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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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• C++: Why don't I need to check if references are invalid/null?

  - by jbu

  Hi all, Reading http://www.cprogramming.com/tutorial/references.html, it says: In general, references should always be valid because you must always initialize a reference. This means that barring some bizarre circumstances (see below), you can be certain that using a reference is just like using a plain old non-reference variable. You don't need to check to make sure that a reference isn't pointing to NULL, and you won't get bitten by an uninitialized reference that you forgot to allocate memory for. My question is how do I know that the object's memory hasn't been freed/deleted AFTER you've initialized the reference. What it comes down to is that I can't take this advice on faith and I need a better explanation. Can anyone shed some light? Thanks, jbu

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• consts and other animals

  - by bks

  Hello i have a cpp code wich i'm having trouble reading. a class B is defined now, i understand the first two lines, but the rest isn't clear enough. is the line "B const * pa2 = pa1" defines a const variable of type class B? if so, what does the next line do? B a2(2); B *pa1 = new B(a2); B const * pa2 = pa1; B const * const pa3 = pa2; also, i'm having trouble figuring out the difference between these two: char const *cst = “abc”; const int ci = 15; thank you

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• Mac OS X Lion no longer recognizes environment.plist?

  - by Michael Irwin

  Just installed Lion today and my PATH env variable is no longer being set by ~/.MacOSX/environment.plist. Did something change? Can't seem to find any info on that or how to fix. Any ideas? Here's the contents of the PLIST: <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"> <plist version="1.0"> <dict> <key>PATH</key> <string>/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/X11/bin:/Users/mdi/bin</string> </dict> </plist>

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• What's the Difference Between These Two Ruby Class Initialaztion Definitions?

  - by michaelmichael

  I'm working through a book on Ruby, and the author used a slightly different form for writing a class initialization definition than he has in previous sections of the book. It looks like this: class Ticket attr_accessor :venue, :date def initialize(venue, date) self.venue = venue self.date = date end end In previous sections of the book, it would've been defined like this: class Ticket attr_accessor :venue, :date def initialize(venue, date) @venue = venue @date = date end end Is there any functional difference between using the setter method, as in the first example vs. using the instance variable in the second? They both seem to work. Even mixing them up seems to work: class Ticket attr_accessor :venue, :date def initialize(venue, date) @venue = venue self.date = date end end

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• [CA_COLOR_OPAQUE] things that make a layer non-opaque. scaled CAGradientLayer?

  - by mahal tertin

  i spent some time with the environment variable CA_COLOR_OPAQUE = 1 and have my findings to share. things that make a CALayer non-opaque (slow, more memory, ...): * contents with alpha (like an NSImage with an icon) * NSImage/CGImage from a pdf as contents (even when the pdf does not contain any alpha and opaque=YES) * backgroundColor = nil * CATextLayer with text in a (because it is contents with alpha) * rounded corners? maybe/sometimes * masksToBounds? not necessarily as we scale most of tree with CATransform3DScale on sublayerTransform i found also these rather irritating non-opaque: * CAGradientLayer that is somewhere down in this scaled tree (even when set all the gradient colors without alpha) * edgeAntialiasingMask != 0 of a layer that is somewhere down in this scaled tree the last two do not make sense to me. why should it be non opaque? what do i see? if anyone has any thoughts on these findings, i'm happy to learn as i couldn't find such a list yet.

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• c style thread creation in python

  - by chandank

  Hi I am new to python and want to create multiple threads in a loop something like (in C style) for (;i < 10; i++) thread[i]= pthread_create(&thread[i],&attr,func) I am not sure how to do the same in python? Basically I want have that thread[] variable as global will create all thread at once and then will start then in once. I have written a similar python program that does it but I think having it in above style will be better. def thread_create(thread_number): command_string = "Thread-" + "%d" %thread_number thread = myThread(thread_number, command_string) thread.start() # Start new Threads for i in range(5): thread_create(i)

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• C++ - Access array (in main) from methods outside main

  - by John Smith

  I have an array in my main class that holds objects that I need to print out for a menu listing. The array is declared and initialized in main. I need to, however, access the same array in a sub-menu function. If I copy the code (for loop that prints out the values) to the sub-menu, nothing is printed (presumably because it can't access the original array and has made a new, blank one). Is there any way (without making the array a global variable) that I can access the array in this sub-menu? Both the main and the sub-menu function are in the same file and the sub-menu is called from main. Maybe to put it more simply, can I use scope resolution to bring me up one 'level' in scope?

