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  • How can I make the output from tapply() into a data.frame

    - by James Thompson
    I have a data.frame in R that looks like this: score rms template aln_id description 1 -261.410 4.951 2f22A.pdb 2F22A_1 S_00001_0000002_0 2 -231.987 21.813 1wb9A.pdb 1WB9A_4 S_00002_0000002_0 3 -263.722 4.903 2f22A.pdb 2F22A_3 S_00003_0000002_0 4 -269.681 17.732 1wbbA.pdb 1WBBA_6 S_00004_0000002_0 5 -258.621 19.098 1rxqA.pdb 1RXQA_3 S_00005_0000002_0 6 -246.805 6.889 1rxqA.pdb 1RXQA_15 S_00006_0000002_0 7 -281.300 16.262 1wbdA.pdb 1WBDA_11 S_00007_0000002_0 8 -271.666 4.193 2f22A.pdb 2F22A_2 S_00008_0000002_0 9 -277.964 13.066 1wb9A.pdb 1WB9A_5 S_00009_0000002_0 10 -261.024 17.153 1yy9A.pdb 1YY9A_2 S_00001_0000003_0 I can calculate summary statistics on the data.frame like this: > tapply( d$score, d$template, mean ) 1rxqA.pdb 1wb9A.pdb 1wbbA.pdb 1wbdA.pdb 1yy9A.pdb 2f22A.pdb -252.7130 -254.9755 -269.6810 -281.3000 -261.0240 -265.5993 Is there an easy way that I coerce this output back into a data.frame? I'd like for it to have these two columns: d$template mean I love tapply, but right now I'm cutting and pasting the results from tapply into a text file and hacking it up a bit to get the summary statistics that I want with appropriate names. This feels very wrong, and I'd like to do something better!

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  • sqlite3.OperationalError: database is locked - non-threaded application

    - by James C
    Hi, I have a Python application which throws the standard sqlite3.OperationalError: database is locked error. I have looked around the internet and could not find any solution which worked (please note that there is no multiprocesses/threading going on, and as you can see I have tried raising the timeout parameter). The sqlite file is stored on the local hard drive. The following function is one of many which accesses the sqlite database, and runs fine the first time it is called, but throws the above error the second time it is called (it is called as part of a for loop in another function): def update_index(filepath): path = get_setting('Local', 'web') stat = os.stat(filepath) modified = stat.st_mtime index_file = get_setting('Local', 'index') connection = sqlite3.connect(index_file, 30) cursor = connection.cursor() head, tail = os.path.split(filepath) cursor.execute('UPDATE hwlive SET date=? WHERE path=? AND name=?;', (modified, head, tail)) connection.commit() connection.close() Many thanks.

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  • How do I Convert ARGB value from string to colour?

    - by James
    I am trying to use the MakeColor method in the GDIPAPI unit but the conversion from int to byte is not returning me the correct value. Example var argbStr: string; A, R, G, B: Byte; begin argbStr := 'ffffcc88'; A := StrToInt('$' + Copy(AValue, 1, 2)); R := StrToInt('$' + Copy(AValue, 3, 2)); G := StrToInt('$' + Copy(AValue, 5, 2)); B := StrToInt('$' + Copy(AValue, 7, 2)); Result := MakeColor(A, R, G, B); end; What am I doing wrong?

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  • Concatenate text files with Windows command line, dropping leading lines

    - by James
    I need to concatenate some relatively large text files, and would prefer to do this via the command line. Unfortunately I only have Windows, and cannot install new software. type file1.txt file2.txt > out.txt allows me to almost get what I want, but I don't want the 1st line of file2.txt to be included in out.txt. I have noticed that more has the +n option to specify a starting line, but I haven't managed to combine these to get the result I want. I'm aware that this may not be possible in Windows, and I can always edit out.txt by hand to get rid of the line, but is there a simple way of doing it from the command line?

