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  • Can anyone tell me why these lines are not working?

    - by user343934
    I am trying to generate tree with fasta file input and Alignment with MuscleCommandline import sys,os, subprocess from Bio import AlignIO from Bio.Align.Applications import MuscleCommandline cline = MuscleCommandline(input="c:\Python26\opuntia.fasta") child= subprocess.Popen(str(cline), stdout = subprocess.PIPE, stderr=subprocess.PIPE, shell=(sys.platform!="win32")) align=AlignIO.read(child.stdout,"fasta") outfile=open('c:\Python26\opuntia.phy','w') AlignIO.write([align],outfile,'phylip') outfile.close() I always encounter with these problems Traceback (most recent call last): File "", line 244, in run_nodebug File "C:\Python26\muscleIO.py", line 11, in align=AlignIO.read(child.stdout,"fasta") File "C:\Python26\Lib\site-packages\Bio\AlignIO_init_.py", line 423, in read raise ValueError("No records found in handle") ValueError: No records found in handle

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  • Compiling VIM on OS X Mountain Lion

    - by Lauri L
    Compiling VIM on Mountain Lion does not work for me. I compile VIM with the following sequence: hg clone https://vim.googlecode.com/hg/ vim cd vim ./configure --enable-rubyinterp --with-features=huge -prefix=/usr make I then try to start the compiled binary with src/vim, but it crashes like this: $ src/vim Vim: Caught deadly signal SEGV Vim: Finished. Segmentation fault: 11 What am I missing here?

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  • UCA + Natural Sorting

    - by Alix Axel
    I recently learnt that PHP already supports the Unicode Collation Algorithm via the intl extension: $array = array ( 'al', 'be', 'Alpha', 'Beta', 'Álpha', 'Àlpha', 'Älpha', '????', 'img10.png', 'img12.png', 'img1.png', 'img2.png', ); if (extension_loaded('intl') === true) { collator_asort(collator_create('root'), $array); } Array ( [0] => al [2] => Alpha [4] => Álpha [5] => Àlpha [6] => Älpha [1] => be [3] => Beta [11] => img1.png [9] => img10.png [8] => img12.png [10] => img2.png [7] => ???? ) As you can see this seems to work perfectly, even with mixed case strings! The only drawback I've encountered so far is that there is no support for natural sorting and I'm wondering what would be the best way to work around that, so that I can merge the best of the two worlds. I've tried to specify the Collator::SORT_NUMERIC sort flag but the result is way messier: collator_asort(collator_create('root'), $array, Collator::SORT_NUMERIC); Array ( [8] => img12.png [7] => ???? [9] => img10.png [10] => img2.png [11] => img1.png [6] => Älpha [5] => Àlpha [1] => be [2] => Alpha [3] => Beta [4] => Álpha [0] => al ) However, if I run the same test with only the img*.png values I get the ideal output: Array ( [3] => img1.png [2] => img2.png [1] => img10.png [0] => img12.png ) Can anyone think of a way to preserve the Unicode sorting while adding natural sorting capabilities?

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  • Mysql select - improve performances