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• Copying blocks (ie: copying them to instance variables) in Objective-C

  - by RyanWilcox

  I'm trying to understand blocks. I get how to use them normally, when passed directly to a method. I'm interested now in taking a block, storing it (say) in an instance variable and calling it later. The blocks programming guide makes it sound like I can do this, by using Block_copy / retain to copy the block away, but when I try to run it I crash my program. - (void) setupStoredBlock { int salt = 42; m_storedBlock = ^(int incoming){ return 2 + incoming + salt; }; [m_storedBlock retain]; } I try to call it later: - (void) runStoredBlock { int outputValue = m_storedBlock(5); NSLog(@"When we ran our stored blockwe got back: %d", outputValue); [m_storedBlock release]; } Anyone have any insights? (Or, is there something I'm not getting with blocks?) Thank you very much!

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• Python - List and Loop in one def

  - by Dunwitch

  I'm trying to get the def wfsc_pod1 and wfsc_ip into the same def. I'm not quite sure how to approach the problem. I want wfsc_pod1 to display all the information for name, subnet and gateway. Then wfsc_ip shows the ip addresses below it. I also get a None value when I run it as it. Not sure why. Anything more pythonic is more appreciated. class OutageAddress: subnet = ["255.255.255.0", "255.255.255.1"] # Gateway order is matched with names gateway = ["192.168.1.1", "192.168.1.2", "192.168.1.3", "192.168.1.4", "192.168.1.5", "192.168.1.6", "192.168.1.7", "192.168.1.8", "192.168.1.9"] name = ["LOC1", "LOC2", "LOC3", "LOC4", "LOC5", "LOC6", "LOC7", "LOC8", "LOC9"] def wfsc_pod1(self): wfsc_1 = "%s\t %s\t %s\t" % (network.name[0],network.subnet[0],network.gateway[0]) return wfsc_1 def wfsc_ip(self): for ip in range(100,110): ip = "192.168.1."+str(ip) print ip network = OutageAddress() print network.wfsc_pod1() print network.wfsc_ip()

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• Small, editable table of strings. Which Forms control do I want? (.NET)

  - by I. J. Kennedy

  I have a small array of structs, each struct has three fields, all strings. I want to display these structs in a grid, let the user edit the strings a la Excel, and then retrieve the edited strings of course. Which WinForms control is best for this? Tried a DataGridView but setting the DataSource to the array of structs doesn't seem to work. There are myriad controls with similar names but I can't figure out what does what. All the examples I've found are geared toward using a database as the data source--I just have a simple array.

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• Getting a unix timestamp as a string in C++

  - by wyatt

  I'm using the function time() in order to get a timestamp in C++, but, after doing so, I need to convert it to a string. I can't use ctime, as I need the timestamp itself (in its 10 character format). Trouble is, I have no idea what form a time_t variable takes, so I don't know what I'm converting it from. cout handles it, so it must be a string of some description, but I have no idea what. If anyone could help me with this it'd be much appreciated, I'm completely stumped. Alternately, can you provide the output of ctime to a MySQL datetime field and have it interpreted correctly? I'd still appreciate an answer to the first part of my question for understanding's sake, but this would solve my problem.

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• inconsistency between Sun JRE javac and Eclipse java compiler?

  - by Jason S

  This confuses me. The following compiles fine under Eclipse. package com.example.gotchas; public class GenericHelper1 { static <T> T fail() throws UnsupportedOperationException { throw new UnsupportedOperationException(); } /** * just calls fail() * @return something maybe */ public boolean argh() { return fail(); } public static void main(String[] args) { // TODO Auto-generated method stub } } But if I try to do a clean build with ant, or at the command line with javac, I get this: src\com\example\gotchas\GenericHelper1.java:14: type parameters of <T>T cannot be determined; no unique maximal instance exists for type variable T with upper bounds boolean,java.lang.Object public boolean argh() { return fail(); } ^ 1 error what gives, and how do I fix it?

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• How do you encode an apostrophe so that it's searchable in mysql?

