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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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• jQuery draggable leaving cloned html behind

  - by Alex Crooks

  I am using jQuery UI; Draggable http://jqueryui.com/demos/draggable invoked like this: $(document).ready(function(){ $("#side_bar").sortable({ revert: true }); $(".draggable").draggable({ containment: 'parent', hascroll: true, handle: 'div.box_header', scrollSensitivity: 100, scrollSpeed: 100, axis: 'y', connectToSortable: '#side_bar', helper: 'clone', opacity: 0.35 }); }); You can see the html structure on http://www.sarsclan.co.uk (right side bar area). It seems to create a transparant clone as your dragging, but when you drop it puts the draggable div in the right place, but leaves the original div in it's place and just appends the dom with a clone of that original div in its new place.

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• Error in SPUtility send email

  - by Faiz

  Hi, I am trying to send an email in the button click event in the webpart.However, the email sending is failed and error is logged in both sharepoint logs and event viewer of the machine. The error is : Cannot connect to SMTP host Outgoing email settings in central admin is already configured. Alerts are also working fine. Below is my code: StringDictionary headers = new StringDictionary(); headers.Add("to", "[email protected]"); headers.Add("from", "MySharePointEmail@myfatblog.co.uk"); headers.Add("subject", "How to use SendEMail from SPUtility"); headers.Add("content-type", "text/html"); string bodyText = "This is the body of my email, in html format."; SPUtility.SendEmail(SPContext.Current.Web, headers, bodyText); Thanks in advance

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• Large number of Google Map Markers and IE6?

  - by Sivakanesh

  I'm working on an application that generates a large number of Google Map markers (2000 - 7000) via JSON. I'm also using MarkerCluster. It works quick on Chrome and FF but IE6 takes few minutes and just crashes the first time I try to zoom in. I'm not doing any more than just adding the markers to a map using JQuery & GMap API. So I looked at the following URL of the regular Google Map. http://maps.google.co.uk/maps?f=q&source=s_q&hl=en&q=hotel&sll=53.182996,-2.581787&sspn=1.494529,4.927368&ie=UTF8&split=1&rq=1&ev=p&hq=hotel&hnear=&ll=53.123702,-2.730103&spn=1.496594,4.927368&t=h&z=8 It shows a lot of tiny markers (~1000) and works fine on IE6. Do you have any ideas why this works and the markers added via the API struggles? Thanks

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• Configuring IoC container from modules/plug-ins ?

  - by rouen

  Hi guys, i am in big dilema.. I am working on highly modular web app in ASP.NET MVC 2 (in fact, core will be super lightweight, all work on modules/plugins). I found MEF pretty useful for modules discovery, but i dont want to us it as IoC container. There is pretty good chance that I will need advanced features of "true" IoC container, so I would like to use Unity. And here is the problem : how to allow modules to configure container (programatically) = register their own types (mvc controllers, custom implementations of services...) at application start without making hard dependency on Unity in all modules ? I know about Common Service Locator project, and it seems pretty good, but this interface co container only allows resolving types, not registering them (afaik). I really hope you can understand my point, I know my english is terrible (I am from non english speaking country :) Thanks a lot !

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• Relative Position in PHP between 2 points (Lat/Long)

  - by Brian H

  I have a database of airports with Latitude and Longitude for each point. I want to run a PHP script to find all airports that are nearby a given airport, with their distance and relative direction. I.e. for Airport KLDJ (40-37-02.810N 074-14-40.539W) Airport Nearby KJFK - John F Kennedy Airport (21.2 nm NE) (40-38-23.104N 073-46-44.132W) I have used code from http://www.movable-type.co.uk/scripts/latlong.html to find distance, and tried to use it to find bearing, which might not be right. //BEARING RHUMB LINE $phi = log(tan($lat2/2+pi/4)/tan($lat1/2+pi/4)); $distance['bearing'] = (rad2deg(atan2($theta, $phi)) +180) % 360; I basically want to run all points through this script and find the distance, which I have already, but then the direction. (i.e. N, S, W, E, NW, SW, NE, SE)

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• preg_match Vs preg_match_all browser error not php?

  - by Phil Jackson

  Hi all i have the following: $str = base64_encode(preg_replace("#\s|\r|\t|\n#", " ", file_get_contents("../www.cms.actwebdesigns.co.uk2/logged.php"))); if(preg_replace("#(PD9waHAg)((?!(Pz4g)).)*#is", $str, )) { #print_r($matches); echo "<xmp>".base64_decode($matches[0]."Pz4g")."</xmp>"; } now this works but i want to be able to use it for all occurrences on page. (finds php segments in page) So i used preg_match_all but returns a browser error (page has been moved or no longer exists) Anyone know why?

