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• Rate my C# code (~300 SLOC) using GDI+/Backgroundworker

  - by sebastianlarsson

  Hi, I want to get some feedback on my code! Below is some background info. I am taking a pre-certification course in C# (Sweden, 15 ECTS). The focus of the course is theoretical and only limited practical work. I dont find the assignments very hard at all to tell you the truth, but since I only have very limited work experience as a developer (I have worked 15h/week at Ericsson since November) I think I would benefit from having the certificate (70-536 and more probably). I am currently reading Martin Fowler's "Refactoring: Improving the design of existing code" and I tried to apply his techniques to my latest lab in the course. I have been on the lookout for a website which have the idea of providing feedback on code, but so far I have yet to discover any. Please take a look on my code and tell me what you think. It is only roughly 300 lines of code divided into a couple of classes. GDI+, backgroundworker and user controls are what the lab is about. I reckon you may have to spend as little as a couple of minutes on looking on the solution. Link to solution: http://www.filefactory.com/file/b18h7d5/n/Lab4_Lab5_SebastianLarsson.zip Regards and thank you, Sebastian

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• Why is there so much XML in Java these days?

  - by BD at Rivenhill

  This is really more of a philosophy/design issue. I did some work in Java back in the middle 90's and again in the early 2000's and now I'm coming back to it after spending a lot of time in C/C++ and it seems like there was an explosion of XML dependency while I was gone. Major build system tools like ant and maven depend on XML for their configuration, but I'm actually more concerned with all the frameworks, such as Spring, Hibernate, etc. My experience is that powerful supporting libraries like these are where a developer can really get leverage for building programs with lots of features without writing a lot of code, but it really seems like I'm getting one language for the price of two here. I write a bunch of Java classes, but then I also write a bunch of XML files to glue them together. The things that get done in the XML are things that I can see reasonable ways of doing in straight code without the middleman, and they don't really seem to be treated exactly like configuration files: they change rarely and they end up getting committed to source code control like the Java code itself, but they are distributed with the resulting application and need to be unpacked and installed in the classpath in order to get the application to work. I'm working with server applications that are not web-based, so maybe the domain is a bit different from what most people are doing, but I just can't help feeling that I must be doing something wrong here. Can someone point me to a good source of information for why these design choices were made and what problems they are meant to solve so that I can analyze my own experiences in this context?

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• How can I "reset" styles for a given HTML element?

  - by Sambo

  I am working on an embeddable javascript which inserts HTML elements onto unknown pages. I have no control of the stylesheets of the pages I'll be inserting HTML into. The problem is that the HTML I insert will mistakenly stylized by the page, and I want to prevent that. What's the least verbose and/or resource intensive to go about ensuring the elements I insert are exactly as I'd like them to be? Is there an easy way to clear all styling for a given HTML element and children? In firebug, for instance, you can remove all styling. I feel like there must, and the very least should, be a native way to exempt certain HTML elements from stylesheet rules? Example: var myHTML = $("<div>my html in here</div>"); myHTML.resetAllStyles(); //<--- what would this function do? myHTML.appendTo("body"); I really want to avoid explicitly stating the attributes I want for each element I insert... PS: I have a lot of experience with JS and CSS, so you can assume that I'll understand pretty much anything you're going to tell me.

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• Is it not possible to make a C++ application "Crash Proof"?

  - by Enno Shioji

  Let's say we have an SDK in C++ that accepts some binary data (like a picture) and does something. Is it not possible to make this SDK "crash-proof"? By crash I primarily mean forceful termination by the OS upon memory access violation, due to invalid input passed by the user (like an abnormally short junk data). I have no experience with C++, but when I googled, I found several means that sounded like a solution (use a vector instead of an array, configure the compiler so that automatic bounds check is performed, etc.). When I presented this to the developer, he said it is still not possible.. Not that I don't believe him, but if so, how is language like Java handling this? I thought the JVM performs everytime a bounds check. If so, why can't one do the same thing in C++ manually? UPDATE By "Crash proof" I don't mean that the application does not terminate. I mean it should not abruptly terminate without information of what happened (I mean it will dump core etc., but is it not possible to display a message like "Argument x was not valid" etc.?)

