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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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  • Joda Time cannot subtract one hour

    - by Leoa
    In my android program, I have a spinner that allows the user to select different times. Each selection is processed with Joda time to subtract the minutes. It works fine for minutes 0 to 59 and 61 and greater. However, when 60 minutes is subtracted, the time is not updated, and the original time is shown. How do I get Joda time to subtract 60 minutes? Spinner: public class MyOnItemSelectedListener implements OnItemSelectedListener { public void onItemSelected(AdapterView<?> parent, View view, int pos, long id1) { String mins = parent.getItemAtPosition(pos).toString(); int intmins=0; // process user's selection of alert time if(mins.equals("5 minutes")){intmins = 5;} if(mins.equals("10 minutes")){intmins = 10;} if(mins.equals("20 minutes")){intmins = 20;} if(mins.equals("30 minutes")){intmins = 30;} if(mins.equals("40 minutes")){intmins = 40;} if(mins.equals("50 minutes")){intmins = 50;} if(mins.equals("60 minutes")){intmins = 60;} if(mins.equals("120 minutes")){intmins = 120;} String stringMinutes=""+intmins; setAlarm(intmins, stringMinutes); } else { } public void onNothingSelected(AdapterView parent) { mLocationDisplay.setText(" " + location); } } public void setAlarm(int intmins, String mins) { // based alarm time on start time of event. TODO get info from database. String currentDate; SimpleDateFormat myFormat = new SimpleDateFormat("MM/dd/yyyy HH:mm:ss"); Date date1 = null; DateTime dt; currentDate = eventdate + " " + startTimeMilitary;// startTimeMilitary; try { date1 = myFormat.parse(currentDate); } catch (ParseException e) { // TODO Auto-generated catch block e.printStackTrace(); } dt = new DateTime(date1); long dateInMillis = dt.getMillis(); String sDateInMillis = Long.toString(dateInMillis); // subtract the selected time from the event's start time String newAlertTime = subtractTime(dt, intmins); newAlertTime = subtractTime(dt, intmins); //......}

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  • search paths where one native library depends on another

    - by carneades
    I'm using JNA and Java but I think this question affects any native-to-nonnative bridge. I have a Java application which relies on lib1.dylib, and lib1.dylib relies on lib2.dylib. I want to put everything inside of my .app file on Mac. I can easily put lib1.dylib inside and set java.classpath (or NativeLibrary.addSearchPath()) to tell the JVM where to find lib1.dylib. The trouble is, I don't know how to communicate that lib1.dylib's dependencies are also in the location I provided. The result is that lib1 is loaded fine, but then lib2 can't be found since it's not in the operating system's library path. Anyone know how I can overcome this problem? I imagine it must come up plenty in big projects with large numbers of shared libraries.

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  • How to override form just on one page?

    - by user363036
    OK so this is my hook form alter function.It is causing all the registration forms on site to be over written which I do not want as I just want it on this page. function special_registration_form_alter(&$form, $form_state, $form_id) { if ($form_id == 'user_register') { drupal_set_title(t('Custom registration')); $form['firstname'] = array('#type' = 'textfield', '#title' = t('First Name: *'), '#required' = TRUE, '#size' = 45, '#weight' = - 100,); $form['lastname'] = array('#type' = 'textfield', '#title' = t('Last Name: *'), '#required' = TRUE, '#size' = 45, '#weight' = - 99,); } I only first name and last name to be captured and stored in a different table just on this page. On other pages I just want the good old fashioned form. Do I still need to change the weight? I know I am missing something elementary.

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  • converting GPS latitude/longitude from different formats to one format (in PHP)

    - by Dave
    Hi. i'm trying to built in support for locations in my application and i'm expecting users to be inputting gps coordinates in a variety of ways. I need to convert all of the below to: latitude - direction (N/s), degres, minutes, seconds; longitude (E/W) - degrees, minuts, seconds. Each user input will be in a single line. eg: 9.182, -39.140625 9.182 / -39.140625 9.182,-39.140625 9.182 -39.140625 21° 16' 674S[some_separator]27° 30' 318E 21 16 674S[some_separator]27 30 318E [some_separator] may be a single space as well... The final format needs to beas: latitude.direction = south latitude.degrees = 21 latitude.minutes = 16 latitude.seconds = 674 longitude.direction = east longitude.degrees = 27 longitude.minutes = 30 longitude.seconds = 318 (a) what is the simplest way of asking ordinary-non-tech users to input the GPS coordinate?s (b) how do i convert the above to the final format? any built in functions that handle these variations in data input? i've seen http://stackoverflow.com/questions/2548943/gps-format-in-php - but i need to handle a more varied input.

