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• How (and where) to get aligned tRNA sequences (and import it into R)

  - by Tal Galili

  (This is a database / R commands question) I wish (for my thesis work), to import tRNA data into R and have it aligned. My questions are: 1) What resources can I use for the data. 2) What commands might help me with the import/alignment. So far, I found two nice repositories that holds such data: http://trnadb.bioinf.uni-leipzig.de/Resulthttp://trnadb.bioinf.uni-leipzig.de/Result http://gtrnadb.ucsc.edu/download.htmlhttp://gtrnadb.ucsc.edu/download.html And also the readFASTA command from Biostrings, that does basic importing of the data into R. My problem still remains with how to handle the alignment of the tRNA. Since I am not from the field, I might be missing a very basic answer (like where I should download the data from, or what command to use). If you might be willing to advice me, that would be most helpful. Many thanks in advance, Tal

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• onclick form submit, open jQuery loading image until form submit complete

  - by Jackson

  Hi Team, Can you offer a bit of advice. I am using a hosted SAAS CMS solution that enables you to create basing apps with a web apps system. I have created a form for members to submit a bunch of images and content to their own area. Everything is working great except if the images being submitted via the form are large, it takes ages for the form to submit and go to the thank you page. I am already using jQuery UI to split the form in to 5 steps and using the jQuery facebox plugin for instructional popups. My question is, what would be the best way to display a loading gif (in facebox or in another suggested overlay) while the form is being submitted? Thanks for your help! Jack

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• Using Python and Mechanize with ASP Forms

  - by tchaymore

  I'm trying to submit a form on an .asp page but Mechanize does not recognize the name of the control. The form code is: <form id="form1" name="frmSearchQuick" method="post"> .... <input type="button" name="btSearchTop" value="SEARCH" class="buttonctl" onClick="uf_Browse('dledir_search_quick.asp');" > My code is as follows: br = mechanize.Browser() br.open(BASE_URL) br.select_form(name='frmSearchQuick') resp = br.click(name='btSearchTop') I've also tried the last line as: resp = br.submit(name='btSearchTop') The error I get is: raise ControlNotFoundError("no control matching "+description) ControlNotFoundError: no control matching name 'btSearchTop', kind 'clickable' If I print br I get this: IgnoreControl(btSearchTop=) But I don't see that anywhere in the HTML. Any advice on how to submit this form?

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• How do you unit test web page authorization using ASP.NET MVC?

  - by Kevin Pang

  Let's say you have a profile page that can only be accessed by the owner of that profile. This profile page is located at: User/Profile/{userID} Now, I imagine in order to prevent access to this page by other users, you could structure your UserController class's Profile function to check the current session's identity: HttpContext.Current.User.Identity.Name If the id matches the one in the url, then you proceed. Otherwise you redirect to some sort of error page. My question is how do you unit test something like this? I'm guessing that you need to use some sort of dependency injection instead of the HttpContext in the controller to do the check on, but I am unclear what the best way to do that is. Any advice would be helpful.

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• How to update primary key

  - by slave016

  Here is my problem: I have 2 tables: 1.WORKER, with coloumns |ID|OTHER_STAF| , where ID is primary key, and 2.FIRM, with coloumns |FPK|ID|SOMETHING_ELSE| , where combination FPK and ID make primary key, and also ID is a foreign key referenced to WORKER.ID (not null, and must have same value as in WORKER). I want to make stored procedure UPDATE_ID_WORKER, where I would like to change the value of specific ID in WORKER, and also in all instances of specific value of ID in FIRM. stored procedure: ........ @id .. ???? ........ Thanks for every advice...

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• Running mongod as a windows service

  - by andreas

  Hello, i have installed mongodb on win32 and i am trying to run it as a service. I have followed the instructions posted here: http://www.deltasdevelopers.com/post/Running-MongoDB-as-a-Windows-Service.aspx but when when windows tries to 'load'/'run' the service there is a problem. I see the service under the services control banner constantly in the 'starting' state. The result: the service is not started and windows is constantly trying to start it without success. The instructions i have followed are: At the command line C:\mongodb\mongod -install then C:\mongodb\mongod -service Then i modified the Win Registry Entry for the MongoDB Service by setting the ImagePath key to the value of C:\mongodb\mongodb.exe -service Any advice? What am i doing wrong?

