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  • Parse large XML file w/ script or use BioPython API ?

    - by jeremy04
    Hey guys this is my first question on here. I'm trying to make a local copy of the UniprotKB in SQL. The UniprotKB is 2.1GB, and it comes in XML and a special text format used by SwissProt Here are my options: 1) Use a SAX parser (XML) - I chose Ruby, and Nokogiri. I started writing the parser, but my initial reaction: how would I map the XML schema to the SAX parser? 2) BioPython - I already have BioSQL/Biopython installed, which literally created my SQL schema for me, and I was able to successfully insert one SwissProt/Uniprot txt file into the database. I'm running it right now (crosses fingers) on the entire 2.1gb. Here is the code I'm running: from Bio import SeqIO from BioSQL import BioSeqDatabase from Bio import SwissProt server = BioSeqDatabase.open_database(driver = "MySQLdb", user = "root", passwd = "", host="localhost", db = "bioseqdb") db = server["uniprot"] iterator = SeqIO.parse(open("/path/to/uniprot_sprot.dat", "r"), "swiss") db.load(iterator) server.commit() Edit: it's now crashing because the transactions are getting locked (since the tables are Innodb) Error Number: 1205 Lock wait timeout exceeded; try restarting transaction. I'm using MySQL version: 5.1.43 Should I switch my database to Postgrelsql ?

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  • How to select number of lines from large text files?

    - by MiNdFrEaK
    I was wondering how to select number of lines from a certain text file. As an example: I have a text file containing the following lines: branch 27 : rect id 23400 rect: -115.475609 -115.474907 31.393650 31.411301 branch 28 : rect id 23398 rect: -115.474907 -115.472282 31.411301 31.417351 branch 29 : rect id 23396 rect: -115.472282 -115.468033 31.417351 31.427151 branch 30 : rect id 23394 rect: -115.468033 -115.458733 31.427151 31.438181 Non-Leaf Node: level=1 count=31 address=53 branch 0 : rect id 42 rect: -115.768539 -106.251556 31.425039 31.717550 branch 1 : rect id 50 rect: -109.559479 -106.009361 31.296721 31.775299 branch 2 : rect id 51 rect: -110.937401 -106.226143 31.285870 31.771971 branch 3 : rect id 54 rect: -109.584412 -106.069092 31.285240 31.775230 branch 4 : rect id 56 rect: -109.570961 -106.000954 31.296721 31.780769 branch 5 : rect id 58 rect: -115.806213 -106.366188 31.400450 31.687519 branch 6 : rect id 59 rect: -113.173859 -106.244057 31.297440 31.627750 branch 7 : rect id 60 rect: -115.811478 -106.278252 31.400450 31.679470 branch 8 : rect id 61 rect: -109.953888 -106.020111 31.325319 31.775270 branch 9 : rect id 64 rect: -113.070969 -106.015968 31.331841 31.704750 branch 10 : rect id 68 rect: -113.065689 -107.034576 31.326300 31.770809 branch 11 : rect id 71 rect: -112.333344 -106.059860 31.284081 31.662920 branch 12 : rect id 73 rect: -115.071083 -106.309677 31.267879 31.466850 branch 13 : rect id 74 rect: -116.094414 -106.286308 31.236290 31.424770 branch 14 : rect id 75 rect: -115.423264 -106.286308 31.229691 31.415510 branch 15 : rect id 76 rect: -116.111656 -106.313110 31.259390 31.478300 branch 16 : rect id 77 rect: -116.247467 -106.309677 31.240231 31.451799 branch 17 : rect id 78 rect: -116.170792 -106.094543 31.156429 31.391781 branch 18 : rect id 79 rect: -116.225723 -106.292709 31.239960 31.442850 branch 19 : rect id 80 rect: -116.268013 -105.769913 31.157240 31.378111 branch 20 : rect id 82 rect: -116.215424 -105.827202 31.198441 31.383421 branch 21 : rect id 83 rect: -116.095734 -105.826439 31.197460 31.373819 branch 22 : rect id 84 rect: -115.423264 -105.815018 31.182640 31.368891 branch 23 : rect id 85 rect: -116.221527 -105.776512 31.160931 31.389830 branch 24 : rect id 86 rect: -116.203369 -106.473831 31.168350 31.367611 branch 25 : rect id 87 rect: -115.727631 -106.501587 31.189100 31.395941 branch 26 : rect id 88 rect: -116.237289 -105.790756 31.164780 31.358959 branch 27 : rect id 89 rect: -115.791344 -105.990044 31.072620 31.349529 branch 28 : rect id 90 rect: -115.736847 -106.495079 31.187969 31.376900 branch 29 : rect id 91 rect: -115.721710 -106.000130 31.160351 31.354601 branch 30 : rect id 92 rect: -115.792236 -106.000793 31.166620 31.378811 Leaf Node: level=0 count=21 address=42 branch 0 : rect id 18312 rect: -106.412270 -106.401367 31.704750 31.717550 branch 1 : rect id 18288 rect: -106.278252 -106.253387 31.520321 31.548361 I just want those lines which are in between Non-Leaf Node level=1 to Leaf Node Level=0 and also there are a lot of segments like this and I need them all.

