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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........................................... -
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. -
Chapter 1: Introduction to the Pencil Code Environment
Chapter 1: Introduction to the Pencil Code Environment In this manual we will show how to use Pencil Code to explore programming. Pencil Code is a free programming tool available at pencilcode.net. Pencil Code was developed by Google engineer David Bau together with his son Anthony Bau, with open-source contributions from many others. Two Ways of Looking at a Program There are two ways of viewing a program. A computer user sees a program by looking at its output. A programmer works with a program’s source code. In Pencil Code, the screen is split into two halves, with the source code on the left and the output on the right. You run programs by by pressing the “play” button in the middle. The Pencil Code interface splits the screen, showing source code on the left and output on the right. The play button in the center runs the code and produces output. Languages and Libraries in Pencil Code Pencil Code supports code in both blocks and text using mainstream web programming languages and useful libraries including: • HTML, the standard HyperText Markup Language for the web. • JavaScript, the standard programming language of web browsers. • CSS, the standard Cascading Style Sheet language for visual styles on the web. • jQuery, a popular library that simplifies programming interactive websites. • CoffeeScript, a language that lets you do more with less typing than JavaScript. • jQuery-turtle, which extends jQuery to simplify graphics and animation for novices. With Pencil Code, students can use these technologies to create web applications with global visibility and impact while exploring fundamental concepts in computational thinking. -
Coffeescript Accelerated Javascript Development, Second Edition
Extracted from: CoffeeScript Accelerated JavaScript Development, Second Edition This PDF file contains pages extracted from CoffeeScript, published by the Prag- matic Bookshelf. For more information or to purchase a paperback or PDF copy, please visit http://www.pragprog.com. Note: This extract contains some colored text (particularly in code listing). This is available only in online versions of the books. The printed versions are black and white. Pagination might vary between the online and printed versions; the content is otherwise identical. Copyright © 2015 The Pragmatic Programmers, LLC. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form, or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior consent of the publisher. The Pragmatic Bookshelf Dallas, Texas • Raleigh, North Carolina CoffeeScript Accelerated JavaScript Development, Second Edition Trevor Burnham The Pragmatic Bookshelf Dallas, Texas • Raleigh, North Carolina Many of the designations used by manufacturers and sellers to distinguish their products are claimed as trademarks. Where those designations appear in this book, and The Pragmatic Programmers, LLC was aware of a trademark claim, the designations have been printed in initial capital letters or in all capitals. The Pragmatic Starter Kit, The Pragmatic Programmer, Pragmatic Programming, Pragmatic Bookshelf, PragProg and the linking g device are trade- marks of The Pragmatic Programmers, LLC. Every precaution was taken in the preparation of this book. However, the publisher assumes no responsibility for errors or omissions, or for damages that may result from the use of information (including program listings) contained herein. Our Pragmatic courses, workshops, and other products can help you and your team create better software and have more fun. -
PHP String Interview Questions
