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• 50 sequences in one line

  - by user343934

  I have Muttiple sequence alignment (clustal) file and i want to read this file and arrange sequences in a such a way that in looks more clear and precise in order. I am doing this from biopython using AlignIO object. My codes like this alignment = AlignIO.read("opuntia.aln", "clustal") print "Number of rows: %i" % len(align) for record in alignment: print "%s - %s" % (record.id, record.seq) My Output-- http://i48.tinypic.com/ae48ew.jpg , it looks messy and long scrolling. What i want to do is print only 50 sequences in each line and continue till the end of alignment file. I wish to have output like this---http://i45.tinypic.com/4vh5rc.jpg from --http://www.ebi.ac.uk/Tools/clustalw2/, sorry two links are just a text due to my reputation. Any suggestions, algorithm and sample code is appreciated Thanks in advance Br,

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• How to set breakpoint in inline Javascript in Google Chrome browser for linux?

  - by Alan McCloud

  When I open Developer Tools in Google Chrome, I see all kinds useless crap like Profiles, Timelines, not to mentions Audits but basic functionality like being able to set breakpoint both in js files and within html javascript code is missing!. I tried to use javascript Console which itself is buggy ( like when once it encounter JS error, cannot get out of it unless refresh the whole page useless when ajax is involved). I am surprised google engineers still have not figured this out if these features still not available. If they are and there is some twisted way to do this, can some one help?

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• What is a class outlet and where is it?

  - by chrish

  I am trying to learn iPhone development and someone passed along the website www.appsamuck.com. On Day 1, the tutorial instructs the developer We need to reference the label in our code so we can update the label * In the document window "File's Owner" * Click: Tools->Idenity Inspector * In the inspector click the + under "Class Outlets" * Change myOutlet1 to "countdownLabel" * Change id to UILabel * Click enter to make sure they commit I really don't want to get hung up on this, but I can't find "Class Outlets" either when creating a new project from scratch or opening the zipped source code project. Is this just a difference in versions of Interface Builder? Where did it go?

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• android compilation

  - by user1241903

  I am trying to compile android source v2.3.4. When I give "make -j32", I am getting result like this.I am using fedora 14(32 bit). [root@localhost WORKING_DIRECTORY]# make -j32 ============================================ PLATFORM_VERSION_CODENAME=REL PLATFORM_VERSION=2.3.4 TARGET_PRODUCT=full TARGET_BUILD_VARIANT=eng TARGET_SIMULATOR=false TARGET_BUILD_TYPE=release TARGET_BUILD_APPS= TARGET_ARCH=arm HOST_ARCH=x86 HOST_OS=linux HOST_BUILD_TYPE=release BUILD_ID=GRJ22 ============================================ Checking build tools versions... build/core/main.mk:76: ************************************************************ build/core/main.mk:77: You are attempting to build on a 32-bit system. build/core/main.mk:78: Only 64-bit build environments are supported beyond froyo/2.2. build/core/main.mk:79: ************************************************************ build/core/main.mk:80: *** stop. Stop. [root@localhost WORKING_DIRECTORY]# Please help me to solve this issue. How to compile android source code on 32 bit os?. Thank You Rajendra

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• Publish web application from MSBuild Script using VS2010 targets resets working directory

  - by Raoul

  I am trying to automatically publish and deploy my .Net 4 web application automatically from a build script to be run by our continuous integration server. I am using the new _WPPCopyWebApplication target from VS2010 to perform the publish, however it appears to reset the current working directory of the msbuild project to c:\ this causes my prebuild steps to fail as they have relative paths to some external tools. The task I am running from our master.build file is as follows: <Target Name="PublishWeb"> <MSBuild Projects="$(ProjectPath)" Targets="ResolveReferences;_WPPCopyWebApplication" Properties="WebProjectOutputDir=$(DeployPath);OutDir=$(TempOutputFolder)$(WebOutputFolder)\;OutputPath=$(ProjectPath)\bin\Debug;" /> </Target> This does not happen when using the legacy _CopyWebApplication. Does anyone have any idea how to resolve this problem?