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  • How can I get a iterable resultset from the database using pdo, instead of a large array?

    - by Tchalvak
    I'm using PDO inside a database abstraction library function query. I'm using fetchAll(), which if you have a lot of results, can get memory intensive, so I want to provide an argument to toggle between a fetchAll associative array and a pdo result set that can be iterated over with foreach and requires less memory (somehow). I remember hearing about this, and I searched the PDO docs, but I couldn't find any useful way to do that. Does anyone know how to get an iterable resultset back from PDO instead of just a flat array? And am I right that using an iterable resultset will be easier on memory? I'm using Postgresql, if it matters in this case. . . . The current query function is as follows, just for clarity. /** * Running bound queries on the database. * * Use: query('select all from players limit :count', array('count'=>10)); * Or: query('select all from players limit :count', array('count'=>array(10, PDO::PARAM_INT))); **/ function query($sql_query, $bindings=array()){ DatabaseConnection::getInstance(); $statement = DatabaseConnection::$pdo->prepare($sql_query); foreach($bindings as $binding => $value){ if(is_array($value)){ $statement->bindParam($binding, $value[0], $value[1]); } else { $statement->bindValue($binding, $value); } } $statement->execute(); // TODO: Return an iterable resultset here, and allow switching between array and iterable resultset. return $statement->fetchAll(PDO::FETCH_ASSOC); }

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  • Syncing large personal school-material -git-repo with things such as casual notes? Rsync, wget and Git -- or some ready tool?

    - by hhh
    My friend wants to store electrically her school -notes and process them fast, with backups. She has over 2GB -size repo already and growing all the time (mostly appended material i.e. more school notes, different formats, pdf, pictures and scanned, some text -files, etc). The goal of my friend is to process fast the notes. I suggested command like this here i.e. "# crontab -e @weekly wget --random-wait -e robots=off -U mozilla -mirror http://VeryLong.com". But I think plugging in Rsync somewhere could make it much better with Git. How would you help my friend to process and store the school -material under Git-version-controlling and still keep the size reasonable? Perhaps related rsync .git directory rsync git big repository Different scope Git/rsync mix for projects with large binaries and text files What's a good way to organize a large collection of personal scripts using git?

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  • Will .NET 4.0 apps work on Win 2008 R2 Server Core?

    - by markus
    When Windows Server 2008 R2 was launched, the "server core" edition started to become useful to me, because it lets me deploy .NET background applications isolated on their own virtual machine instance with only a small fraction of all the disk space overhead of a default Windows Server installation, and very few Windows Updates. It comes with a subset of .NET 3.5 SP1 integrated (as an optional feature). Now that .NET 4.0 is released, the redistributables explicitly state that it's not support on Server Core. Any chance that there will be a separate download available for Server Core (e. g. without WPF) any time soon, has anybody heard about it?

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  • Why does File::Find finished short of completely traversing a large directory?

    - by Stan
    A directory exists with a total of 2,153,425 items (according to Windows folder Properties). It contains .jpg and .gif image files located within a few subdirectories. The task was to move the images into a different location while querying each file's name to retrieve some relevant info and store it elsewhere. The script that used File::Find finished at 20462 files. Out of curiosity I wrote a tiny recursive function to count the items which returned a count of 1,734,802. I suppose the difference can be accounted for by the fact that it didn't count folders, only files that passed the -f test. The problem itself can be solved differently by querying for file names first instead of traversing the directory. I'm just wondering what could've caused File::Find to finish at a small fraction of all files. The data is stored on an NTFS file system.