    - by realshadow
    Hey, I am working on an e-shop which sells products only via loans. I display 10 products per page in any category, each product has 3 different price tags - 3 different loan types. Everything went pretty well during testing time, query execution time was perfect, but today when transfered the changes to the production server, the site "collapsed" in about 2 minutes. The query that is used to select loan types sometimes hangs for ~10 seconds and it happens frequently and thus it cant keep up and its hella slow. The table that is used to store the data has approximately 2 milion records and each select looks like this: SELECT * FROM products_loans WHERE KOD IN("X17/Q30-10", "X17/12", "X17/5-24") AND 369.27 BETWEEN CENA_OD AND CENA_DO; 3 loan types and the price that needs to be in range between CENA_OD and CENA_DO, thus 3 rows are returned. But since I need to display 10 products per page, I need to run it trough a modified select using OR, since I didnt find any other solution to this. I have asked about it here, but got no answer. As mentioned in the referencing post, this has to be done separately since there is no column that could be used in a join (except of course price and code, but that ended very, very badly). Here is the show create table, kod and CENA_OD/CENA_DO very indexed via INDEX. CREATE TABLE `products_loans` ( `KOEF_ID` bigint(20) NOT NULL, `KOD` varchar(30) NOT NULL, `AKONTACIA` int(11) NOT NULL, `POCET_SPLATOK` int(11) NOT NULL, `koeficient` decimal(10,2) NOT NULL default '0.00', `CENA_OD` decimal(10,2) default NULL, `CENA_DO` decimal(10,2) default NULL, `PREDAJNA_CENA` decimal(10,2) default NULL, `AKONTACIA_SUMA` decimal(10,2) default NULL, `TYP_VYHODY` varchar(4) default NULL, `stage` smallint(6) NOT NULL default '1', PRIMARY KEY (`KOEF_ID`), KEY `CENA_OD` (`CENA_OD`), KEY `CENA_DO` (`CENA_DO`), KEY `KOD` (`KOD`), KEY `stage` (`stage`) ) ENGINE=InnoDB DEFAULT CHARSET=utf8 And also selecting all loan types and later filtering them trough php doesnt work good, since each type has over 50k records and the select takes too much time as well... Any ides about improving the speed are appreciated. Edit: Here is the explain +----+-------------+----------------+-------+---------------------+------+---------+------+--------+-------------+ | id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra | +----+-------------+----------------+-------+---------------------+------+---------+------+--------+-------------+ | 1 | SIMPLE | products_loans | range | CENA_OD,CENA_DO,KOD | KOD | 92 | NULL | 190158 | Using where | +----+-------------+----------------+-------+---------------------+------+---------+------+--------+-------------+ I have tried the combined index and it improved the performance on the test server from 0.44 sec to 0.06 sec, I cant access the production server from home though, so I will have to try it tomorrow.

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  • Change size of ImageIcon in a JRadioButton

    - by Frederik Wordenskjold
    I simply want to change the size (diameter) of the actual (default) ImageIcon of my JRadioButton. I've changed the size of the font displayed in the widget, so it really looks silly with such a large radiobutton. JRadioButton button = new JRadioButton("Button"); button.setFont(new Font("Lucida Grande",Font.PLAIN, 11)); gives me this giant button: Do I really have to create my own ImageIcon? Or can I somehow scale the default one, without too much of a hassle?

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  • How do I write sql data into a textbox after a submit type event

    - by Matt
    Finishing up some homework and Im having trouble with figuring out how to take information generated in sql column(a primary key set up to assign a record number to a customer example 1046) at submit and writing it to my redirected recipt page. I call it recipt.aspx. Any takers Professor says to use a datareader...but things go bad after that. public partial class _Default : System.Web.UI.Page { String cnStr = "EDITED FOR THE PURPOSE OF NOT DISPLAYED SQL SERVERta Source=111.11.111.11; uid=xxxxxxx; password=xxxx; database=xxxxxx; "; String insertStr; SqlDataReader reader; SqlConnection myConnection = new SqlConnection(); protected void submitbutton_Click(object sender, EventArgs e) { myConnection.ConnectionString = cnStr; try { //more magic happens as myConnection opens myConnection.Open(); insertStr = "insert into connectAssignment values ('" + TextBox2.Text + "','" + TextBox3.Text + "','" + TextBox4.Text + "','" + TextBox5.Text + "','" + bigtextthing.Text + "','" + DropDownList1.SelectedItem.Value + "')"; //magic happens as Connection string is assigned to connection object and passes in the SQL statment //associate the command to the the myConnection connection object SqlCommand cmd = new SqlCommand(insertStr, myConnection); cmd.ExecuteNonQuery(); Session["passmyvalue1"] = TextBox2.Text; Session["passmyvalue2"] = TextBox3.Text; Session["passmyvalue3"] = TextBox4.Text; Session["passmyvalue4"] = TextBox5.Text; Session["passmyvalue5"] = bigtextthing.Text; Session["I NEED SOME HELP RIGHT HERE"] =Textbox6.Text; Response.Redirect("receipt.aspx"); } catch { bigtextthing.Text = "Error submitting" + "Possible casues: Internet is down,server is down, check your settings!"; } finally { myConnection.Close(); TextBox2.Text = ""; TextBox3.Text = ""; TextBox4.Text = ""; TextBox5.Text = ""; bigtextthing.Text = ""; } //reset validators? } The recipt page public partial class _Default : System.Web.UI.Page { protected void Page_Load(object sender, EventArgs e) { if(Session["passmyvalue1"] != null) { TextBox1.Text = (string)Session["passmyvalue1"]; TextBox2.Text = (string)Session["passmyvalue2"]; TextBox3.Text = (string)Session["passmyvalue3"]; TextBox4.Text = (string)Session["passmyvalue4"]; TextBox5.Text = (string)Session["passmyvalue5"]; TextBox6.Text = I don't know ; } } } THanks for the help