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• Erlang Supervisor Strategy For Restarting Connections to Downed Hosts

  - by derdewey

  I'm using erlang as a bridge between services and I was wondering what advice people had for handling downed connections? I'm taking input from local files and piping them out to AMQP and it's conceivable that the AMQP broker could go down. For that case I would want to keep retrying to connect to the AMQP server but I don't want to peg the CPU with those connections attempts. My inclination is to put a sleep into the reboot of the AMQP code. Wouldn't that 'hack' essentially circumvent the purpose of failing quickly and letting erlang handle it? More generally, should the erlang supervisor behavior be used for handling downed connections?

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• per build configuration files on iPhone ?

  - by Matt

  I'm looking for the best way to store per-Build configuration information for an iPhone app. In my iPhone app there are several url's and storage location settings that are specific to a particular build (DEBUG RELEASE etc) Currently i have three recipients for my app, QA/Test, myself and the customer, each has specific settings for the url's and storage locations mentioned above. whats the best way to do this? NOTE: they don't necessarily have to be defined in the build but what im looking for is advice on the best way to store alternate configuration settings. ALSO NOTE: i do not want these settings to be editable through the settings app thanks

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• Pool Billiard AI

  - by Sebi

  Im implementing a pool billiard game in Java and it all works fine. It is a multiplayer game, but nevertheless, it should also be possible to play it alone. For this purpose I'm trying to implement a simple KI. At the moment, the KI choose just randomly a direction and a random intensity of the impulse (don't know the correct english word for that). Of course this AI is very poor and unlikely to ever challenge a player. So i thought about improving the KI, but there are several hard to solve problems. First I thought of just choosing the nearest ball and to try to put it directly into the nearest hole. This isn't that bad, but if there other balls in the line between, it isn't really working anymore. Additionally this dosn't solve te problem of calculating the intensity of the impulse. So are there any general advice? Or any ideas? Best practices?

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• C# parsing txt files IF name format is desired format

  - by jakesankey

  OK, I have txt files that I am parsing and saving into a sql db. The names are formatted like R306025COMP_272A4075_20090929_080159.txt However, there are a select few (out of thousands of files) with names that are formatted differently (particularly files that were generated as tests), example R306025COMP_SU2_TestBottom_20090915_101441.txt The reason this causes a problem for me is that I am using Split('_')[1,2,etc] to extract the R number, the 272A4075 portion, and the 20090929 (date) portion. When the application comes across the oddly named files, it fails because it is trying to parse 'TestBottom' as a date and inserts 'SU2' instead of the 272 number. Basically I want the app to recognize that if the file's name is not formatted like my first example, skip it. Any advice?

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• Need multiple views to respond to a touch event in an iPhone app

  - by Joel

  Setup: I have two views that I need to respond to the touch event, and they are layered out on top of one another. View 1 is on top of View 2. View 2 is a UIWebView. View 1 is sublclassed to capture the touch event. My problem is that if I try to call the UIWebView event handlers (touchesBegan: and touchesEnded:) from within the event handlers of View 1, which is the first responder, nothing happens. However if I set View 1 to userInteractionEnabled = NO, then the touch goes through that view and is processed properly by the 2nd view. Any ideas on how I can have 2 views respond to a touch event? Unfortunately the 2nd view is a UIWebView, so I need to actually call the event handler and not a different method, etc... Thanks in advance for any advice, Joel

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• XNA, WPF light show visualizer

  - by Bgnt44

  HI all, I'm developing a software to control light show ( through DMX protocol ), i use C# and wpf to develop my main software (.net 4.0) To help people preview their show, i would like to make a live 3D visualizer... First, i thought that i could use wpf 3D to make the visualizer, but i need to work with light .. My main application should send property ( beam angle, orientation (X,Y), position(X,Y), Brush ( color,shape,effect)) to the 3D visualizer But i would like to be able to move light (position in the scene) by mouse during execution and had value in return... So .. Does XNA is the easiest way to doing that ? Can you help me for that : Generating light (orientation , bitmap like filter in front of light ) Dynamically moving object with mouse and get position in return Dynamically add or remove fixture All of your advice, sample, example are very welcome ... I don't espect to have a perfect result at the first time but i need to understand the main concepts for doing that Thank You !!

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• How can I update multiple columns with a Replace in SQL server?