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• What do you call a generalized (non-GUI-related) "Model-View-Controller" architecture?

  - by dcuccia

  I am currently refactoring code that coordinates multiple hardware components for data acquisition, and feeling a bit like I'm recreating the wheel. In particular, an MVC-like pattern seems to be emerging. Except, this has nothing to do with a GUI and I'm worried that I'm forcing this particular pattern where another might be more appropriate. Here's my scenario: Individual hardware "component" classes obey interface contracts for each hardware type. Previously, component instances were orchestrated by a single monolithic InstrumentController class, which relied heavily on configuration + branching logic for executing a specific acquisition sequence. After an iteration, I have a separate controller for each component, with these controllers all managed by a small InstrumentControllerBase (or its derivatives). The composite system will receive "input" either programmatically or via inter-hardware component triggering - in either case these interactions are routed to, and handled by, the appropriate controller. So, I have something that feels MVC-esque, but I don't know if that's because I'm forcing the point. With little direct MVC experience in application development, it's hard to know if I'm just trying to make my scenario fit MVC, where another pattern might be a good alternative or complimentary. My problem is, search results and wiki documentation of these family of patterns seems to immediately drop me into GUI-specific discussions. I understand "M means Model data and the V means View" - but do you call the superset pattern? Component-Commander-Controller? Whence can I exhume examples exemplary?

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• trying to reenter IT field after a break of over 5 years

  - by josephj1989

  Hello I have had some misfortune in life - I was unwell and had to stay out of work for an extended period of about 5 years.Before that I used to work as an Oracle/Oracle Ebusiness suite consultant (I was charging very good contract rates). But now I am fully recovered ,feeling sharper than ever. But there arent many opportunities in my areas of expertise in a small market like New Zealand and the long absence is no help either. So for the last 5 months I have been training myself in C# ,ASP .NET,WEB technologies like HTML,JQuery,CSS and also SQL Server.I had some previous experience with JAVA and VB .NET (few months). But I am fully confident of my abilities and believe I can hit the ground running given a chance.I used to be an expert with SQL and C language and these skills are portable to SQL Server and C#. Another problem I face is my age- I am over 50. What is your opinion - Am I doing the right thing. Can I get back into an IT career-I am willing to start all over again at a junior level, I am really facing a crisis in my life.

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• WCF hosting: Can access svc file but cannot go to wsdl link

  - by Impulse

  Hello, I have a WCF service that is hosted in IIS 7.5. I have two servers, one for test and one for production. The service works fine on test server, but on the production server I have the following error. When I access the address http//..../service.svc I can see the default page that says: You have created a service. To test this service, you will need to create a client and use it to call the service. You can do this using the svcutil.exe tool from the command line with the following syntax: svcutil.exe http://..../service.svc?wsdl This will generate a configuration file and a code file that contains the client class. Add the two files to your client application and use the generated client class to call the Service. But when I click the wsdl link, I cannot go to the wsdl page. It returns me to this default web page without any errors. I am suspecting a network/firewall authorization error but does anybody have an experience like this one? All IIS settings are the same for test and production servers. Thank you, Best Regards.

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• Design for fastest page download

  - by mexxican

  I have a file with millions of URLs/IPs and have to write a program to download the pages really fast. The connection rate should be at least 6000/s and file download speed at least 2000 with avg. 15kb file size. The network bandwidth is 1 Gbps. My approach so far has been: Creating 600 socket threads with each having 60 sockets and using WSAEventSelect to wait for data to read. As soon as a file download is complete, add that memory address(of the downloaded file) to a pipeline( a simple vector ) and fire another request. When the total download is more than 50Mb among all socket threads, write all the files downloaded to the disk and free the memory. So far, this approach has been not very successful with the rate at which I could hit not shooting beyond 2900 connections/s and downloaded data rate even less. Can somebody suggest an alternative approach which could give me better stats. Also I am working windows server 2008 machine with 8 Gig of memory. Also, do we need to hack the kernel so as we could use more threads and memory. Currently I can create a max. of 1500 threads and memory usage not going beyond 2 gigs [ which technically should be much more as this is a 64-bit machine ]. And IOCP is out of question as I have no experience in that so far and have to fix this application today. Thanks Guys!