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• Find Loding performance of the Website

  - by pandora

  How to find the site performance, there is a tools like YSLOW, Speed traker in google that shows the speed of the website. I have done a php project on LMS with Zend Framework, Everything is in live. When user post contents for a subject that may be size 200K and submitted to the server takes too slow. Sometime server may get DOWN. I login to server(PUTTY) and checked i found that there is more resource occupied in my server. It uses full memory on the server. When i cleared the resource the site loads well. Site is in Dedicated server with 3 more domains with 4GB Ram. Because of this LMS website all the website gets down. I need to check what is wrong in my website. How do i Start?

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• Parsing a website

  - by Phenom

  I want to make a program that takes as user input a website address. The program then goes to that website, downloads it, and then parses the information inside. It outputs a new html file using the information from the website. Specifically, what this program will do is take certain links from the website, and put the links in the output html file, and it will discard everything else. Right now I just want to make it for websites that don't require a login, but later on I want to make it work for sites where you have to login, so it will have to be able to deal with cookies. I'll also want to later on have the program be able to explore certain links and download information from those other sites. What are the best programming languages or tools to do this?

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• Can we view objects in the JVM memory?

  - by Sebastien Lorber

  Hey, At work we found that on some instances (particulary the slow ones) we have a different behaviour, acquired at the reboot. We guess a cache is not initialized correctly, or maybe a concurrency problem... Anyway it's not reproductible in any other env than production. We actually don't have loggers to activate... it's an old component... Thus i'd like to know if there are tools that can help us to see the different objets present in the JVM memory in order to check the content of the cache... Thank you!

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• Emacs on Windows for C++ development configuration?

  - by rbnn

  Has anyone set up cygwin and some emacs to work well under a 64-bit Windows 7? I tried downloading cygwin recently, and by default not even dired works reliably, there are odd shell prompt characters, I get a lot of warnings, in one case C-c was read as C-g and caused various errors. (Neither xemacs nor emacs worked for me, where by "work" I mean that dired and shell work, and without warnings). I just want the usual emacs development tools: gdb-mode, shell-mode, compiling, tag-search to work as normal. I was hoping someone who has done this recently with cygwin could share whatever relevant shell files, emacs files, environment variables, and so on to make this all work. Should all these things just work out of the box?

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• Devising a test strategy

  - by Simon Callan

  As part of a new job, I have to devise and implement a complete test strategy for the companies new product. So far, all I really know about it is that it is written in C++, uses an SQL database and has a web API which is used by a browser client written using GWT. As far as I know, there isn't much of an existing strategy, except for using Python scripts to test the web API. I need to develop and implement a suitable strategy for unit, system, regression and release testing, preferably a fully automated one. I'm looking for good references for : Devising the complete test strategy. Testing the web API. Testing the GWT based application. Unit testing C++ code. In addition, any suitable tools would be appreciate

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• How to install Multiple ActiveX Controls per one step?

  - by Eugene

  My .ocx contains two ActiveX controls and I use both of them on one page. When user comes to page he gets two install confirmations for the same binary. After the first installation and page reload he gets one control displayed and “the website wants to run the following add-on...” yellow bar with control’s run confirmation for the other. I have only two possible solutions: Adding my CLSID’s to IE’s pre-approved control list, but I guess I cannot do it in the case of Non-Admin installation. Besides I consider this way as unreliable. Use the third control-container for hosting all other controls. It seems to my too complicated. Actually I’m not sure it can be done. Controls are used from the WEB, so I cannot use any administrative tools for installation. Is it possible to do all installation actions with one step without twice installation or run confirmation? Are there any “Best practices” for my case?