  - by Kettenbach

  How do I update different columns and rows across a table? I want to do something similiar to replace a string in SQL server I want to do this but the value exists in multiple columns of the same type. The values are foreign keys varchars to an employee table. Each column represents a task, so the same employee may be assigned to several tasks in a record and those tasks will vary between records. How can I do this effectively? Basically something of a replace all accross varying columns throughout a table. Thanks for any help or advice. Cheers, ~ck in San Diego

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• Career Day in kindergarten: how to demonstrate programming in 20 minutes?

  - by Péter Török

  I was invited to the kindergarten group of my elder daughter to talk, and aswer the kids' questions, about my profession. There are 26 kids of age 4-6 in the group (plus 3 teachers who are fairly scared of anything related to programming and IT themselves, but bold enough to learn new tricks). I would have about 20-30 minutes, without projector or anything. (They have an old computer though, which by its look may be a 486, and I am not even sure if it's functioning.) My research turned up excellent earlier threads, with lots of good tips: How would you explain your job to a 5-year old? Career Day: how do I make “computer programmer” sound cool to 8 year olds? What things can I teach a group of children about programming in one day? My situation is different from each of the above though. So any advice on how to teach the kids (and their teachers) in a fun way about programming is appreciated.

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• Resources for Programmatic Rendering of Topology Maps

  - by bn

  Servus, Do you know of any frameworks, APIS, languages, or other resources that are well suited for drawing topology maps that allow a user to interact with objects on the map? I am not constrained by language choice and the program can be web-based, or stand-alone. I thought I would check before rolling my own. My goal is not to draw cartographic maps, but more like this picture: http://www.fineconnection.com/files/images/GraphicalNM.PNG, or if you are familiar with Edward Tufte's books, the data-visualization mechanisms he describes such as a map of a metro or subway. Also, if you have had any experience rendering these types of user interfaces or usage of underlying datastructures, I would be grateful to hear any thoughts you have on the subject, advice, any "gotchas." Thank you very for your time, -bn

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• Reading UDP Packets

  - by Thomas Mathiesen

  I am having some trouble dissecting a UDP packet. I am receiving the packets and storing the data and sender-address in variables 'data' and 'addr' with: data,addr = UDPSock.recvfrom(buf) This parses the data as a string, that I am now unable to turn into bytes. I know the structure of the datagram packet which is a total of 28 bytes, and that the data I am trying to get out is in bytes 17:28. I have tried doing this: mybytes = data[16:19] print struct.unpack('>I', mybytes) --> struct.error: unpack str size does not match format And this: response = (0, 0, data[16], data[17], 6) bytes = array('B', response[:-1]) print struct.unpack('>I', bytes) --> TypeError: Type not compatible with array type And this: print "\nData byte 17:", str.encode(data[17]) --> UnicodeEncodeError: 'ascii' codec can't encode character u'\xff' in position 0: ordinal not in range(128) And I am not sure what to try next. I am completely new to sockets and byte-conversions in Python, so any advice would be helpful :) Thanks, Thomas

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• Java sound doesn't work under Linux

  - by Cliff

  Help! I'm getting frustrated by the individual hoops I have to go through to eek sound out of my speakers when running Java apps on Linux platforms! I just installed Fedora 12 and after downloading and running the Java Sound Demo I get exceptions. If I run just a vanilla Java program that plays a wav file it runs silently with no sound and no exceptions. Every other app seems to play sound. I also took some advice from this thread in the Ubuntu forums which almost seemed to work. (Installing aoss got rid of the initial exceptions in the sound demo but I still hear nothing when I play.) can somebody help me figure out what's wrong?

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• What is the correct way to backup ZODB blobs?

  - by joeforker

  I am using plone.app.blob to store large ZODB objects in a blobstorage directory. This reduces size pressure on Data.fs but I have not been able to find any advice on backing up this data. I am already backing up Data.fs by pointing a network backup tool at a directory of repozo backups. Should I simply point that tool at the blobstorage directory to backup my blobs? What if the database is being repacked or blobs are being added and deleted while the copy is taking place? Are there files in the blobstorage directory that must be copied over in a certain order?

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• SqlServer / MySql Connection pool: is it really important ?

  - by stighy

  Hy guys, after a lot of problem with my hoster, i decided to disable connection pooling of my application. The problem was related to the number of concurrent connections : only five. So i decided to disable connection pooling: the result is that my web app don't crash. So i'm asking you: are there some "collateral" effect disabling connection pooling ? Is it so important ? I didn't noticed bad performance after disabling it. Thank you for your (i'm sure) precious advice!