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  • OOP design for DMS that allows searching and grouping

    - by James P.
    I'd like to make a searchable Document Management System and allow a user to group documents together. On one hand, there would be a functionality that registers/fingerprints in a linear fashion and, on the other, one that associates documents into groups. How could I compromise between the two in terms of object design?

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  • Statistics Question: Kernel Smoothing in R

    - by James Thompson
    I have data of this form: x y 1 0.19 2 0.26 3 0.40 4 0.58 5 0.59 6 1.24 7 0.68 8 0.60 9 1.12 10 0.80 11 1.20 12 1.17 13 0.39 I'm currently plotting a kernel-smoothed density estimate of the x versus y using this code: smoothed = ksmooth( d$resi, d$score, bandwidth = 6 ) plot( smoothed ) I simply want a plot of the x versus smoothed(y) values, which is ## Heading ## However, the documentation for ksmooth suggests that this isn't the best kernel-smoothing package available: This function is implemented purely for compatibility with S, although it is nowhere near as slow as the S function. Better kernel smoothers are available in other packages. What other kernel smoothers are better can these smoothers be found?

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  • Right align text in an image with imagettftext(), PHP

    - by James Simpson
    I am setting up dynamic forum signature images for my users and I want to be able to put their username on the image. I am able to do this just fine, but since usernames are different lengths and I want to right align the username, how can I go about doing this when I have to set x & y coordinates. $im = imagecreatefromjpeg("/path/to/base/image.jpg"); $text = "Username"; $font = "Font.ttf"; $black = imagecolorallocate($im, 0, 0, 0); imagettftext($im, 10, 0, 217, 15, $black, $font, $text); imagejpeg($im, null, 90);

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  • Maven Assembly: include a dependency with a different classifier

    - by James Kingsbery
    I would like to build two different versions of a WAR in Maven (I know that's a no-no, that's just the way it is given the current situation). In the version of a WAR depicted by an assembly, I want to replace a dependency by the same dependency with a different classifier. For example, I was expecting this assembly to work: <assembly> <id>end-user</id> <formats> <format>war</format> </formats> <dependencySets> <dependencySet> <excludes> <exclude>group:artifact:jar:${project.version}</exclude> </excludes> <includes> <include>group:artifact:jar:${project.version}:end-user</include> </includes> </dependencySet> </dependencySets> </assembly> This doesn't work, but am I heading in the right direction? I've already read all the pages on the Maven assembly page and the section on the Maven Definitive Guide that seems relevant. Any pointers would be helpful.

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  • how to diff / align Python lists using arbitrary matching function?

    - by James Tauber
    I'd like to align two lists in a similar way to what difflib.Differ would do except I want to be able to define a match function for comparing items, not just use string equality, and preferably a match function that can return a number between 0.0 and 1.0, not just a boolean. So, for example, say I had the two lists: L1 = [('A', 1), ('B', 3), ('C', 7)] L2 = ['A', 'b', 'C'] and I want to be able to write a match function like this: def match(item1, item2): if item1[0] == item2: return 1.0 elif item1[0].lower() == item2.lower(): return 0.5 else: return 0 and then do: d = Differ(match_func=match) d.compare(L1, L2) and have it diff using the match function. Like difflib, I'd rather the algorithm gave more intuitive Ratcliff-Obershelp type results rather than a purely minimal Levenshtein distance.

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  • Quick and easy flood protection?

    - by James P
    I have a site where a user submits a message using AJAX to a file called like.php. In this file the users message is submitted to a database and it then sends a link back to the user. In my Javascript code I disabled the text box the user types into when they submit the AJAX request. The only problem is, a malicious user can just constantly send POST requests to like.php and flood my database. So I would like to implement simple flood protection. I don't really want the hassle of another database table logging users IPs and such... as if they are flooding my site there will be a lot of database read/writes slowing it down. I thought about using sessions, like have a session that contains a timestamp that gets checked every time they send data to like.php, and if the current time is before the timestamp let them add data to the database, otherwise send out an error and block them. If they are allowed to enter something into the database, update their session with a new timestamp. What do you think? Would this be the best way to go about it or are there easier alternatives? Thanks for any help. :)