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• Adding a new view to a Window-based app (re: MapKit tutorial)

  - by blackkettle

  I'm trying add a new view in a window-based application but not really getting anywhere. I've been going through a great MapKit tutorial lately, http://mithin.in/2009/06/22/using-iphone-sdk-mapkit-framework-a-tutorial/ and have successfully set it up and added some further buttons and customizations. However I've gotten stuck at what I assume ought to be a brain-dead simple step. I have added a toolbar to the bottom of the app, and a 'settings' style button. Following this I created a SettingsViewController complete with it's own view. Now I'd like to connect them but I've had absolutely no luck trying to figure out how to do this. I've also gone through several other good tutorials lately, http://miketeo.net/wp/index.php/2008/08/31/simple-iphone-tutorial-part-1.html http://blog.webscale.co.in/?p=228 http://www.iphonesdkarticles.com/2009/01/uitableview-searching-table-view.html but I've gotten lost trying to tie these two bits together. I'm sure it is quite trivial to link these two items but I've had no luck.

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• How to stop Javascript from showing default image and only text for link?

  - by tokyowp

  The Javascript below has a default image, but I would like display text "only text url" for this link instead of this button at this link http://developer.mixi.co.jp/wp-content/uploads/2010/09/bt_check_1.gif that this script defaults to. Is this possible? <div> <a href="http://mixi.jp/share.pl" class="mixi-check-button" data-key="some-data-key" data-url="http://someurl.com">only text url </a> <script type="text/javascript" src="http://static.mixi.jp/js/share.js"></script> </div>

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• C# define string format of double/floats to be US english by default

  - by neil

  Hi, I have got several thousands of lines of a web application source code, initially written on a US development system, to maintain. It makes heavy use of SQL statement strings, which are combined on the fly, e.g. string SQL = "select * from table where double_value = " + Math.Round(double_value, 2); Don't comment on bad programming style, that doesn't help me in this case :) The cruix: My system uses a German locale, which in turn leads to wrong SQL statements, like this: "select * from table where double_value = 15,5" (Note the comma as decimal separator instead of a point). Question: What is the most "elegant" way to change the locale of the web app in this case) to US or UK in order to prevent being forced to change and inspect every single line of code? .net 3.5 is not an option (would give me the chance to overwrite ToString() in an extension class) Kind regards

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• Storing dates as UTC in database

  - by James

  I am storing date/times in the database as UTC and computing them inside my application back to local time based on the specific timezone. Say for example I have the following date/time: 01/01/2010 00:00 Say it is for a country e.g. UK which observes DST (Daylight Savings Time) and at this particular time we are in daylight savings. When I convert this date to UTC and store it in the database it is actually stored as: 31/12/2009 23:00 As the date would be adjusted -1 hours for DST. This works fine when your observing DST. However, what happens when the clock is adjusted back? When I pull that date from the database and convert it to local time that particular datetime would be seen as 31/12/2009 23:00 when in reality it was processed as 01/01/2010 00:00. Correct me if I am wrong but isn't this a bit of a flaw when storing times as UTC?

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• How do I show/hide an element in YUI as in jQuery?

  - by Chad Johnson

  In jQuery, when I want to show or hide something, I do this: $('#elementId').show(); $('#elementId').hide(); How do I do this with YUI? I've tried YAHOO.util.Dom.get('elementId').hide(), asked my co-workers, looked at the documentation, and searched Google, and I've found nothing helpful. From the documentation, it looks like this should work YAHOO.util.Dom.get('elementId').setStyle('display', 'none') but of course it does not. All I can think of is this, which sucks because then I'm not using a framework: document.getElementById('elementId').style.display = 'none';

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• Why JPA injection not works on @PersistentUnit

  - by Dewfy

  Hello colleagues! It is continues of question ( http://stackoverflow.com/questions/2570976/struts-2-bean-is-not-created ) I'm using struts2 + toplink in my very simple web application under Tomcat. On the page I would like use iteration tag. That is why I've declared some factory (SomeFactory) that resolves collection of entities (Entity). Per article: http://download-uk.oracle.com/docs/cd/B32110_01/web.1013/b28221/usclient005.htm#CIHCEHHG the only thing I need is declaration: @PersistenceContext(unitName="name_in_persistence_xml") public class SomeFactory { @PersistenceUnit(unitName="name_in_persistence_xml") EntityManagerFactory emf; public EntityManager getEntityManager() { assert(emf != null); //HERE every time it is null return emf.createEntityManager(); } public Collection<Entity> getAll() { return getEntityManager().createNamedQuery("Entity.findAll").getResultList(); } } What is wrong? May be i miss something in web.xml? How to pre-init toplink for web application to allow injection happen?