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  • Why is it a bad idea to use ClientLogin for web apps in the Google API?

    - by Onema
    I just picked up the Google API today to allow some users of our site to upload videos to our own organization YouTube account. I Don't want our users to know our user name and password, but rather give them the option if they want to upload videos to youtube or not. If they choose to do it, they check on a check box and hit the submit button. I keep seeing over, and over in the Developers guide that ClientLogin, which to me looks like the best option to implement what I want to do, is not a good idea for user authentication in web applicaitons. The "AuthSub for web applications" doesn't seem to be the best mechanism for what I want to implement! Any ideas on what to do? Thank you

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  • What are CAD apps written in, and how are they organized ?

    - by ldigas
    What are CAD applications (Rhino, Autocad) of today written in and how are they organized internally ? I gave as an example, Autocad and Rhino, although I would love to hear of other examples as well. I'm particularly interested in knowing what is their backend written in (multilanguage ?) and how is it organized, and how do they handle their frontend (GUI) in real time ? Do they use native windows API's or some libraries of their own, since I imagine, as good as may be, the open source solutions on today's market won't cut it. I may be wrong ... As most of you who have used them know, they handle amongs other things relatively complex rotational operations in realtime (shading is not interesting me). I've been doing some experiments with several packages recently, and for some larger models found that there is considerable difference in speed in, for example, programed rotation (big full ship models) amongst some of them (which I won't name). So I'm wondering about their internals ... Also, if someone knows of some book on the subject, I'd be interested to hear of it.

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  • Shared WCF client code between .NET and Silverlight apps?

    - by Eduardo Scoz
    I'm developing a .NET application that will have both a WinForms and a Silverlight client. Although the majority of code will be in the server, I'll need to have quite a bit of logic in the clients as well, and I would like to keep the client library code the same. From what I could figure out so far, I need to have two different project types, a class library and a Silverlight class library, and link the files from one project to the other. This seems kind of lame, but it works for simple code. My problem, though, is that the code generated by the SVCUtil.exe to access WCF services is different from the code generated by the slsvcutil.exe, and the silverlight code is actually incompatible with the .NET one: I get a bunch of problems with the System.ServiceModel.Channel classes when I try to import the class into .NET. Has anybody done anything similar to this before? What am I doing wrong?

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  • Is is possible to parse a web page from the client side for a large number of words and if so, how?

    - by Technoh
    I have a list of keywords, about 25,000 of them. I would like people who add a certain < script tag on their web page to have these keywords transformed into links. What would be the best way to go and achieve this? I have tried the simple javascript approach (an array with lots of elements and regexping/replacing each) and it obviously slows down the browser. I could always process the content server-side if there was a way, from the client, to send the page's content to a cross-domain server script (I'm partial to PHP but it could be anything) but I don't know of any way to do this. Any other working solution is also welcome.

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  • What's the most scalable way to handle somewhat large file uploads in a Python webapp?

    - by Jason Baker
    We have a web application that takes file uploads for some parts. The file uploads aren't terribly big (mostly word documents and such), but they're much larger than your typical web request and they tend to tie up our threaded servers (zope 2 servers running behind an Apache proxy). I'm mostly in the brainstorming phase right now and trying to figure out a general technique to use. Some ideas I have are: Using a python asynchronous server like tornado or diesel or gunicorn. Writing something in twisted to handle it. Just using nginx to handle the actual file uploads. It's surprisingly difficult to find information on which approach I should be taking. I'm sure there are plenty of details that would be needed to make an actual decision, but I'm more worried about figuring out how to make this decision than anything else. Can anyone give me some advice about how to proceed with this?

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  • Does anyone know of a good free bulk upload tool for web apps?