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  • Loading large amounts of data to an Oracle SQL Database

    - by James
    Hey all, I was wondering if anyone had any experience with what I am about to embark on. I have several csv files which are all around a GB or so in size and I need to load them into a an oracle database. While most of my work after loading will be read-only I will need to load updates from time to time. Basically I just need a good tool for loading several rows of data at a time up to my db. Here is what I have found so far: I could use SQL Loader t do a lot of the work I could use Bulk-Insert commands Some sort of batch insert. Using prepared statement somehow might be a good idea. I guess I was wondering what everyone thinks is the fastest way to get this insert done. Any tips?

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  • Dynamicall Rendering in a Scrollable Area

    - by James
    What is the generic algorithm or process that is commonly used to dynamically render portions of a scrolling area? For example, in Google Maps, when the user scrolls past the bounds of the currently rendered area, a grey checkerboard pattern is displayed within the not-yet-rendered portions while the application loads and renders those areas. I'm looking specifically for the approach, or the mathematics, related to filling a graphics area in chunks based on what has just come into view. If possible, I'm looking for anything relevant to the GDI+ process of doing so.

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  • How to define RequestMapping prioritization

    - by James Skidmore
    I have a situation where I need the following RequestMapping: @RequestMapping(value={"/{section}"}) ...method implementation here... @RequestMapping(value={"/support"}) ...method implementation here... There is an obvious conflict. My hope was that Spring would resolve this automatically and map /support to the second method, and everything else to the first, but it instead maps /support to the first method. How can I tell Spring to allow an explicit RequestMapping to override a RequestMapping with a PathVariable in the same place? (Edit - this is simplified, I know that having those two RequestMapping alone wouldn't make much sense)

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  • Rendering a CGPDFPage into a UIImage

    - by James Antrobus
    I'm trying to render a CGPDFPage (selected from a CGPDFDocument) into a UIImage to display on a view. I have the following code in MonoTouch which gets me part way there. RectangleF PDFRectangle = new RectangleF(0, 0, UIScreen.MainScreen.Bounds.Width, UIScreen.MainScreen.Bounds.Height); public override void ViewDidLoad () { UIGraphics.BeginImageContext(new SizeF(PDFRectangle.Width, PDFRectangle.Height)); CGContext context = UIGraphics.GetCurrentContext(); context.SaveState(); CGPDFDocument pdfDoc = CGPDFDocument.FromFile("test.pdf"); CGPDFPage pdfPage = pdfDoc.GetPage(1); context.DrawPDFPage(pdfPage); UIImage testImage = UIGraphics.GetImageFromCurrentImageContext(); pdfDoc.Dispose(); context.RestoreState(); UIImageView imageView = new UIImageView(testImage); UIGraphics.EndImageContext(); View.AddSubview(imageView); } A section of the CGPDFPage is displayed but rotated back-to-front and upside down. My question is, how do I select the full pdf page and flip it round to display correctly. I have seen a few examples using ScaleCTM and TranslateCTM but couldn't seem to get them working. Any examples in ObjectiveC are fine, I'll take all the help I can get :) Thanks

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  • CakePHP HABTM Filtering

    - by James Haigh
    Hi, I've got two tables - users and servers, and for the HABTM relationship, users_servers. Users HABTM servers and vice versa. I'm trying to find a way for Cake to select the servers that a user is assigned to. I'm trying things like $this->User->Server->find('all'); which just returns all the servers, regardless of whether they belong to the user. $this->User->Server->find('all', array('conditions' => array('Server.user_id' => 1))) just gives an unknown column SQL error. I'm sure I'm missing something obvious but just need someone to point me in the right direction. Thanks!