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  • One way Has-Many-Through

    - by Hock
    Hello, I have a Category, a Subcategory and a Product model. I have: Category has_many Subcategories Subcategory has_many Products Subcategory belongs_to Category Product belongs_to Subcategory Is there a way to have something like Category has_many Projects through Subcategories ? The 'normal' rails way wouldn't work because "subcategory" doesn't belongs to product so product does not have a subcategory_id field. Instead, I need the query to be something like SELECT * FROM products WHERE id IN category.subcategory_ids Is there a way to do that? Thanks, Nicolás Hock Isaza

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  • copy file from one location to another location in linux using java program

    - by Mouli
    Using JSP am trying to move customer logo into another location in linux but its not working. thanks in advance Here is my program String customerLogo = request.getParameter("uploadCustomerLogo").trim(); StringBuffer absoluteFolderPath = new StringBuffer(); absoluteFolderPath.append("/zoniac"); absoluteFolderPath.append("/Companies/"); absoluteFolderPath.append("companyCode/"); absoluteFolderPath.append("custom/"); String destination = absoluteFolderPath.toString(); File sourcefile = new File(customerLogo); File destfile = new File(destination+sourcefile.getName()); FileUtils.copyFile(sourcefile,destfile);

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  • Naive Bayesian classification (spam filtering) - Doubt in one calculation? Which one is right? Plz c

    - by Microkernel
    Hi guys, I am implementing Naive Bayesian classifier for spam filtering. I have doubt on some calculation. Please clarify me what to do. Here is my question. In this method, you have to calculate P(S|W) - Probability that Message is spam given word W occurs in it. P(W|S) - Probability that word W occurs in a spam message. P(W|H) - Probability that word W occurs in a Ham message. So to calculate P(W|S), should I do (1) (Number of times W occuring in spam)/(total number of times W occurs in all the messages) OR (2) (Number of times word W occurs in Spam)/(Total number of words in the spam message) So, to calculate P(W|S), should I do (1) or (2)? (I thought it to be (2), but I am not sure, so plz clarify me) I am refering http://en.wikipedia.org/wiki/Bayesian_spam_filtering for the info by the way. I got to complete the implementation by this weekend :( Thanks and regards, MicroKernel :) @sth: Hmm... Shouldn't repeated occurrence of word 'W' increase a message's spam score? In the your approach it wouldn't, right?. Lets take a scenario and discuss... Lets say, we have 100 training messages, out of which 50 are spam and 50 are Ham. and say word_count of each message = 100. And lets say, in spam messages word W occurs 5 times in each message and word W occurs 1 time in Ham message. So total number of times W occuring in all the spam message = 5*50 = 250 times. And total number of times W occuring in all Ham messages = 1*50 = 50 times. Total occurance of W in all of the training messages = (250+50) = 300 times. So, in this scenario, how do u calculate P(W|S) and P(W|H) ? Naturally we should expect, P(W|S) P(W|H)??? right. Please share your thought...

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  • SQL 2005 Merge / concatenate multiple rows to one column

    - by Dave
    Hi, We have a bit of a SQL quandry. Say I have a results that look like this... 61E77D90-D53D-4E2E-A09E-9D6F012EB59C | A 61E77D90-D53D-4E2E-A09E-9D6F012EB59C | B 61E77D90-D53D-4E2E-A09E-9D6F012EB59C | C 61E77D90-D53D-4E2E-A09E-9D6F012EB59C | D 7ce953ca-a55b-4c55-a52c-9d6f012ea903 | E 7ce953ca-a55b-4c55-a52c-9d6f012ea903 | F is there a way I can group these results within SQL to return as 61E77D90-D53D-4E2E-A09E-9D6F012EB59C | A B C D 7ce953ca-a55b-4c55-a52c-9d6f012ea903 | E F Any ideas people? Many thanks Dave