By OnlineInterviewQuestions.com String Interview Questions in PHP Q1. What is String in PHP? The String is a collection or set of characters in sequence in PHP. The String in PHP is used to save and manipulate like an update, delete and read the data. Q2. How to cast a php string to integer? The int or integer used for a variable into an integer in PHP. Q3. How to perform string concatenation in PHP? The string concatenation means two strings connect together. The dot ( . ) sign used in PHP to combine two string. Example:- <?php $stringa = " creative "; $stringb = "writing "; echo $stringa . $stringb; ?> Q4. How to get php string length? To determine the string length in PHP, strlen() function used. Example:- echo strlen(“creative writing”); Q5. List some escape characters in PHP? Some list escape characters in PHP there are:- \’ \” \\ \n \t \r Q6. How to convert special characters to unicode in php? There is function json_encode() which is converted special characters to Unicode in PHP. Example:- $stringa = " I am good at smiling"; print_r(json_encode($stringa)); Q7. How to add double quotes in string in php? The double quotes in string using (" ") sign and write content under this sign. The double quotes convert variable as value. An example is below:- $str8 = " need to read data where has to go "; echo $str 8output: double quotes in the string echo “ PHP work $str8 output: PHP work need to read data where has to go Q8. Explain how php string interpolation is done? The interpolation is adding variables in among a string data. PHP parses the interpolate variables and replaces this variable with own value while processing the string. -
Learning HTML5 Game Programming Addison-Wesley Learning Series
Learning HTML5 Game Programming Addison-Wesley Learning Series Visit informit.com/learningseries for a complete list of available publications. The Addison-Wesley Learning Series is a collection of hands-on programming guides that help you quickly learn a new technology or language so you can apply what you’ve learned right away. Each title comes with sample code for the application or applications built in the text. This code is fully annotated and can be reused in your own projects with no strings attached. Many chapters end with a series of exercises to encourage you to reexamine what you have just learned, and to tweak or adjust the code as a way of learning. Titles in this series take a simple approach: they get you going right away and leave you with the ability to walk off and build your own application and apply the language or technology to whatever you are working on. Learning HTML5 Game Programming A Hands-on Guide to Building Online Games Using Canvas, SVG, and WebGL James L. Williams Upper Saddle River, NJ • Boston • Indianapolis • San Francisco New York • Toronto • Montreal • London • Munich • Paris • Madrid Cape Town • Sydney • Tokyo • Singapore • Mexico City Many of the designations used by manufacturers and sellers to distinguish their products Associate are claimed as trademarks. Where those designations appear in this book, and the publish- Publisher er was aware of a trademark claim, the designations have been printed with initial capital Mark Taub letters or in all capitals. Senior Acquisitions The author and publisher have taken care in the preparation of this book, but make no Editor expressed or implied warranty of any kind and assume no responsibility for errors or omis- Trina MacDonald sions. -
Coding 101: Learn Ruby in 15 Minutes Visit
Coding 101: Learn Ruby in 15 minutes Visit www.makers.tech 1 Contents 2 Contents 10 Challenge 3 3 About us 11 Defining Methods 4 Installing Ruby 12 Challenge 4 4 Checking you’ve got Ruby 12 Challenge 5 5 Method calls 12 Challenge 6 5 Variables 13 Arrays 6 Truth and Falsehood 14 Hashes 7 Strings, objects and Methods 14 Challenge 7 8 Challenge 1 15 Iterations 8 Challenge 2 16 Challenge 8 9 Method Chaining 16 Challenge 9 10 Conditionals 18 Extra Challenges 2 About Us At Makers, we are creating a new generation of tech talent who are skilled and ready for the changing world of work. We are inspired by the idea of discovering and unlocking potential in people for the benefit of 21st century business and society. We believe in alternative ways to learn how to code, how to be ready for work and how to be of value to an organisation. At our core, Makers combines tech education with employment possibilities that transform lives. Our intensive four-month program (which includes a month-long PreCourse) sets you up to become a high quality professional software engineer. Makers is the only coding bootcamp with 5 years experience training software developers remotely. Your virtual experience will be exactly the same as Makers on-site, just delivered differently. If you’d like to learn more, check out www.makers.tech. 3 Installing Checking Ruby you’ve got Ruby You’ll be happy to know that Ruby comes preinstalled on all Apple computers. However we can’t simply use the system defaults - just in case we mess something up! Open the terminal on your computer and then type in If you’ve got your laptop set up already you can skip this section. -