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• Embeding EasyVideoPlayer Code into Wordpress Theme - Video not showing

  - by bbacarat

  I'm attempting to place some embed code into a Premium WordPress Theme. NOTE: I'm not great when it comes to php. The embed code is produced by a video player called EasyVideoPlayer. (Basically it allows me to use Amazon S3 and gives me feedback on when people stop watching the video.) This is the embed code I have: _evpInit('ZXh0cmEtbW9uZXktZnJvbS1ob21lLTEubW92'); I've opened the index.php wordpress file and placed this video embed code in between the that represents the area of the website I want it to show up. However the video is not showing. If we place both the theme and video player aside, would you expect the php code to accept what I've done or is this not the way to go about adding this embed code? NOTE:I've contacted both the Wordpress Premium Theme support at Woothemes.com and the video players support for EasyVideoPlayer.com However both tend to stop at the point that another paid product is involved! Grrreat. website is www.extramoneyfromhome.co.uk

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• Calculating probability that a string has been randomized? - Python

  - by RadiantHex

  Hi folks, this is correlated to a question I asked earlier (question) I have a list of manually created strings such as: lucy87 gordan_king fancy_unicorn77 joplucky_kanga90 base_belong_to_narwhals and a list of randomized strings: johnkdf pancake90kgjd fancy_jagookfk manhattanljg What gives away that the last set of strings are randomized is that sequences such as 'kjg', 'jgf', 'lkd', ... . Any clever way I could separate strings that contain these apparently randomized strings from the crowd? I guess that this plays a lot on the fact that certain characters are more likely to be placed next to others (e.g. 'co', 'ka', 'ja', ...). Any ideas on this one? Kylotan mentioned Reverend, but I am not sure if it can be used fr such purpose. Help would be much appreciated!

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• Layered Architecture and Static Methods

  - by BigBoss

  I need suggestion for three layered architecture I am planning to implement. Scenario Am Working in ASP.NET c# 3.5 Environment. DLHelper: Methods to get data from database. DAL : Contains Methods which collects data from database with help of DLHelper classes. Most of the methods in this layer are not referencing any page level object, hence can be declared static. BL : Same as DAL Layer, most of the methods are not referencing any page other page level object, hence can be declared static. UI Layer: As per above scenario UI Layer call to BL Layer is like BLClass.Method - DALClass.Method Question I would like to know is this standardise way to do it. As per discussion with my co-worker, we should have corresponding object of BL/DAL layer. But am still looking for more convencing answer.

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• Device Emulator Mananger and ActiveSync

  - by Vaccano

  I use Device Emulator Manager to fire up my Windows Mobile 5 Emulator. I then right click on the device (in the Device Emulator Manager list) and select cradle. ActiveSync then ties to connect. After a few seconds I get this message: Then if I open up the connection options and press connect: Then it works just fine. So, my question is, how can I get it to connect every time. Right as I cradle. I do this enough times that it is annoying to have the extra step. Has anyone ever been able to figure this out? (Does anyone have this problem too?) FYI My co-workers have the same issue Connecting a real device does not have this issue (It is just when I use an emulator)

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• What format do I use to store a relatively small amount of user data

  - by wcm

  I am writing a small program for our local high school (pro bono). The program has an interface allows the user to enter school holidays. This is a simple stand alone Windows app. What format should I use to store the data? A big relational data is obviously overkill. My initial plan was to store the data in an XML file. Co-workers have been suggesting that I use JSON files, Access Databases, SQL Lite, and SQL Server Express. There was even a suggestion of old school INI files.

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• Filling a screen width

  - by lorna

  I'm really struggling to tidy up a web site I am building for someone. I've spent hours on trying to figure this out! I have limited knowledge so the code would be helpful. They want the section at the top (originally two images, now I'm trying background images and css) to fill the width of the browser- no matter what size it is. Does anyone know how to do this? Similarly, is there a setting to get text to fill 100% width of the box, no matter what? I would seriously appreciate even someone helping me move on a step! they want everything to sit tight and inline, in some browsers/screens it does but on mine it spreads out with lots of white space. www.thegees.co.uk is the site.