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• Database (and ORM) choice for an small-medium size .NET Application

  - by jim

  I have a requirement to develop a .NET-based application whose data requirements are likely to exceed the 4 gig limit of SQL 2005 Express Edition. There may be other customers of the same application (in the future) with a requirement to use a specific DB platform (such as Oracle or SQL Server) due to in-house DBA expertise. Questions What RDBMS would you guys recommend? From the looks of it the major choices are PostGreSQL, MySQL or FireBird. I've only got experience of MYSQL from these. Which ORM tool (if any) would you recommend using - ideally one that can be swapped out between DB platforms with minimal effort? I like the look of the entity framework but unsure as to the degree to which platforms other than SQL Server are supported. If it helps, we'll be using the 3.5 version of the Framework. I'm open to the idea of using a tool such as NHibernate. On the other hand, if it's going to be easier, I'm happy to write my own stored procedures / DAL code - there won't be that many tables (perhaps 30-35).

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• Type-safe generic data structures in plain-old C?

  - by Bradford Larsen

  I have done far more C++ programming than "plain old C" programming. One thing I sorely miss when programming in plain C is type-safe generic data structures, which are provided in C++ via templates. For sake of concreteness, consider a generic singly linked list. In C++, it is a simple matter to define your own template class, and then instantiate it for the types you need. In C, I can think of a few ways of implementing a generic singly linked list: Write the linked list type(s) and supporting procedures once, using void pointers to go around the type system. Write preprocessor macros taking the necessary type names, etc, to generate a type-specific version of the data structure and supporting procedures. Use a more sophisticated, stand-alone tool to generate the code for the types you need. I don't like option 1, as it is subverts the type system, and would likely have worse performance than a specialized type-specific implementation. Using a uniform representation of the data structure for all types, and casting to/from void pointers, so far as I can see, necessitates an indirection that would be avoided by an implementation specialized for the element type. Option 2 doesn't require any extra tools, but it feels somewhat clunky, and could give bad compiler errors when used improperly. Option 3 could give better compiler error messages than option 2, as the specialized data structure code would reside in expanded form that could be opened in an editor and inspected by the programmer (as opposed to code generated by preprocessor macros). However, this option is the most heavyweight, a sort of "poor-man's templates". I have used this approach before, using a simple sed script to specialize a "templated" version of some C code. I would like to program my future "low-level" projects in C rather than C++, but have been frightened by the thought of rewriting common data structures for each specific type. What experience do people have with this issue? Are there good libraries of generic data structures and algorithms in C that do not go with Option 1 (i.e. casting to and from void pointers, which sacrifices type safety and adds a level of indirection)?

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• Performance difference between functions and pattern matching in Mathematica

  - by Samsdram

  So Mathematica is different from other dialects of lisp because it blurs the lines between functions and macros. In Mathematica if a user wanted to write a mathematical function they would likely use pattern matching like f[x_]:= x*x instead of f=Function[{x},x*x] though both would return the same result when called with f[x]. My understanding is that the first approach is something equivalent to a lisp macro and in my experience is favored because of the more concise syntax. So I have two questions, is there a performance difference between executing functions versus the pattern matching/macro approach? Though part of me wouldn't be surprised if functions were actually transformed into some version of macros to allow features like Listable to be implemented. The reason I care about this question is because of the recent set of questions (1) (2) about trying to catch Mathematica errors in large programs. If most of the computations were defined in terms of Functions, it seems to me that keeping track of the order of evaluation and where the error originated would be easier than trying to catch the error after the input has been rewritten by the successive application of macros/patterns.