    - by Ev
    I have a web application in which a user has to upload images to a gallery. At the moment they need to upload one image at a time so it's pretty tedious. I'd like to implement a system where they could potentially drag and drop files into the browser, or select a folder to upload. Any ideas? Thanks in advance! (By the way; it's a .Net App if it makes a difference, but I was thinking most of the work would be happening client side so shouldn't matter) -Ev

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  • C# slowdown while creating a bitmap - calculating distances from a large List of places for each pixel

    - by user576849
    I'm creating a graphic of the glow of lights above a geographic location based upon Walkers Law: Skyglow=0.01*Population*DistanceFromCenter^-2.5 I have a CSV file of places with 66,000 records using 5 fields (id,name,population,latitude,longitude), parsed on the FormLoad event and stored it in: List<string[]> placeDataList Then I set up nested loops to fill in a bitmap using SetPixel. For each pixel on the bitmap, which represents a coordinate on a map (latitude and longitude), the program loops through placeDataList – calculating the distance from that coordinate (pixel) to each place record. The distance (along with population) is used in a calculation to find how much cumulative sky glow is contributed to the coordinate from each place record. So, for every pixel, 66,000 distance calculations must be made. The problem is, this is predictably EXTREMELY slow – on the order of one line of pixels per 30 seconds or so on a 320 pixel wide image. This is unrelated to SetPixel, which I know is also slow, because the speed is similarly slow when adding the distance calculation results to an array. I don’t actually need to test all 66,000 records for every pixel, only the records within 150 miles (i.e. no skyglow is contributed to a coordinate from a small town 3000 miles away). But to find which records are within 150 miles of my coordinate I would still need to loop through all the records for each pixel. I can't use a smaller number of records because all 66,000 places contribute to skyglow for SOME coordinate in my map as it loops. This seems like a Catch-22, so I know there must be a better method out there. Like I mentioned, the slowdown is related to how many calculations I’m making per pixel, not anything to do with the bitmap. Any suggestions? private void fillPixels(int width) { Color pixelColor; int pixel_w = width; int pixel_h = (int)Math.Floor((width * 0.424088664)); Bitmap bmp = new Bitmap(pixel_w, pixel_h); for (int i = 0; i < pixel_h; i++) for (int j = 0; j < pixel_w; j++) { pixelColor = getPixelColor(i, j); bmp.SetPixel(j, i, pixelColor); } bmp.Save("Nightfall", System.Drawing.Imaging.ImageFormat.Jpeg); pictureBox1.Image = bmp; MessageBox.Show("Done"); } private Color getPixelColor(int height, int width) { int c; double glow,d,cityLat,cityLon,cityPop; double testLat, testLon; int size_h = (int)Math.Floor((size_w * 0.424088664)); ; testLat = (height * (24.443136 / size_h)) + 24.548874; testLon = (width * (57.636853 / size_w)) -124.640767; glow = 0; for (int i = 0; i < placeDataList.Count; i++) { cityPop=Convert.ToDouble(placeDataList[i][2]); cityLat=Convert.ToDouble(placeDataList[i][3]); cityLon=Convert.ToDouble(placeDataList[i][4]); d = distance(testLat, testLon, cityLat, cityLon,"M"); if(d<150) glow = glow+(0.01 * cityPop * Math.Pow(d, -2.5)); } if (glow >= 1) glow=1; c = (int)Math.Ceiling(glow * 255); return Color.FromArgb(c, c, c); }

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  • Does anybody have any suggestions on which of these two approaches is better for large delete?

    - by RPS
    Approach #1: DECLARE @count int SET @count = 2000 DECLARE @rowcount int SET @rowcount = @count WHILE @rowcount = @count BEGIN DELETE TOP (@count) FROM ProductOrderInfo WHERE ProductId = @product_id AND bCopied = 1 AND FileNameCRC = @localNameCrc SELECT @rowcount = @@ROWCOUNT WAITFOR DELAY '000:00:00.400' Approach #2: DECLARE @count int SET @count = 2000 DECLARE @rowcount int SET @rowcount = @count WHILE @rowcount = @count BEGIN DELETE FROM ProductOrderInfo WHERE ProductId = @product_id AND FileNameCRC IN ( SELECT TOP(@count) FileNameCRC FROM ProductOrderInfo WITH (NOLOCK) WHERE bCopied = 1 AND FileNameCRC = @localNameCrc ) SELECT @rowcount = @@ROWCOUNT WAITFOR DELAY '000:00:00.400' END

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  • Is there a performance gain from defining routes in app.yaml versus one large mapping in a WSGIAppli