Open Source on IBM I Webinar Series Day 2 ERWIN EARLEY ([email protected]), SR
Open Source on IBM i Webinar Series Day 2 ERWIN EARLEY ([email protected]), SR. SOLUTIONS CONSULTANT, PERFORCE, NOVEMBER 2019 2 | COMMON Webinar Series: Open Source on IBM i | November 2019 zend.com Day 1 Review • Introduction to Open Source on IBM i • Why is Open Source on IBM i Important • Understanding the PASE environment as the enabler of Open Source on IBM i • Getting Familiar with the PASE environment 2 | Zend by Perforce © 2019 Perforce Software, Inc. zend.com 3 | COMMON Webinar Series: Open Source on IBM i | November 2019 zend.com Day 2 Agenda • Setting up OSS EcoSystem on IBM i – ACS version • Exploring Containers on IBM i • Managing Open Source on IBM i • Exploring Open Source Programming Languages ▪ Integration with Db2 and ILE • After-Hours Lab: Containers & Setting up Development Environment • After-Hours Lab: Open Source Programming Languages 3 | Zend by Perforce © 2019 Perforce Software, Inc. zend.com IBM Systems Technical University © 3 4 | COMMON Webinar Series: Open Source on IBM i | November 2019 zend.com Setting up OSS Ecosystem on IBM i – ACS Version 4 | Zend by Perforce © 2019 Perforce Software, Inc. zend.com 5 | COMMON Webinar Series: Open Source on IBM i | November 2019 zend.com The directory structure Before installing the Open Source ecosystem / dev home lib sbin tmp usr var Directory Contents bin Commands dev Device Files etc Configuration files home User Home Directories lib Libraries pkgs Package files / commands sbin Privileged commands tmp Temporary files usr Utilities & Applications var Variable files -
Webassembly: High Speed at Low Cost for Everyone
WebAssembly: high speed at low cost for everyone Andreas Rossberg Google [email protected] Abstract instructions that are widely available on modern CPUs. They map WebAssembly is a new language- and platform-independent bi- to machine code in a predictable manner and with predictable nary code format bringing native-code performance to the web. We performance on all relevant platforms. present its design and report our experience with specifying its se- High-level Data Flow. WebAssembly is an expression language: mantics via a reference interpreter written in OCaml, that currently it is defined as an AST in which machine operators return values serves as a proxy for a future formal specification. and can be used as operands to other operators. The binary format is a post-order serialisation of this AST. This design provides for 1. Introduction more compact binaries than 3-address code or SSA form would. Like it or not, the Web has become one of the most important Low-level Control Flow. Control flow is available mainly in the platforms for application development. Yet there is only one pro- form of sequential blocks and branch instructions, plus a structured gramming language that the Web understands: JavaScript. Liter- conditional. However, branches are still structured: they can only ally hundreds of compilers have been written that translate almost break out of an expression, not jump into one. This prevents ir- every imaginable language into JavaScript in order to run on the reducible control flow and associated complications (it’s the pro- Web [1]. Unfortunately, JavaScript is not the most delightful com- ducers’ responsibility to transform irreducible control flow into pilation target: it’s brittle and often slow in unpredictable ways, all structured form [6]). -
A Typescript Program Generator Based on Alloy
Federal University of Pernambuco Center of Informatics Bachelor’s Program in Computer Engineering A TypeScript program generator based on Alloy Gabriela Araujo Britto Recife 2020 Federal University of Pernambuco Center of Informatics Gabriela Araujo Britto A TypeScript program generator based on Alloy A B.Sc. Dissertation presented to the Bachelor’s Program in Computer Engineering of the Center of Informatics of Federal University of Pernambuco in partial fulfillment of the requirements for the degree of Bachelor of Science in Computer Engineering. Advisor: Leopoldo Motta Teixeira Recife 2020 Abstract Refactoring is the process of modifying code to improve its internal structure, without altering its external behavior. To aid the programmer in the process of applying common refactorings to code, many IDEs