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• Entity Framework Decorator Pattern

  - by Anthony Compton

  In my line of business we have Products. These products can be modified by a user by adding Modifications to them. Modifications can do things such as alter the price and alter properties of the Product. This, to me, seems to fit the Decorator pattern perfectly. Now, envision a database in which Products exist in one table and Modifications exist in another table and the database is hooked up to my app through the Entity Framework. How would I go about getting the Product objects and the Modification objects to implement the same interface so that I could use them interchangeably? For instance, the kind of things I would like to be able to do: Given a Modification object, call .GetNumThings(), which would then return the number of things in the original object, plus or minus the number of things added by the modification. This question may be stemming from a pretty serious lack of exposure to the nitty-gritty of EF (all of my experience so far has been pretty straight-forward LOB Silverlight apps), and if that's the case, please feel free to tell me to RTFM. Thanks in advance!

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• [PHP/MySQL] How to create text diff web app

  - by Adam Kiss

  Hello, idea I would like to create a little app for myself to store ideas (the thing is - I want it to do MY WAY) database I'm thinking going simple: id - unique id of revision in database text_id - identification number of text rev_id - number of revision flags - various purposes - expl. later title - self expl. desc - description text - self expl . flags - if I (i.e.) add flag rb;65, instead of storing whole text, I just said, that whenever I ask for latest revision, I go again in DB and check revision 65 Question: Is this setup the best? Is it better to store the diff, or whole text (i know, place is cheap...)? Does that revision flag make sense (wouldn't it be better to just copy text - more disk space, but less db and php processing. php I'm thinking, that I'll go with PEAR here. Although main point is to open-edit-save, possiblity to view revisions can't be that hard to program and can be life-saver in certain situations (good ideas got deleted, saving wrong version, etc...). However, I've never used PEAR in a long-time or full-project relationship, however, brief encounters in my previous experience left rather bad feeling - as I remember, it was too difficult to implement, slow and humongous to play with, so I don't know, if there's anything better. why? Although there are bazillions of various time/project/idea management tools, everything lacks something for me, whether it's sharing with users, syncing on more PCs, time-tracking, project management... And I believe, that this text diff webapp will be for internal use with various different tools later. So if you know any good and nice-UI-having project management app with support for text-heavy usage, just let me know, so I'll save my time for something better than redesigning the weel.

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• Paypal Sandbox 2014 Non US test account Sign Up proper link

  - by Flood Gravemind

  Ok I had a Paypal Sandbox account a year ago. I am developing a new site for a client and when I try to Login it won't recognize my email address. I tried forgot my password forgot password still nothing. So I guessed that maybe due to inactivity for such a long time they may have deleted my account. So then I try to Sign Up for a new one. I entered my details 3 times now and spent 6 hours trying to figure out what is the proper link to do this. Then I went to another Sandbox link which required me to entered a US Zip code and its a dead end. I am not even sure which Paypal account I signed up for those three times. No email nothing at all. I am a Non US developer and the FAQ link for Non US developers just points to their REST API. Can someone please guide me to the proper Paypal Sandbox Setup for Non US developers including the proper sign up links please. And I know Stackoverflow does not like rants but from my experience dealing with Paypal, GTA 6 should make a satirical Paypal company in their next Game with Paypal Developer Rampage mode for the main protagonist who also happens to be a Developer. EDIT: REST API does not include UK :(

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• Upload .txt and keep formating

  - by s2xi

  I have been trying to upload a .txt to my server via a simple php script I made. Everything seems to uploaded correctly, if I open the .txt in Dreamweaver I can see all the formatting is still in tact with spaces and paragraph breaks. The problem I have is when I try to open that file with PHP and import the contents onto my site. I'm not using an editor right now, just a simple div where the contents are echoed. I don't have much experience with uploading/downloading using PHP. Am I not using a command to handle the file contents and keep the initial formatting? In the end I want the user to upload a file, and have PHP read the file and extract certain elements from it based on the number of spaces between paragraph breaks and such. I was able to actually echo the .txt using URLENCODE() which kept the formatting and made all my spaces +'s. Thats the closes I got, but the original file isn't uploaded in the format so I can't do a count for +'s and select x characters after the last +. Hmmm, if someone knows of a script already available that can do this or similar to with me just tweaking that would be awesome.