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• Ajax and sophisticated graphics in Java web-app

  - by EugeneP

  In my opinion WWW will sooner or later come to full-blown AJAX web-sites, so that we wouldn't have page reloads every time you click somewhere. Now I want you to ask this. What tools and frameworks can one use to make a Java Web-application running on Tomcat have AJAX functionality like "in-place, with no page reloading" table sorting by clicking on its column header, multi-tabs that enable opening at once the new screen to the user without reloading a page, saving data in the database without reloading a page, and other similar things that we do not usually see on web pages. That's all should probably be based on AJAX. But how to integrate this AJAX functionality with existing java web-frameworks, let's say Spring MVC? Or maybe there are other frameworks that better suit such needs but that can be integrated with core Spring?

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• How do I diff two spreadsheets?

  - by neu242

  We have a lot of spreadsheets (xls) in our subversion repository. These are usually edited with gnumeric or openoffice.org, and are mostly used to populate databases for unit testing with dbUnit. There are no easy ways of doing diffs on xls files that I know of, and this makes merging extremely tedious and error prone. I've found Spreadsheet Compare, but it requires Excel 2000 or later. I've also tried to convert the spreadsheets to xml and doing a regular diff, but it really feels as a last resort. Are there any tools for diffing two spreadsheets (xls or ods)? I am primarily looking for a multi-platform/open source tool.

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• What is a good approach for a Data Access Layer?

  - by Adil Mughal

  Our software is a customized Human Resource Management System (HRMS) using ASP.NET with Oracle as the database and now we are actually moving to make it a product that supports multiple tenants with their own databases. Our options: Use NHibernate to support Multiple databases and use of OO. But we concern related to NHibernate learning curve and any problem we faced. Make a generalized DAL which will continue working with Oracle using stored procedures and use tools to convert it to other databases such as SQL Server or MySql. There is a risk associated with having to support multiple database-dependent versions of a single script. Provide the software as a Service (SaaS) and maintain the way we conduct business. However there can may be clients who do not want or trust the Cloud or other SaaS business models. With this in mind, what's the best Data access layer technique?

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• is there any cross platform process manager tool

  - by lvlv

  I need a program that is able to launch a set of processes according to a schedule/configuration; the program would run in the background and restart the processes in case they crash. There are standard tools for this kind of task on both windows and unix - what I need is a cross platform program which could run on different operating systems using the same configuration. A portable C/C++ library which implements the basic functionality (i.e. create processes, signal process termination events and all that) would be ok too.

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• VSTO install package How to check for prerequisites and skip them

  - by ticky

  I created Setup project for my Excel add-in project according to the article: Deploying a Visual Studio Tools for the Office System 3.0 Solution for the 2007 Microsoft Office System Using Windows Installer http://msdn.microsoft.com/en-us/library/cc563937(office.12).aspx I add prerequisites such as 2007 Interop assemblies(Office2007PIA) and when I run my setup file it does install it. But the problem is : That my setup ALWAYS installs it even if my computer already has Office2007PIA. How can I configure my setup project that it will first check if Office2007PIA is installed and continue the installation of my project without installing Office2007PIA? Thanks!

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• Measuring CPU time per-thread on Windows

  - by Eli Courtwright

  I'm developing a long-running multi-threaded Python application for Windows, and I want the process to know the CPU time that each of its threads has taken. I can get the overall times for the entire process with os.times() but I need to know the per-thread times. I know that there are external tools such as the Sysinternals Process Explorer, but my program itself needs to have this information. If I were on Linux, I look in the /proc filesystem, as described here. If I were writing C code, I'd use the GetThreadTimes call, as described here. So how can I accomplish this on Windows using Python?

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• How best to debug Delphi using the IDE and/or FOSS?

  - by LeonixSolutions

  I am currently using Delphi 7 and unsure whether to upgrade. I see the following means of debugging and wonder if there are others or which FOSS tools a small company can use (we don't do much Windows programming). 1 Debug in the IDE, by setting breakpoints, using watches, etc 2 Debug in the IDE, by using the Event Log I got some good info from this page and tweaked it to add timestamps and indent/outdent on procedure call/return, so that I can see nested calls more quickly. Does anyone know of anything better ? 3 Using a profiler 4 Any others? Such as MadExcept, etc?