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  • Reverse regular expressions to generate data

    - by Anton Gogolev
    In one of the StackOverflow Podcasts (the one where guys were discussing data generation for testing DBs -- either #11 or #12), Jeff mentioned something like "reverse regular expressions", which are used exactly for that purpose: given a regex, produce a string which will eventually match said regex. What is the correct term for this whole concept? Is this a well-known concept?

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  • JS text to array

    - by Sonny
    Hi i got this text 2/92/20 3/32/32 4/62/6 5/22/28 6/60/61 7/33/32 8/34/31 9/31/19 10/19/19 11/34/39 12/32/32 14/19/25 15/45/37 16/32/32 17/84/36 18/72/33 and i need it to be like // 2/92/20 chars[0][0]=2; chars[0][1]=92; chars[0][2]=20; How should i make that PS: the split must be in $.ajax({ type: "POST", url: "char_info2.php", dataType: "html", success: function(data) { //here }

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  • What are PHP 5.2 settnigs which affect compatibility with old code (developed for PHP 4 and 3)?

    - by Ivan
    What are PHP 5.2 settnigs which affect compatibility with old code (developed for PHP 4 and 3)? A web application using XTemplate 0.2.4-2 (officially meant for 3.0.11) works fine on one server running PHP 5.2 but works incorrect (seems that the form can't be submitted or processed correctly) on new PHP 5.2 and 5.3 installations. What may I need to tweak on new servers to make them able to run legacy code?

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  • LINQ + Find count of non-null values

    - by Ashutosh
    I have a table with the below structure. ID VALUE 1 3.2 2 NULL 4 NULL 5 NULL 7 NULL 10 1.8 11 NULL 12 3.2 15 4.7 17 NULL 22 NULL 24 NULL 25 NULL 27 NULL 28 7 I would like to get the max count of consecutive null values in the table. Any help would be greatly appreciated. THanks Ashutosh

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  • Crystal reports CSV incorrect generation

    - by yauhen
    When setting ExportFormatType.CharacterSeparatedValues crystal report generates every row of data prefixed with column names (Report Headers). Why it does this? How it could be fixed? Usually it is preferred to have single header. For excel export type - generated report looks ok (only single header for all rows). I am using crystal reports 11.5.3700.0. Visual studio 2008, .net 3.5 sp1

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  • MySQL float values jumping around on insert?

    - by dubayou
    So i have a SQL table setup as such CREATE TABLE IF NOT EXISTS `points` ( `id` int(11) NOT NULL auto_increment, `lat` float(10,6) NOT NULL, `lng` float(10,6) NOT NULL, PRIMARY KEY (`id`) ) ENGINE=MyISAM; And im inserting stuff like INSERT INTO `points` (`lat`, `lng`) VALUES ('89.123456','-12.123456'); Gives me a row with lat and lng being 89.123459 and -12.123455 Whats up?