    - by jgeewax
    Scenario 1 This involves using one "gateway" route in app.yaml and then choosing the RequestHandler in the WSGIApplication. app.yaml - url: /.* script: main.py main.py from google.appengine.ext import webapp class Page1(webapp.RequestHandler): def get(self): self.response.out.write("Page 1") class Page2(webapp.RequestHandler): def get(self): self.response.out.write("Page 2") application = webapp.WSGIApplication([ ('/page1/', Page1), ('/page2/', Page2), ], debug=True) def main(): wsgiref.handlers.CGIHandler().run(application) if __name__ == '__main__': main() Scenario 2: This involves defining two routes in app.yaml and then two separate scripts for each (page1.py and page2.py). app.yaml - url: /page1/ script: page1.py - url: /page2/ script: page2.py page1.py from google.appengine.ext import webapp class Page1(webapp.RequestHandler): def get(self): self.response.out.write("Page 1") application = webapp.WSGIApplication([ ('/page1/', Page1), ], debug=True) def main(): wsgiref.handlers.CGIHandler().run(application) if __name__ == '__main__': main() page2.py from google.appengine.ext import webapp class Page2(webapp.RequestHandler): def get(self): self.response.out.write("Page 2") application = webapp.WSGIApplication([ ('/page2/', Page2), ], debug=True) def main(): wsgiref.handlers.CGIHandler().run(application) if __name__ == '__main__': main() Question What are the benefits and drawbacks of each pattern? Is one much faster than the other?

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  • How to create beautiful Screencasts for your web apps?

    - by Abs
    Hello all, I am trying to create a screen cast for my new web app. I have just come across a great example of a screencast and I am wondering what is used to do this: Click on the video to play on this page. I am impressed with the animation when the mouse is clicked and zooming into images from different angles. Is this done with Actionscript or is there software that will make my life easier to do this? Thanks all for any help

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  • Setting up SVN (subvsersion) to manage our companies files, how to exclude large files from being ve

    - by Roeland
    Me and two other guys recently started our own web development company. We each work from our homes and have decided we want to keep one central location for all of our files. These files include word documents, spreadsheets, client files, designs.. etc. Anything pertaining to our company. I have a pretty solid internet connection and a windows 2008 server box sitting at home so I set up a subversion repository. Our file repository will look something like this. Clients Company A Design (photoshop files, wireframes, concepts) Documents ( logins, quotes, proposals etc) Site Backups Company B Design Documents Site Backups Prospects Company C Company D Our Company Our Website Documents (contract, operating procudres) My question is in regards to design files. The photoshop files that my designer works with range in sizes from 10mb to 100mb. I don't think we need to keep these files version-ed as this would eat up space incredibly fast. How do I go about controlling which files get version-ed, and which files are just stored. What I am thinking is that all documents need to be version-ed, and any files other then that should not be. Any help would be appreciated, thanks! Edit I am also curious whether this is the way to go. I just like this system since it keeps version of all my documents and at the same time. Also essentially I will have 3 backups in 3 different locations (3 local copies) so no need for backing it up. I am unsure of how svn would perform as purely a huge file repository.

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  • How do Go web apps function from a server perspective?

    - by Metropolis
    Hey Everyone, I followed the directions on how to create web applications using Go, and I was able to get an application working great. One thing I am confused about though is, when you run the application (./8.out), the terminal will sit there and listen on port 8080 until somebody accesses a page. Does the terminal need to stay up all of the time to run the web application? Does the application act like apache? Does apache need to be run next to this app? Setting this up on a server environment seems very confusing to me right now because I dont understand what the best way to do this is. Thanks for any help on this, Metropolis

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  • Why did File::Find finish short of completely traversing a large directory?

    - by Stan
    A directory exists with a total of 2,153,425 items (according to Windows folder Properties). It contains .jpg and .gif image files located within a few subdirectories. The task was to move the images into a different location while querying each file's name to retrieve some relevant info and store it elsewhere. The script that used File::Find finished at 20462 files. Out of curiosity I wrote a tiny recursive function to count the items which returned a count of 1,734,802. I suppose the difference can be accounted for by the fact that it didn't count folders, only files that passed the -f test. The problem itself can be solved differently by querying for file names first instead of traversing the directory. I'm just wondering what could've caused File::Find to finish at a small fraction of all files. The data is stored on an NTFS file system. Here is the meat of the script; I don't think including DBI stuff would be relevant since I reran the script with nothing but a counter in process_img() which returned the same number. find(\&process_img, $path_from); sub process_img { eval { return if ($_ eq "." or $_ eq ".."); ## Omitted querying and composing new paths for brevity. make_path("$path_to\\img\\$dir_area\\$dir_address\\$type"); copy($File::Find::name, "$path_to\\img\\$dir_area\\$dir_address\\$type\\$new_name"); }; if ($@) { print STDERR "eval barks: $@\n"; return } } And here is another method I used to count files: count_images($path_from); sub count_images { my $path = shift; opendir my $images, $path or die "died opening $path"; while (my $item = readdir $images) { next if $item eq '.' or $item eq '..'; $img_counter++ && next if -f "$path/$item"; count_images("$path/$item") if -d "$path/$item"; } closedir $images or die "died closing $path"; } print $img_counter;