  - by Yegor

  I don't think that was the most clear question, but an example should make it a little clearer. I have a table filled with movie names, some of which contain apostrophes. I have a search box which is used to find movies. If I perform searches via mov_title = '$search_keywords' it all works, but this method will not yield any results for partial searches, so I have to use this mov_title LIKE '%$search_keywords%' This method works fine for titles that are A-Za-z0-9, but if a title has an apostrophe, it's not able to find the movie, even if I do an exact match. Before the titles are stored in the DB, I put them through this: $search_keywords = htmlspecialchars(mysql_escape_string($_GET["search_keywords"])); So in the DB, there is a forward slash before every single apostrophe. The only way to match a movie title with an apostrophe is to physically put a forward slash in front of the apostrophe, in the search box. This seems so trivial, and I'm sure the solution is painfully obvious, but I'm just not seeing it.

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• Returning the html from .ajax call

  - by coffeeaddict

  I'm getting undefined for some reason when I try to return the html via the callback function: function getDataFromUrl(urlWithContent) { // jQuery async request $.ajax( { url: urlWithContent, dataType: "html", success: function(data) { return $('.result').html(data); }, error: function(e) { alert('Error: ' + e); } }); } I know I'm getting data back, I see it in firebug in the response and also when I alert out the data, I see the entire page content come up in the alert box. When I call my function, I am doing the following: var divContent = getDataFromUrl(dialogDiv.attr("href")); if(divContent) dialogDiv.innerHTML = divContent; when I alert out the divContent (before the if statement) I'm getting undefined. Maybe I'm just going about this wrong on how I'm returning back the data? I also tried just return data; same thing, I get undefined after the call to this method when set to my variable.

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• Aren't passwords written in inputbox vulnerable through a stack trace ?

  - by loursonwinny

  Hello, I am not a guru of the stack tracing, at all. I even don't know how to get some. Anyway, I am wondering if entering a password entered in an inputbox is safe. Can't it be retrieved by getting a stack trace ? A password entered that way will be found in many places : Caption property of the TEdit Result of the function which creates the inputbox probably, a variable that stores the Result of the InputBox Command etc... If the answer is "yes, it is a vulnerability", then my world collapses :p. What can be done to avoid that vulnerability hole ? NOTE : The InputBox is an example but it can be with a "homebrewed" login prompt. InputBox is a Delphi command but I haven't tagged the question with the Delphi tag because I suppose that the question concerns any language. Thanks for reading

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• Jquery - Convert ascii chars back to HTML

  - by sdmiller

  I am reading data from an html file to load into a div. The problem I am having is, the program that writes the html files is converting to <br /> SO when I execute $('#items').load('/News/list.aspx'); it displays as a string on my page instead of reading it as a page break. I have tried to read the above file into a variable to do a string replace on the <br /> but it doesn't seem to work. Any suggestions?

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• how to display the grid in div tag..

  - by kumar

  <script type="text/javascript"> var showGrid = function() { $("#Grid1").load('/friends/names/fried'); }; </script> <div> <%= Html.Trirand().JQGrid(Model.OrdersGrid, "JqGrid1")%> </div> <div> </div> /////// i need to dispaly the Grid1 here? can anyone tell me? thanks

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• write.table in R screws up header when has rownames

  - by Yannick Wurm

  Hello, check this example: > a = matrix(1:9, nrow = 3, ncol = 3, dimnames = list(LETTERS[1:3], LETTERS[1:3])) > a A B C A 1 4 7 B 2 5 8 C 3 6 9 the table displays correctly. There are two different ways of writing it to file... write.csv(a, 'a.csv') which gives as expected: "","A","B","C" "A",1,4,7 "B",2,5,8 "C",3,6,9 and write.table(a, 'a.txt') which screws up "A" "B" "C" "A" 1 4 7 "B" 2 5 8 "C" 3 6 9 indeed, an empty tab is missing.... which is a pain in the butt for downstream things. Is this a bug or a feature? Is there a workaround? (other than write.table(cbind(rownames(a), a), 'a.txt', row.names=FALSE) Cheers, yannick

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• BASH Expression to replace beginning and ending of a string in one operation?