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  • How to export C++ function as a dll that throws exception?

    - by ShaChris23
    When I try to export the following function as a dll: extern "C" __declspec(dllexport) void some_func() { throw std::runtime_error("test throwing exception"); } Visual C++ 2008 gives me the following warning: 1>.\SampleTrainer.cpp(11) : warning C4297: 'some_func' : function assumed not to throw an exception but does 1> The function is extern "C" and /EHc was specified I need to extern "C" because I use Qt QLibrary to load the dll and resolve the function name. Without extern "C" it can't find the some_func() function.

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  • spatial indexing mysql

    - by shaiju
    i have to integrate spatial indexing in mysql .i got an example i almost done it.in that example INSERT INTO address VALUES('Foobar street 12', GeomFromText('POINT(2671 2500)')); inplace of 2671 and 2500 i have to insert latitude and longitude in below format 35.177 ,-77.11. How is it possibe .Please help me

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  • Simple 301 redirect; how do I get it to drop the query string?

    - by Throlkim
    Hopefully there's a simple solution to this. I'm setting up a redirect for old search listings, but I don't want any of the query string to carry over. The current rule is: redirect 301 /blog http://newdomain.com But this would redirect the following: http://www.olddomain.com/blog/2009/11/article-name-etc To this: http://newdomain.com/2009/11/article-name-etc When I just want: http://newdomain.com Can this be done in the simple 301 redirect, or will I have to write a mod_rewrite rule?

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  • base-n series generator for a given number in java,,

    - by Senthil
    I want to create a program for generating the series for the given base-n. , for example if my input is 2,then series shuould be, 00,01,10,11,etc.,(binary) if my input is 10,then series shuould be,1,2,3,4,5,etc.,(decimal) is there any general mechanism to find these numbers so that I can program for base-n.,

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  • issue while synchronising PHP (reading file) and Ajax (jquery ui slider)

    - by Boris
    Hello, I got an issue while trying to display a jquery UI slider with its range based on a values read with PHP from a text file. Its seems that it's a syncrhonising issue as I get the error: "An attempt was made to use an object that is not, or is no longer, usable" code: 11" Is there a way I can force the jquery UI slider to wait for the value to be present or to work in synchrone mode ? Thanks in advance.

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  • Mysql Syntax Error

    - by tarnfeld
    Any idea why this is popping up :( ? You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'CREATE TABLE `clocks` ( `id` int(11) NOT NULL AUTO_INCREMENT, ' at line 6

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  • plane bombing problems- help