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• CSS Overflow issue in IE7

  - by BrynJ

  I'm working on a site for a client at the moment, and have it working correctly in all browsers except IE7 (IE6 and IE8 tested fine). It's a WordPress site and the theme is a child theme of the Thematic framework. This is an example of a page that is not displayed correctly in IE7: http://roynesbitt.credit-medics.co.uk/our-donors The main content is forcing vertical and horizontal scrollbars on the main wrapper and is also not pushing the footer down, so that is appearing midway through it. The irony is that this works correctly in IE6, it's just IE7 that is displaying this issue. Any suggestions on how to fix are gratefully received.

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• Why does MySQL autoincrement increase on failed inserts?

  - by Sorcy

  A co-worker just made me aware of a very strange MySQL behavior. Assuming you have a table with an auto_increment field and another field that is set to unique (e.g. a username-field). When trying to insert a row with a username thats already in the table the insert fails, as expected. Yet the auto_increment value is increased as can be seen when you insert a valid new entry after several failed attempts. For example, when our last entry looks like this... ID: 10 Username: myname ...and we try five new entries with the same username value on our next insert we will have created a new row like so: ID: 16 Username: mynewname While this is not a big problem in itself it seems like a very silly attack vector to kill a table by flooding it with failed insert requests, as the MySQL Reference Manual states: "The behavior of the auto-increment mechanism is not defined if [...] the value becomes bigger than the maximum integer that can be stored in the specified integer type." Is this expected behavior?

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• How important is caching for a site's speed with PHP?

  - by benhowdle89

  I've just made a user-content orientated website http://www.humanisms.co.uk Its done in PHP, MySQL and jQuery's AJAX, at the moment there is only a dozen or so submissions and already i can feel it lagging slightly when it goes to a new page (therefore running a new mysql query) Is it most important for me to try and optimise my mysql queries (by prepared statements) or is it worth in looking at CDN's (amazon s3) and caching (much like the WordPress plugin WP Super Cache) which works by serving static HTML files when there hasnt been new content submitted. Which route is the most beneficial, for me as a developer, to take, ie. where am i better off concentrating my efforts to speed up the site?

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• Using @NotNull in a project where both IntelliJ and Eclipse developers are working

  - by Gugussee

  A co-worker on IntelliJ IDEA (working on another project) showed me the amazing @NotNull annotation. I've read messages here on SO about how starting to add @NotNull everywhere saved lots of time and headaches (and IntelliJ 10 can even add automatically @NotNull to old code when it detects that null would break havoc). Since I read my first "Probable @NotNull violation" message (in real-time, in the IDE, even on a partial .java file that doesn't compile yet) my jaw dropped and I got hooked. So I was wondering: is there anything that needs to be known if we want to start using @NotNull in a project where developers are using both Eclipse and IntelliJ? I know IntelliJ ships with the annotations.jar. Is this compatible with Eclipse?

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• How do you reach a "flow" state while programming?

  - by acrosman

  I'm not talking about program flow, but as in the state of working called flow, the state where you can get great work done the most effectively. I find that my current work environment while good in many ways does not allow me to get into a good state of mind for writing code most of the time (my job includes many other functions). If it's critical to get something done I'll often put on head-phones with classical music and try to drown out the office noise around me (and discourage co-workings from asking me questions). I am best able to get work done late in the evening when the house is quite and I've been thinking about the project for most of the day. What tricks have you found when working in less then perfect office environments?

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• Pre approve expenditure batch in oracle apps project module

  - by nil

  hi to all i have to crete one pre approve expence batch when i crete batch and then go to india local payble (MHE) but when i run the request Expense Report Import Report then i got following out put hear some error Rejection Reason = no location so my problem is that where i have to define location please give me guidance for that Total Functional Currency Invoice Amount: 100.00 Elecon Engineering Co. Ltd. Expense Report Import Report 17-MAY-10 16:57 Page: 2 Source: Oracle Projects Exceptions Report Supplier Supplier Invoice Invoice Invoice Invoice Name Number Name Number Number Date Currency Amount Rejection Reason ------------ Megha, Nilesh M. 90054 XSAM R17-MAY-1 31-MAY-10 INR 400.00 No Location Megha, Nilesh M. 90054 XT2 R17-MAY-10 31-MAY-10 INR 100.00 No Location Total Expense Reports Rejected: 2 Total Functional Currency Invoice Amount: 500.00 Edited by: user12921822 on May 17, 2010 9:00 PM

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