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  • How do you specify a really large character in UIButton?

    - by Epsilon Prime
    I have a series of buttons that have suit symbols on them. Currently I provide these suit symbols as bitmaps. In preparation for iPhone 4 I'd like to use text instead. However Interface Builder rescales the button to account for whitespace underneath the symbol so I can't get the image to fill the button completely. Any hints on getting Interface Builder to behave?

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  • CoreGraphics taking a while to show on a large view - can i get it to repeat pixels?

    - by Andrew
    This is my coregraphics code: void drawTopPaperBackground(CGContextRef context, CGRect rect) { CGRect paper3 = CGRectMake(10, 14, 300, rect.size.height - 14); CGRect paper2 = CGRectMake(13, 12, 294, rect.size.height - 12); CGRect paper1 = CGRectMake(16, 10, 288, rect.size.height - 10); //Shadow CGContextSetShadowWithColor(context, CGSizeMake(0,0), 10, [[UIColor colorWithWhite:0 alpha:0.5]CGColor]); CGPathRef path = createRoundedRectForRect(paper3, 0); CGContextSetFillColorWithColor(context, [[UIColor blackColor] CGColor]); CGContextAddPath(context, path); CGContextFillPath(context); //Layers of paper //CGContextSaveGState(context); drawPaper(context, paper3); drawPaper(context, paper2); drawPaper(context, paper1); //CGContextRestoreGState(context); } void drawPaper(CGContextRef context, CGRect rect) { //Shadow CGContextSaveGState(context); CGContextSetShadowWithColor(context, CGSizeMake(0,0), 1, [[UIColor colorWithWhite:0 alpha:0.5]CGColor]); CGPathRef path = createRoundedRectForRect(rect, 0); CGContextSetFillColorWithColor(context, [[UIColor blackColor] CGColor]); CGContextAddPath(context, path); CGContextFillPath(context); //CGContextRestoreGState(context); //Gradient //CGContextSaveGState(context); CGColorRef startColor = [UIColor colorWithWhite:0.92 alpha:1.0].CGColor; CGColorRef endColor = [UIColor colorWithWhite:0.94 alpha:1.0].CGColor; CGRect firstHalf = CGRectMake(rect.origin.x, rect.origin.y, rect.size.width / 2, rect.size.height); CGRect secondHalf = CGRectMake(rect.origin.x + (rect.size.width / 2), rect.origin.y, rect.size.width / 2, rect.size.height); drawVerticalGradient(context, firstHalf, startColor, endColor); drawVerticalGradient(context, secondHalf, endColor, startColor); //CGContextRestoreGState(context); //CGContextSaveGState(context); CGRect redRect = rectForRectWithInset(rect, -1); CGMutablePathRef redPath = createRoundedRectForRect(redRect, 0); //CGContextSaveGState(context); CGContextSetStrokeColorWithColor(context, [[UIColor blackColor] CGColor]); CGContextAddPath(context, path); CGContextClip(context); CGContextAddPath(context, redPath); CGContextSetShadowWithColor(context, CGSizeMake(0, 0), 15.0, [[UIColor colorWithWhite:0 alpha:0.1] CGColor]); CGContextStrokePath(context); CGContextRestoreGState(context); } The view is a UIScrollView, which contains a textview. Every time the user types something and goes onto a new line, I call [self setNeedsDisplay]; and it redraws the code. But when the view starts to get long - around 1000 height, it has very noticeable lag. How can i make this code more efficient? Can i take a line of pixels and make it just repeat that, or stretch it, all the way down?

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