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• PHP include taking too long

  - by wxiiir

  I have a php file with around 100mb which is full of arrays (only arrays). I've made a script that includes this file (for processing), first it exhausted the default Xampp 128mb memory limit, i've raised it to 1024mb but it just takes forever and doesn't do anything. I'm sure the problem is being created by the sheer size of the file because i've tried removing all lines of code and just leaving the include and an echo for me to know when it finishes executing, and it does the same thing (which is taking forever), i've also tried to run the 100mb file in separate and same thing again. A 10mb file is taking forever as well but a similar 1mb file is almost instantly read and executed so the problem must be more than just the file size. I was avoiding using c++ for a simple project as this and would rather not to as php is easier for me and the task that will be executed doesn't need to benefit from the added speed that it would have if it had been done in c++ but if i have no luck in solving this problem i guess i'll have to. EDIT Reasons for not using a database: 1-Whoever made it didn't used a database and it will be pretty hard to store this in an organized database if i'm not able to do something with it first, like just reading it, copying parts from it or putting in memory or something. 2-I don't have experience working with databases as pretty much all stuff i've ever done in php didn't needed large amounts of stored data, 50kb at best, if i was thinking about a big project or huge chunks of data as this one, i definitely would, but i didn't made this mess to start with and now i have to undo it. 3-The logic for having to store a small portion of data like 10mb in hard drive when now every computer has pretty much enough ram to fit the whole OS in it is pretty much incomprehensible unless someone gives a good explanation about it, if i had to access a lot of said files simultaneously i would understand but like i said, this is a simple project, this is the only file that will be accessed at a given time this isn't even to make some kind of website, it's to run a few times and be done with it.

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• What's the best way to link formal specs to JIRA enchancement requests?

  - by Adam

  What's the best way to link formal specs to JIRA enhancement requests? I want to track changes to specifications using JIRA. Ideally, I'd like to refer to a functional ID reference in a JIRA ticket (e.g. MYAPPAPPROVAL LOGICMAIN SCREEN), so that program managers can retrospectively categorise defects. The reason for this, is so that QA scripts and documentation tickets can be searched/categorised meaningfully in the tracking system. There seems to be a million possible ways to do this, e.g. should I write a custom component to select functional IDs from a tree? should I write the specs in confluence, or another CMS with a TrackBack facility? should I include a link to the documentation URL? should I use some other 3rd party plugin application? should I use some Atlassian application that i'm unaware of? am I using the wrong tracking tool/process to measure spec growth? What's the best way, in your experience?

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• Should programmers use boolean variables to "document" their code?

  - by froadie

  I'm reading McConell's Code Complete, and he discusses using boolean variables to document your code. For example, instead of: if((elementIndex < 0) || (MAX_ELEMENTS < elementIndex) || (elementIndex == lastElementIndex)){ ... } He suggests: finished = ((elementIndex < 0) || (MAX_ELEMENTS < elementIndex)); repeatedEntry = (elementIndex == lastElementIndex); if(finished || repeatedEntry){ ... } This strikes me as logical, good practice, and very self-documenting. However, I'm hesitant to start using this technique regularly as I've almost never come across it; and perhaps it would be confusing just by virtue of being rare. However, my experience is not very vast yet, so I'm interested in hearing programmers' opinion of this technique, and I'd be curious to know if anyone uses this technique regularly or has seen it often when reading code. Is this a worthwhile convention/style/technique to adopt? Will other programmers understand and appreciate it, or consider it strange?