  - by swestrup

  Here's a simple problem that's been bugging me for some time. I often find I have a number of input files in some directory, and I want to construct output file names by replacing beginning and ending portions. For example, given this: source/foo.c source/bar.c source/foo_bar.c I often end up writing BASH expressions like: for f in source/*.c; do a="obj/${f##*/}" b="${a%.*}.obj" process "$f" "$b" done to generate the commands process "source/foo.c" "obj/foo.obj" process "source/bar.c "obj/bar.obj" process "source/foo_bar.c "obj/foo_bar.obj" The above works, but its a lot wordier than I like, and I would prefer to avoid the temporary variables. Ideally there would be some command that could replace the beginning and ends of a string in one shot, so that I could just write something like: for f in source/*.c; do process "$f" "obj/${f##*/%.*}.obj"; done Of course, the above doesn't work. Does anyone know something that will? I'm just trying to save myself some typing here.

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• Alternative to latex / a way to typeset good looking documents from Java to PDF

  - by drasto

  I'm working on application in Java that will maintain database of song lyrics in plain text and print out some songbooks/chordbooks(that is create PDF file from selected songs). I was planing that the Java application will generate source code for pdflatex and after compiling this source user will get PDF file. Lately I've run into a lot of problems because of latex limitation: fixed memory size (some pictures will also be drawn to PDF) - error when exceeded, no way to query end of line or and of page dynamically, it's very hard to override latex placement algorithm in a complex way,... see also some my other questions regarding latex. I come to conclusion that latex is not good option for automated PDF generation. So I need replacement. I need to be able to typeset: Chords over lyrics when the lyrics are in variable char width so I need to be able to measure text width Chord diagrams that means I'll have to draw quite complex pictures Each song on separate double page Different fonts etc. Thanks for all answers

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• How can I add a border to all the elements that share a class when the mouse has hovered over one of

  - by Siracuse

  I have a generated HTML file which has large blocks of text with span's sprinkled throughout it with generated class names: This <span class="21232">an example</span> of what <span class="332423"> I'm talking</span> about. There are span's with <span class="21232"> generated ID's </span>. Now, what I'm seeking to do, is if I hover over any of my spans, they will add a border to not only that span, but all other spans that share that same class. So, if I were to hover over the first span, it would wrap a border around "an example" and "generated ID's" because the first and third span share the same class name. I was pretty sure I couldn't do it in straight CSS. Is this possible using jQuery? If so, can anyone point me in the right direction for doing this as simply as possible?

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• How would I create a VIM or Vi command to delete all text after a certain character for every line i

  - by Jason Down

  Scenario: I have a text file that has pipe (as in the "|" character) delimited data. Each field of data in the pipe delimited fields can be of variable length, so counting characters won't work (or using some sort of substring function... if that even exists in VIM). Is it possible, using VIM / Vi to delete all data from the second pipe to the end of the line for the entire file? There are approx 150,000 lines, so doing this manually would only be appealing to a masochist... e.g. Change the following lines from: 1111|random sized text 12345|more random data la la la|1111|abcde 2222|random sized text abcdefghijk|la la la la|2222|defgh 3333|random sized text|more random data|33333|ijklmnop to: 1111|random sized text 12345 2222|random sized text abcdefghijk 3333|random sized text I'm sure this can be done somehow... I hope. TIA UPDATE: I should have mentioned that I'm running this on Windows XP, so I don't have access to some of the mentioned *nix commands (CUT is not recognized on Windows).

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• MooTools Problem in IE with Request

  - by trobrock

  I have this class method in a mootools class: getData : function(){ var r = new Request.JSON({ url : this.container.getAttribute('data-url'), method : 'post', onSuccess : function(j){ this.cards = j; this.prepareQuiz(); }.bind(this) }).send(); }, In any browser aside from IE this works fine, but in IE I get a this.cards is not defined in a method that occurs after the this.prepareQuiz method does it's stuff. I narrowed the problem to this section by adding an if ($defined(this.cards)) before the this.prepareQuiz call and if I just keep refreshing the page 1 out of every 5 or so times it will work. So the this.cards variable is not being set some of the time for some reason. Why would this happen?

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• How do I dynamically point an interface to a specific class at runtime?

  - by Jon

  As a simple example, I have an xml file with a list of names of classes which actually carry out the work and all implement interface IDoWork with a method Process(). I loop through the items in the xml file. How do I actually dynamically assign the class to the interface from a string name? e.g. var IDoWork = new "DoWorkType1"(); IDoWork.Process(); <work> <item id="DoWorkType1"> </item> <item id="DoWorkType2"> </item> </work> I want to achieve a plugin type architecture, except the plugin isn't at an assembly level only a class level within my program.

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