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• How can an animator do animation targeted for the iPhone

  - by teepusink

  Hi, I'm working with an animator for the iPhone. The animator I'm working with isn't a programmer and has a background in Flash. (right now she's doing the animation in Flash and I need to convert to Objective C). For some it's ok because I can just use image frames, but there are more complex animation that would take longer for me to convert to Objective C. Is there any tools out there that can help the work flow easier? Just trying to find a way so I can just take the animation and stick it into the project. Thanks, Tee

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• Any ideas for developing a Risc Processor friendly string allocator?

  - by Richard Fabian

  I'm working on some tools to enable high throughput data-oriented development, and one thing that I've not got an immediate answer for is how you go about allocating strings quickly. On risc processors you've got another problem of implementation that the CPU doesn't like branching, which is what I'm trying to minimise or avoid. Also, cache coherence is important on most CPUs, so that's gotta be influential in the design too. So, how would you go about reducing the overhead for a generic string allocator? Sometimes it's easier to solve a more explicit problem, so any ideas for string sizes of 5-30?

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• How to get the right order for creation of stored procedure, user-defined functions and triggers

  - by PeeWee2201

  I read that object dependencies have been improved in SQL server 2008. I have a rather complex database schema containing stored procedure, user-defined functions, triggers. Can anybody give me a query that would return the right order of creation of those items based on their dependencies ? I read here that there are tools that can do the job, but I am looking for something scriptable. Also, they often give the dependencies of one object and I would like a database-wide solution. Thank you.

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• How can I check that I didn't break anything when refactoring?

  - by Nathan Fellman

  I'm about to embark on a bout of refactoring of some functions in my code. I have a nice amount of unit tests that will ensure I didn't break anything, but I'm not sure about the coverage they give me. Are there any tools that can analyze the code and see that the functionality remains the same? I plan to refactor some rather isolated code, so I don't need to check the entire program, just the areas that I'm working on. For context, the code I'm working on is in C/C++, and I work in Linux with GCC and VIM.

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• ORA-12560: TNS:protocol adaptor error after delete one database

  - by malihe

  i have oracle11g desktop. For my project I create 3 databases via configuration assistant tools. Then I delete one of them and after this I have the error: ora-12560. By mistake both of my databases have the same pasword, for example: when i want to connect one of these data bases with system user, i have one pasword and perhaps the databases dont know connect which one. I start all services set oracle_sid=orcl. I run lsnrctl tnsping check tansname.ora & my listener.ora and I logon with sysdba@oracle_sid but i have this error again pleas help me tnx

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• Tracing\profiling instructions

  - by LeChuck2k

  Hi Y'all. I'd like to statistically profile my C code at the instruction level. I need to know how many additions, multiplications, devides, etc,... I'm performing. This is not your usual run of the mill code profiling requirement. I'm an algorithm developer and I want to estimate the cost of converting my code to hardware implementations. For this, I'm being asked the instruction call breakdown during run-time (parsing the compiled assembly isn't sufficient as it doesn't consider loops in the code). After looking around, It seems VMWare may offer a possible solution, but I still couldn't find the specific feature that will allow me to trace the instruction call stream of my process. Are you aware of any profiling tools which enable this?

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• From .NET to Delphi, an ERP on Delphi

  - by emray

  I have learned programming on .NET. It's been 4 years since I have started (serious) programming, I gained experience in VBA, JavaScript but mainly C#. I have spent a lot of time trying to grasp the good coding practices, object orientation etc. Now finally I have a job. The job is fixing/upgrading an ERP on a daily basis. Creating reports and maybe sometimes new stuff. I have absolutely no experience in Delphi, and no motivation to learn it especially when people are moving to .NEt from Delphi not in the reverse direction sa my manager expects :) The question is that are there any tools that I write C# code and compile into this object pascal or whatever it is. Thanks in advance.

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