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• Logic: Best way to sample & count bytes of a 100MB+ file

  - by Jami

  Let's say I have this 170mb file (roughly 180 million bytes). What I need to do is to create a table that lists: all 4096 byte combinations found [column 'bytes'], and the number of times each byte combination appeared in it [column 'occurrences'] Assume two things: I can save data very fast, but I can update my saved data very slow. How should I sample the file and save the needed information? Here're some suggestions that are (extremely) slow: Go through each 4096 byte combinations in the file, save each data, but search the table first for existing combinations and update it's values. this is unbelievably slow Go through each 4096 byte combinations in the file, save until 1 million rows of data in a temporary table. Go through that table and fix the entries (combine repeating byte combinations), then copy to the big table. Repeat going through another 1 million rows of data and repeat the process. this is faster by a bit, but still unbelievably slow This is kind of like taking the statistics of the file. NOTE: I know that sampling the file can generate tons of data (around 22Gb from experience), and I know that any solution posted would take a bit of time to finish. I need the most efficient saving process

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• Labview + National Instruments hardware or ???

  - by NSL

  I'm in the processes of buying a new data acquisition system for my company to use for various projects. At first, it's primary purpose will be to monitor up to 20 thermocouples and control the temperature of a composites oven. However, I also plan on using it to monitor accelerometers, strain gauges, and to act as a signal generator. I probably won't be the only one to use it, but I have a good bit of programming experience with Atmel microcontrollers (C). I've used Labview before, but ~5 years ago. Labview would be good because it is easy to pick up on for both me and my coworkers. On the flip side, it's expensive. Right now I have a NI CompactDAQ system with 2 voltage and one thermocouple cards + Labview speced out and it's going to cost $5779! I'm going to try to get the same I/O capabilities with different NI hardware for less $ + labview to see if I can get it for less $. I'd like to see if anyone has any suggestions other than Labview for me. Thanks in advance!

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• Is there any library/software available that can give me useful measurements of image quality?

  - by Thor84no

  I realise measuring image quality in software is going to be really difficult, and I'm not looking for a quick-fix. Googling this is largely showing up research papers and discussions that go a bit over my head, so I was wondering if anyone in the SO community had any experience with doing any rough image quality assessment? I want to use this to scan a few thousand images and whittle it down to a few dozen images that are most likely of poor quality. I could then show these to a user and leave the rest to them. Obviously there are many metrics that can be a part of whether an image is of high/low quality, I'd be happy with anything that could take an image as an input and give some reasonable metrics to any of the basic image quality metrics like sharpness, dynamic range, noise, etc., leaving it up to my software to determine what's acceptable and what isn't. Some of the images are poor quality because they've been up-scaled drastically. If there isn't a way of getting metrics like I suggested above, is there any way to detect that an image has been up-scaled like this?

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• JMS message. Model to include data or pointers to data?

  - by John

  I am trying to resolve a design difference of opinion where neither of us has experience with JMS. We want to use JMS to communicate between a j2ee application and the stand-alone application when a new event occurs. We would be using a single point-to-point queue. Both sides are Java-based. The question is whether to send the event data itself in the JMS message body or to send a pointer to the data so that the stand-alone program can retrieve it. Details below. I have a j2ee application that supports data entry of new and updated persons and related events. The person records and associated events are written to an Oracle database. There are also stand-alone, separate programs that contribute new person and event records to the database. When a new event occurs through any of 5-10 different application functions, I need to notify remote systems through an outbound interface using an industry-specific standard messaging protocol. The outbound interface has been designed as a stand-alone application to support scalability through asynchronous operation and by moving it to a separate server. The j2ee application currently has most of the data in memory at the time the event is entered. The data would consist of approximately 6 different objects; a person object and some with multiple instances for an average size in the range of 3000 to 20,000 bytes. Some special cases could be many times this amount. From a performance and reliability perspective, should I model the JMS message to pass all the data needed to create the interface message, or model the JMS message to contain record keys for the data and have the stand-alone Java application retrieve the data to create the interface message?