    - by peiska
    I'm training code problems, and on this one I am having problems to solve it, can you give me some tips how to solve it please. The problem is something like this: Your task is to find the sequence of points on the map that the bomber is expected to travel such that it hits all vital links. A link from A to B is vital when its absence isolates completely A from B. In other words, the only way to go from A to B (or vice versa) is via that link. Notice that if we destroy for example link (d,e), it becomes impossible to go from d to e,m,l or n in any way. A vital link can be hit at any point that lies in its segment (e.g. a hit close to d is as valid as a hit close to e). Of course, only one hit is enough to neutralize a vital link. Moreover, each bomb affects an exact circle of radius R, i.e., every segment that intersects that circle is considered hit. Due to enemy counter-attack, the plane may have to retreat at any moment, so the plane should follow, at each moment, to the closest vital link possible, even if in the end the total distance grows larger. Given all coordinates (the initial position of the plane and the nodes in the map) and the range R, you have to determine the sequence of positions in which the plane has to drop bombs. This sequence should start (takeoff) and finish (landing) at the initial position. Except for the start and finish, all the other positions have to fall exactly in a segment of the map (i.e. it should correspond to a point in a non-hit vital link segment). The coordinate system used will be UTM (Universal Transverse Mercator) northing and easting, which basically corresponds to a Euclidian perspective of the world (X=Easting; Y=Northing). Input Each input file will start with three floating point numbers indicating the X0 and Y0 coordinates of the airport and the range R. The second line contains an integer, N, indicating the number of nodes in the road network graph. Then, the next N (<10000) lines will each contain a pair of floating point numbers indicating the Xi and Yi coordinates (1 No two links will ever cross with each other. Output The program will print the sequence of coordinates (pairs of floating point numbers with exactly one decimal place), each one at a line, in the order that the plane should visit (starting and ending in the airport). Sample input 1 102.3 553.9 0.2 14 342.2 832.5 596.2 638.5 479.7 991.3 720.4 874.8 744.3 1284.1 1294.6 924.2 1467.5 659.6 1802.6 659.6 1686.2 860.7 1548.6 1111.2 1834.4 1054.8 564.4 1442.8 850.1 1460.5 1294.6 1485.1 17 1 2 1 3 2 4 3 4 4 5 4 6 6 7 7 8 8 9 8 10 9 10 10 11 6 11 5 12 5 13 12 13 13 14 Sample output 1 102.3 553.9 720.4 874.8 850.1 1460.5 102.3 553.9

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  • How can I multiply each item in an array easily with PHP?

    - by Henry
    I have an array called $times. It is a list of small numbers (15,14,11,9,3,2). These will be user submitted and are supposed to be minutes. As PHP time works on seconds, I would like to multiply each element of my array by 60. I've been playing around with array_walk and array_map but I can't get those working :S Thanks.

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  • Converting a list into a select with jquery

    - by Davemof
    I'm trying to convert the following list into a select list so it can be submitted via a form - the element within the lists will become the value of each option: <ul class="selected connected-list ui-sortable" style="height: 279px;"> <li class="ui-helper-hidden-accessible" style=""></li> <li title="Owner Name 1 - " class="ui-state-default ui-element ui-draggable" style="display: block; position: relative; top: 0px; left: 0px;"><span class="ui-icon-arrowthick-2-n-s ui-icon"></span>Owner Name 1 - <em class="thenumber">4.4796E+11</em><a class="action" href="#"><span class="ui-corner-all ui-icon ui-icon-minus"></span></a></li> <li title="David Moffat - " class="ui-state-default ui-element" style="display: block; position: relative; top: 0px; left: 0px;"><span class="ui-icon ui-icon-arrowthick-2-n-s"></span>David Moffat - <em class="thenumber">07730423005</em><a class="action" href="#"><span class="ui-corner-all ui-icon ui-icon-minus"></span></a></li> </ul> This should convert to the following format: <select style="display:none" class="selectoption" name="p_num[]" multiple="multiple"> <option value="">4.4796E+11</option> <option value="">07730423007</option> </select> I have tried the following jquery code, but after many hours I'm pulling my hair out: $('a.sendform').click(function(){ $('ul.selected').each(function() { var $select = $('<select />'); $(this).find('li').each(function() { var $option = $('<option />'); $option.attr('value', $(this).('em')).html($(this).html()); $select.append($option); }); $(this).replaceWith($select); }); }); Any help might save my remaining hair. Many thanks David

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  • How to optimize this Python code?

    - by RandomVector
    def maxVote(nLabels): count = {} maxList = [] maxCount = 0 for nLabel in nLabels: if nLabel in count: count[nLabel] += 1 else: count[nLabel] = 1 #Check if the count is max if count[nLabel] > maxCount: maxCount = count[nLabel] maxList = [nLabel,] elif count[nLabel]==maxCount: maxList.append(nLabel) return random.choice(maxList) nLabels contains a list of integers. The above function returns the integer with highest frequency, if more than one have same frequency then a randomly selected integer from them is returned. E.g. maxVote([1,3,4,5,5,5,3,12,11]) is 5

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