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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 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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• How to do concurrent modification testing for grails application

  - by werner5471

  I'd like to run tests that simulate users modifying certain data at the same time for a grails application. Are there any plug-ins / tools / mechanisms I can use to do this efficiently? They don't have to be grails specific. It should be possible to fire multiple actions in parallel. I'd prefer to run the tests on functional level (so far I'm using Selenium for other tests) to see the results from the user perspective. Of course this can be done in addition to integration testing if you'd recommend to run concurrent modification tests on integration level as well.

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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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• 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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• 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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• 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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• WPF component for 2D tree diagram

  - by pdm2011

  I'm looking for a well-documented, supported WPF component that provides an API for visualisation of 2D tree diagrams. Ideally something easy to use, customisable (i.e. supports various flavours of nodes and splines) and preferably with automated layout control. Tools that look good so far are GoXam (http://www.nwoods.com/components/silverlight-wpf/goxam-overview.htm) and yFiles WPF (http://www.yworks.com/en/products_yfileswpf_about.html). Just wondering if anyone has experience with either of these, or can recommend an alternative? Thanks!

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• design question for transportation agency/workflow system

  - by George2

  Hello everyone, I am designing a transportation agency/workflow system, and it including 3 types of people, customer who requests to transport some stuff, drivers who deliver the stuff, and truck manager who manages transport source/destination truck coordination and communicates/organizes drivers. The system is expected to be a web site, and 3 kinds of people could use the web site to submit request, accept request, monitor status of specific stuff transportation, etc. The web site is more like an open agency or a workflow system. I am wondering whether there are any existing technologies, tools or projects (better to be open source, but not a must) which I could build my application faster based on? I prefer to use .Net technologies, but not a must. thanks in advance, George

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• Bitwise operators versus .NET abstractions for bit manipulation in C# prespective

  - by Leron

  I'm trying to get basic skills in working with bits using C#.NET. I posted an example yesterday with a simple problem that needs bit manipulation which led me to the fact that there are two main approaches - using bitwise operators or using .NET abstractions such as BitArray (Please let me know if there are more build-in tools for working with bits other than BitArray in .NET and how to find more info for them if there are?). I understand that bitwise operators work faster but using BitArray is something much more easier for me, but one thing I really try to avoid is learning bad practices. Even though my personal preferences are for the .NET abstraction(s) I want to know which i actually better to learn and use in a real program. Thinking about it I'm tempted to think that .NET abstractions are not that bad at, after all there must be reason to be there and maybe being a beginner it's more natural to learn the abstraction and later on improve my skills with low level operations, but this is just random thoughts.

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• Is there a way to write System.Drawing.Graphics to PDF from C#?

  - by Brett Ryan

  I have a whole bunch of 2D graphics that is being used for both rendering controls on screen and used to print, it's pretty custom graphics that couldn't be done by any 3rd party reporting tools or off the shelf controls. The program can generate PDF files of the printed content but when I wrote it I cheated and just print the Graphics object to an in memory image and then embed that into the PDF page. Since the users are emailing the documents they're finding they are too large. I've started writing the PDF from scratch using iText, however is there a way to get System.Drawing.Graphics content directly into PDF? The way iText works and Graphics works is completely different.

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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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• Please recommend good books for telemetry / SCADA system design & programming

  - by Mawg

  I am looking at several projects, all with roughly the same fucntionality. Some instruments collect some data (or control some functionality). They commmunicate by Internet (Etehrnet/wifi/GPRS/sasatellite) with a databse server which stores the measurements and provides a browser based means of qeurying the data, prodcuing reports, etc (and possibly also allows control of the remote equipment). Can anyone recommend a good book describing an approach to developing such a software architecture, keeping it generic, which tools, languages. test methods, etc to use? (note to self: ask a similar question about possible existing frameworks)

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• What is the best book in client server programming ?

  - by Nayef

  What is the best "new" book in client server programming with C#? I mean principles of inter-network architecture and communication protocols. Open systems and interoperability. Case studies of particular protocols from network layer and above. Socket programming. Remoting. Selected examples of networked client-server applications such as e-mail, news, file-transfer, HTTP. Client-Server Programming Project(s). Using APIs. Software tools and environments.

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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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• 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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• Eclipse debugging "source not found"

  - by James

  I just started using Eclipse so go easy on me ;). But when trying to debug a JUnit test case I get a dialog that states the the source is not found when I get to this line in the code in my test method: Assert.assertEquals(1, contents.size()); I know I should probably go and try and download the source from somewhere, but I really don't want to because I have no interest in stepping into the JUnit code. I have the JUnit runtime jar so Why does Eclipse expect me to have all the referenced tools source code in order to debug my own code (seems somewhat silly)? My main question is though, how can I tell Eclipse to skip this dialog when the source is not available and allow me to continue to debug my own code? [Edit] I've isolated the cause of this. It seems that Eclipse seems to think it needs the source when an exception is thrown by the internal JUnit code. In general is there anyway to tell it that it doesn't and just have it throw up an error dialog of some kind instead?

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• JQuery Tooltip and Scrollable Fix

  - by KrippledShark

  I have set up the navigation on my site using a scrollable div created with Flowplayer's JQuery tools. I also want to add a tooltip to the individual images within the scrollable div. The problem is the tooltip needs to appear outside of the div. I can adjust the height of the div so you can see the tooltip, but the tooltip is still constrained inside another div. Here is the link to my code. http://staging.asla.org/sustainablesites/TestAGAIN.html Is there a way to make this tooltip (div) appear out of it's containing divs?

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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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• Generating report from an xml file

  - by Vignesh

  I want to generate a report from an xml, preferably html. The html here should be dynamic to allow limiting the view based on some user entered values, preferably selecting from a drop down of categories, which inturn is populated from the xml. I also want to have links in the report to more info which is stored in another xml file. I started off with javascript with xslt for display and I'm still long way in acheiving my desires. Are there any other ways to do it?? Any automated Open sources tools, for this, rather than reinventing.

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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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• Why not speed up testing by using function dependency graph?

  - by Maltrap

  It seems logical to me that if you have a dependency graph of your source code (tree showing call stack of all functions in your code base) you should be able to save a tremendous amount of time doing functional and integration tests after each release. Essentially you will be able to tell the testers exactly what functionality to test as the rest of the features remain unchanged from a source code point of view. If for instance you change a spelling mistake in once piece of the code, there is no reason to run through your whole test script again "just in case" you introduced a critical bug. My question, why are dependency trees not used in software engineering and if you use them, how do you maintain them? What tools are available that generate these trees for C# .NET, C++ and C source code?

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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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• Best Ruby ORM for Wrapping around Legacy SQL Server Database?

  - by Technocrat

  Hi. I found this answer and it sounds like almost exactly what I'm doing. I have heard mixed answers about whether or not datamapper can support SQL Server through dataobjects. Basically, we have an app that uses a consistently structured database, consistently named tables, etc in SQL Server. We're making all kinds of tools and stuff that have to interact with it, some of them remotely and so I decided that we need to create some common, simple access point to do read/write operations on the SQL Server app since it's API is all C# and other things I despise. Now my question is if anyone has any examples or projects they know of where a ruby ORM can essentially create models for another application's legacy database by defining the conventions of each model's pkeys, fkeys, table names, etc. Sequel is the only ORM I've used with SQL Server but never to do anything quite like this. Any suggestions?

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