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• PC to Macbook Pro Transition - Getting (re)started?

  - by Torus Linvald

  I'm in my second computer science course right now. I've enjoyed programming so far, but really have just scraped my way by. I've not done much programming outside of required class work. For similar reasons, I never really invested in downloading/learning software to help me program (IDE's, editors, compilers, etc). I know it sounds tedious, but my current setup is: notepad++ for coding; Filezilla to transfer .cpp & .h files to school's aludra/unix and compiling; unix tells me where my bugs are and I go back to notepad++ to debug; repeat until done. This isn't fun - and I know it could be easier. But I put it off knowing that I was soon going to switch to a Mac. And, tomorrow, I'm switching. So... How should I set up my Macbook for the best programming experience? What IDEs and editors and debuggers and so on should I download? How will Mac programming differ from PC? I'm open to all ideas and comments, even the most basic. (Background - I'm learning/programming in C++ right now. Next semester, my classes switch to Java. I'm also going to take a class in web development, with HTML/CSS/Javascript/PHP. My new laptop will be a late 2009 Macbook Pro with Leopard, or maybe Snow Leopard. Free would be preferrable for all programs.) Thank you all.

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• C++ IDE for Linux?

  - by Sven

  I want to expand my programming horizons to Linux. A good, dependable basic toolset is important, and what is more basic than an IDE? I could find these SO topics: Lightweight IDE for linux and What tools do you use to develop C++ applications on Linux? I'm not looking for a lightweight IDE. If an IDE is worth the money, then I will pay for it, so it need not be free. My question, then: What good, C++ programming IDE is available for Linux? The minimums are fairly standard: syntax highlighting, code completion (like intellisense or its Eclipse counterpart) and integrated debugging (e.g., basic breakpoints). I have searched for it myself, but there are so many that it is almost impossible to separate the good from the bads by hand, especially for someone like me who has little C++ coding experience in Linux. I know that Eclipse supports C++, and I really like that IDE for Java, but is it any good for C++ and is there something better? The second post actually has some good suggestions, but what I am missing is what exactly makes the sugested IDE so good for the user, what are its (dis)advantages? Maybe my question should therefore be: What IDE do you propose (given your experiences), and why?

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• How to parse a string (by a "new" markup) with R ?

  - by Tal Galili

  Hi all, I want to use R to do string parsing that (I think) is like a simplistic HTML parsing. For example, let's say we have the following two variables: Seq <- "GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCGGGGCA" Str <- ">>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<." Say that I want to parse "Seq" According to "Str", by using the legend here Seq: GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCGGGGCA Str: >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<. | | | | | | | || | +-----+ +--------------+ +---------------+ +---------------++-----+ | Stem 1 Stem 2 Stem 3 | | | +----------------------------------------------------------------+ Stem 0 Assume that we always have 4 stems (0 to 3), but that the length of letters before and after each of them can very. The output should be something like the following list structure: list( "Stem 0 opening" = "GCCTCGA", "before Stem 1" = "TA", "Stem 1" = list(opening = "GCTC", inside = "AGTTGGGA", closing = "GAGC" ), "between Stem 1 and 2" = "G", "Stem 2" = list(opening = "TACGA", inside = "CTGAAGA", closing = "TCGTA" ), "between Stem 2 and 3" = "AGGtC", "Stem 3" = list(opening = "ACCAG", inside = "TTCGATC", closing = "CTGGT" ), "After Stem 3" = "", "Stem 0 closing" = "TCGGGGC" ) I don't have any experience with programming a parser, and would like advices as to what strategy to use when programming something like this (and any recommended R commands to use). What I was thinking of is to first get rid of the "Stem 0", then go through the inner string with a recursive function (let's call it "seperate.stem") that each time will split the string into: 1. before stem 2. opening stem 3. inside stem 4. closing stem 5. after stem Where the "after stem" will then be recursively entered into the same function ("seperate.stem") The thing is that I am not sure how to try and do this coding without using a loop. Any advices will be most welcomed.

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