: · https://rhn.redhat.com/errata/RHSA-2009-1101.html 2. Avaya System Products using RHEL3 or RHEL4 with cscope installed: None 3. Avaya Software-Only Products: Avaya software-only products operate on general-purpose operating systems. Occasionally vulnerabilities may be discovered in the underlying operating system or applications that come with the operating system. These vulnerabilities often do not impact the software-only product directly but may threaten the integrity of the underlying platform. In the case of this advisory Avaya software-only products are not affected by the vulnerability directly but the underlying Linux platform may be. Customers should determine on which Linux operating system the product was installed and then follow that vendor's guidance. -
Maximal-Munch” Tokenization in Linear Time Tom Reps [TOPLAS 1998]
Fall 2016-2017 Compiler Principles Lecture 1: Lexical Analysis Roman Manevich Ben-Gurion University of the Negev Agenda • Understand role of lexical analysis in a compiler • Regular languages reminder • Lexical analysis algorithms • Scanner generation 2 Javascript example • Can you some identify basic units in this code? var currOption = 0; // Choose content to display in lower pane. function choose ( id ) { var menu = ["about-me", "publications", "teaching", "software", "activities"]; for (i = 0; i < menu.length; i++) { currOption = menu[i]; var elt = document.getElementById(currOption); if (currOption == id && elt.style.display == "none") { elt.style.display = "block"; } else { elt.style.display = "none"; } } } 3 Javascript example • Can you some identify basic units in this code? keyword ? ? ? ? ? var currOption = 0; // Choose content to display in lower pane. ? function choose ( id ) { var menu = ["about-me", "publications", "teaching", "software", "activities"]; ? for (i = 0; i < menu.length; i++) { currOption = menu[i]; var elt = document.getElementById(currOption); if (currOption == id && elt.style.display == "none") { elt.style.display = "block"; } else { elt.style.display = "none"; } } } 4 Javascript example • Can you some identify basic units in this code? keyword identifier operator numeric literal punctuation comment var currOption = 0; // Choose content to display in lower pane. string literal function choose ( id ) { var menu = ["about-me", "publications", "teaching", "software", "activities"]; whitespace for (i = 0; i < menu.length; i++) { currOption = menu[i]; var elt = document.getElementById(currOption); if (currOption == id && elt.style.display == "none") { elt.style.display = "block"; } else { elt.style.display = "none"; } } } 5 Role of lexical analysis • First part of compiler front-end Lexical Syntax AST Symbol Inter. Code High-level Analysis Analysis Table Rep. -
A Command-Line Interface for Analysis of Molecular Dynamics Simulations
taurenmd: A command-line interface for analysis of Molecular Dynamics simulations. João M.C. Teixeira1, 2 1 Previous, Biomolecular NMR Laboratory, Organic Chemistry Section, Inorganic and Organic Chemistry Department, University of Barcelona, Baldiri Reixac 10-12, Barcelona 08028, Spain 2 DOI: 10.21105/joss.02175 Current, Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Software Canada • Review Summary • Repository • Archive Molecular dynamics (MD) simulations of biological molecules have evolved drastically since its application was first demonstrated four decades ago (McCammon, Gelin, & Karplus, 1977) and, nowadays, simulation of systems comprising millions of atoms is possible due to the latest Editor: Richard Gowers advances in computation and data storage capacity – and the scientific community’s interest Reviewers: is growing (Hospital, Battistini, Soliva, Gelpí, & Orozco, 2019). Academic groups develop most of the MD methods and software for MD data handling and analysis. The MD analysis • @amritagos libraries developed solely for the latter scope nicely address the needs of manipulating raw data • @luthaf and calculating structural parameters, such as: MDAnalysis (Gowers et al., 2016; Michaud- Agrawal, Denning, Woolf, & Beckstein, 2011); (McGibbon et al., 2015); (Romo, Submitted: 03 March 2020 MDTraj LOOS Published: 02 June 2020 Leioatts, & Grossfield, 2014); and PyTraj (Hai Nguyen, 2016; Roe & Cheatham, 2013), each with its advantages and drawbacks inherent to their implementation strategies. This diversity License enriches the field with a panoply of strategies that the community can utilize. Authors of papers retain copyright and release the work The MD analysis software libraries widely distributed and adopted by the community share under a Creative Commons two main characteristics: 1) they are written in pure Python (Rossum, 1995), or provide a Attribution 4.0 International Python interface; and 2) they are libraries: highly versatile and powerful pieces of software that, License (CC BY 4.0).