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  • My PHP script for sending emails wont send

    - by James
    Well I'm working on a school project, and I uploaded my script to send emails. I'm pretty much using whats defined here: http://www.webcheatsheet.com/PHP/send_email_text_html_attachment.php . Now, all I really changed(other than the contents), is the receiver, to my email address. However, I'm not getting it in my inbox. Is there something else I need? Do I need to do something with the settings on the server(or have my school enable something)?

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  • How to create relationship mapping via Entity framework

    - by James
    I have following domain model: User { int Id; } City { int Id; } UserCity { int UserId, int CityId, dateTime StartDate } In the function where I have to attach a user to a city, the following code is working for me: UserCity uc = new UserCity(); //This is a db hit uc.User = MyEntityFrameworkDBContext.User.FirstOrDefault(u => u.ID == currentUserId); //this is a db hit uc.City = MyEntityFrameworkDBContext.City.FirstOrDefault(c => c.ID == currentCityId); uc.StartDate = userCityStartDate; //this is a db hit MyEntityFrameworkDBContext.SaveChanges(); Is there any way I can create relationships with just one single DB hit? The first two db hits are not required, actually.

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  • Configure ERP conectivity to a Flex application via a web service

    - by James
    I am developing a Flex application that will need to 'pull' information from an ERP system such as SAP or Peoplesoft via the clients web service. My application will need to pass credentials & query to a Query_URL and receive the returned data. I saw a Flash Builder 4 presentation where the Adobe evangelist created a similar application using Twitter. Insights or links to example code would be appreciated.

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  • Accessing elements from an array in objective c

    - by James
    I am trying to access individual elements of my array. This is an example of the contents of the array i am trying to access. <City: 0x4b77fd0> (entity: Spot; id: 0x4b7e580 <x-coredata://D902D50B-C945-42E2-8F71-EDB62222C0A7/Spot/p5> ; data: { CityToProvince = 0x4b7dbd0 <x-coredata://D902D50B-C945-42E2-8F71-EDB62222C0A7/County/p15>; Description = "Friend"; Email = "[email protected]"; Age = 21; Name = "Adam"; Phone = "+44175240"; }), The elements i am trying to access are Name, Phone, etc ... How would i go about doing this?

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  • finding N contiguous zero bits in an integer to the left of the MSB from another

    - by James Morris
    First we find the MSB of the first integer, and then try to find a region of N contiguous zero bits within the second number which is to the left of the MSB from the first integer. Here is the C code for my solution: typedef unsigned int t; unsigned const t_bits = sizeof(t) * CHAR_BIT; _Bool test_fit_within_left_of_msb( unsigned width, t val1, t val2, unsigned* offset_result) { unsigned offbit = 0; unsigned msb = 0; t mask; t b; while(val1 >>= 1) ++msb; while(offbit + width < t_bits - msb) { mask = (((t)1 << width) - 1) << (t_bits - width - offbit); b = val2 & mask; if (!b) { *offset_result = offbit; return true; } if (offbit++) /* this conditional bothers me! */ b <<= offbit - 1; while(b <<= 1) offbit++; } return false; } Aside from faster ways of finding the MSB of the first integer, the commented test for a zero offbit seems a bit extraneous, but necessary to skip the highest bit of type t if it is set. I have also implemented similar algorithms but working to the right of the MSB of the first number, so they don't require this seemingly extra condition. How can I get rid of this extra condition, or even, are there far more optimal solutions?

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  • Copy of Access mdb database being updated by live database

    - by James
    I'm trying to compute statistics for data held in an Access .mdb database. In order to avoid interfering with the live database, I'm working from a copy which I made by simply using copy-paste in Windows Explorer. The copy resides in the same directory, but with a different name. I'm using R and RODBC to connect to the copy of the file. The strange thing is that new data that is being updated on the original live database is appearing in my queries. This is despite the file timestamps of the copy not changing at all. It is also causing some slowdown in the live database. My understanding is that the .mdb files are standalone, or is this not the case? Should I have copied the database in a different way?

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