provide refactoring implementations that automate the refactoring process. However, in doing so, the refactoring developers must concern themselves with guaranteeing that their refactoring does not change program behavior. Formally verifying that a refactoring preserves behavior is a complex and costly task. Therefore, in practice, developers use tests as an alternative. Testing a refactoring implementation requires programs as test inputs. Manually writing such programs can be tedious and difficult, as there may be many language features to consider. This work proposes a technique for generating TypeScript programs that can be used as input to test refactorings. We implement this technique in a tool called TSDolly. TSDolly uses an Alloy specification of TypeScript language and the Alloy Analyzer to generate instances for this specification, which are then transformed into TypeScript programs. The majority of the generated programs (at least 97.45%) compiled without errors. -
Archive and Compressed [Edit]
Archive and compressed [edit] Main article: List of archive formats • .?Q? – files compressed by the SQ program • 7z – 7-Zip compressed file • AAC – Advanced Audio Coding • ace – ACE compressed file • ALZ – ALZip compressed file • APK – Applications installable on Android • AT3 – Sony's UMD Data compression • .bke – BackupEarth.com Data compression • ARC • ARJ – ARJ compressed file • BA – Scifer Archive (.ba), Scifer External Archive Type • big – Special file compression format used by Electronic Arts for compressing the data for many of EA's games • BIK (.bik) – Bink Video file. A video compression system developed by RAD Game Tools • BKF (.bkf) – Microsoft backup created by NTBACKUP.EXE • bzip2 – (.bz2) • bld - Skyscraper Simulator Building • c4 – JEDMICS image files, a DOD system • cab – Microsoft Cabinet • cals – JEDMICS image files, a DOD system • cpt/sea – Compact Pro (Macintosh) • DAA – Closed-format, Windows-only compressed disk image • deb – Debian Linux install package • DMG – an Apple compressed/encrypted format • DDZ – a file which can only be used by the "daydreamer engine" created by "fever-dreamer", a program similar to RAGS, it's mainly used to make somewhat short games. • DPE – Package of AVE documents made with Aquafadas digital publishing tools. • EEA – An encrypted CAB, ostensibly for protecting email attachments • .egg – Alzip Egg Edition compressed file • EGT (.egt) – EGT Universal Document also used to create compressed cabinet files replaces .ecab • ECAB (.ECAB, .ezip) – EGT Compressed Folder used in advanced systems to compress entire system folders, replaced by EGT Universal Document • ESS (.ess) – EGT SmartSense File, detects files compressed using the EGT compression system. • GHO (.gho, .ghs) – Norton Ghost • gzip (.gz) – Compressed file • IPG (.ipg) – Format in which Apple Inc. -
Specialising Dynamic Techniques for Implementing the Ruby Programming Language
SPECIALISING DYNAMIC TECHNIQUES FOR IMPLEMENTING THE RUBY PROGRAMMING LANGUAGE A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Engineering and Physical Sciences 2015 By Chris Seaton School of Computer Science This published copy of the thesis contains a couple of minor typographical corrections from the version deposited in the University of Manchester Library. [email protected] chrisseaton.com/phd 2 Contents List of Listings7 List of Tables9 List of Figures 11 Abstract 15 Declaration 17 Copyright 19 Acknowledgements 21 1 Introduction 23 1.1 Dynamic Programming Languages.................. 23 1.2 Idiomatic Ruby............................ 25 1.3 Research Questions.......................... 27 1.4 Implementation Work......................... 27 1.5 Contributions............................. 28 1.6 Publications.............................. 29 1.7 Thesis Structure............................ 31 2 Characteristics of Dynamic Languages 35 2.1 Ruby.................................. 35 2.2 Ruby on Rails............................. 36 2.3 Case Study: Idiomatic Ruby..................... 37 2.4 Summary............................... 49 3 3 Implementation of Dynamic Languages 51 3.1 Foundational Techniques....................... 51 3.2 Applied Techniques.......................... 59 3.3 Implementations of Ruby....................... 65 3.4 Parallelism and Concurrency..................... 72 3.5 Summary............................... 73 4 Evaluation Methodology 75 4.1 Evaluation Philosophy