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• Override delete behaviour in NHibernate

  - by David

  Hi all In my application users cannot truly delete records. Rather, the record's Deleted field gets set to 1, which hides it from selects. I need to maintain this behaviour and I'm looking into whether NHibernate is appropriate for my app. Can I override NHibnernate's delete behaviour so that instead of issuing DELETE statements, it issues UPDATES, as described above? I would obviously also need to override its SELECT behaviour to include the 'AND Deleted = 0' clause. Or read from a view instead. I dunno. TIA for your advice. David

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• Rewriting subdomain to subfolder with htaccess

  - by Owen Allen

  I'm attempting to use .htaccess in the root folder of an Ubuntu/Apache2 server in order to mask a subdomain to subfolder and I keep getting a 500 Internal Error. I know that I'm doing something stupidly wrong and it is some silly error causing the problem. I've checked all of the similar threads on SO and online and whenever I try their advice the 500 continues. Here's my code. RewriteEngine on RewriteCond %{HTTP_HOST} ^admin\.mydomain\.com.*$ RewriteRule (.*) intranet/$1 [L] What I want to occur is that if a user visits admin.mydomain.com they will get the contents of the folder admin.mydomain.com/intranet/ but their URL bar will still be admin.mydomain.com. Any idea what I'm doing wrong? In addition, some of the threads online talked about possible problems with this system. Is this the best way of doing this masking, should I be using a vhost setup?

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• C++ Primer (Stanley Lipmann) or The C++ programming language (special edition)

  - by Kim

  I have a Computer Science degree (long2 time ago) .. I do know Java OOP but i am now trying to pick up C++. I do have C and of course data structure using C or pascal. I have started reading Bjarne Stroustrup book (The C++ Programming Language - Special Edition) but find it extremely difficult esp. some section which i don't have exposure such as Recursive Descent Parser (chapter 6). In terms of the language i don't foresee i have problem but i have problem as mentioned cos' those topic are usually covered in a Master Degree program such as construction of compiler. I just bought a book called C++ primer (Stanley Lipmann) which i heard it is a very good book for C++. Only setback is it's of course no match with the amount of information from the original C++ creator. Please advice. Thanks.

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• How to sort an array by some specific key?

  - by vinothkumar

  I have an array look like below. $array[0]['keyword'] = 'cricket '; $array[0]['noofhits'] = '26'; $array[0]['keyword'] = 'food '; $array[0]['noofhits'] = '17'; $array[0]['keyword'] = 'mypax'; $array[0]['noofhits'] = '22'; $array[0]['keyword'] = 'next'; $array[0]['noofhits'] = '22'; $array[0]['keyword'] = 'nextbutton'; $array[0]['noofhits'] = '22'; $array[0]['keyword'] = 'picture'; $array[0]['noofhits'] = '18'; I want to sort the array using the noofhits. How can I do? Advance Thanks for your advice.

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• strongly typed dataset Insert record with C# problem

  - by Eyla

  Greetings, I'm using strongly typed data-set in windows application and I'm creating table adapter object to call insert function. The problem that there is nothing inserted to the table after calling the function and no error produced. here is my code: public PacketsDBDataSet1TableAdapters.packetsTableAdapter ds = new PacketsDBDataSet1TableAdapters.packetsTableAdapter(); private void btnSavePacketsInFile_Click(object sender, EventArgs e) { byte[] w = null; ds.InsertPackets("s", "s", "s", "s", "s", w); } I'm using same same code with ASP.Net but it is working OK. any advice??

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• DLL export of a static function

  - by Begbie00

  Hi all - I have the following static function: static inline HandVal StdDeck_StdRules_EVAL_N( StdDeck_CardMask cards, int n_cards ) Can I export this function in a DLL? If so, how? Thanks, Mike Background information: I'm doing this because the original source code came with a VS project designed to compile as a static (.lib) library. In order to use ctypes/Python, I'm converting the project to a DLL. I started a VS project as a DLL and imported the original source code. The project builds into a DLL, but none of the functions (including functions such as the one listed above) are exported (as confirmed by both the absence of dllexport in the source code and tools such as DLL Export Viewer). I tried to follow the general advice here (create an exportable wrapper function within the header) to no avail...functions still don't appear to be exported.

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