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  • Jython java call throws exception asking for 2 args when only one arg is coded

    - by clutch
    I have an Java method I want to call within my Jython servlet running on tomcat5. It looks like this: @SuppressWarnings("unchecked") public School loadByName(String name) { List<School> school; school = getHibernateTemplate().find("from " + getPersistentClass().getName() + " where name = ?", name); return uniqueResult(school); } I call it in Jython using: foobar = SchoolDAOHibernate.loadByName('Univeristy') It throws an error that says loadByName() expects 2 args; got 1. What other argument could it be looking for?

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  • Can one form have multiple actions?

    - by Brook Julias
    I am wanting to submit a form to different places based on selections made in the form. If the user wants to delete elements go to page 1. If the user wants to edit/update elements go to page 2. If the user wants to group/attach elements go to page 3.

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  • Ajax problem after deleting a div, then creating a new one

    - by Matt Nathanson
    I'm building a custom CMS where you can add and delete clients using ajax and jquery 1.4.2. My problem lies after I delete a div. The ajax is used to complete this and refresh automatically.. But when I go to create a new div (without a hard refresh) it puts it back in the slot of the div I just deleted. How can I get this to completely forget about the div i just deleted and place the new div in the next database table? link for reference: http://staging.sneakattackmedia.com/cms/ //Add New client // function AddNewClient() { dataToLoad = 'addClient=yes'; $.ajax({ type: 'post', url: '/clients/controller.php', datatype: 'html', data: dataToLoad, target: ('#clientssidebar'), async: false, success: function(html){ $(this).click(function() {reInitialize()}); //$('#clientssidebar').html(html); $('div#' + clientID).slideDown(800); $(this).click(function() { ExpandSidebar()});}, error: function() { alert('An error occured! 222');} });}; //Delete Client // function DeleteClient(){ var yes = confirm("Whoa there chief! Do you really want to DELETE this client?"); if (yes == 1) { dataToLoad = 'clientID=' + clientID + '&deleteClient=yes', $.ajax({ type: 'post', url: '/clients/controller.php', datatype: 'html', data: dataToLoad, success: function(html) { alert('Client' + clientID + ' should have been deleted from the database.'); $(this).click(function() {reInitialize()}); $('div#' +clientID).slideUp(800); }, error: function() { alert('error'); }});};}; //Re Initialize // function reInitialize() { $('#addnew').click(function() {AddNewClient()}); $('.deletebutton').click(function() {clientID = $(this).parent().attr('id'); DeleteClient()}) $('.clientblock').click(function() {clientID = $(this).attr('id'); ExpandSidebar()});}; //Document Ready // $(document).ready(function(){ if ($('isCMS')){ editCMS = 1; $('.deletebutton').click(function() {clientID = $(this).parent().attr('id'); DeleteClient()}); $('#addnew').click(function() {AddNewClient()}); $('.clientblock').click(function() {clientID = $(this).attr('id'); ExpandSidebar()}); $('.clientblock').click(function() {if (clickClient ==true) { $(this).css('background-image', 'url(/images/highlightclient.png)'); $(this).css('margin-left' , '30px'); }; $(this).click(function(){ $(this).css('background-image', ''); }); $('.uploadbutton').click(function(){UploadThings()}); }); } else ($('#clientscontainer')) { $('#editbutton').css('display', 'none'); }; }); Please help!!!

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  • JPA One to Many using JoinTable Error

    - by user553015
    I am trying to model 1:N (Person & Address) relationship using a junction table (Person_Address). 1.Person (personId PK) 2.Address (addressId PK) 3.PersonAddress ( personId, addressId composite PK, personId FK references Person, addressid FK references Address ) @Entity public class Person { @OneToMany @JoinTable( name="PersonAddress", joinColumns = @JoinColumn( name="personId"), inverseJoinColumns = @JoinColumn( name="addressId") ) public Set<Address> getAddresses() {...} ... } I encounter following error. Not able to find any solution. Caused by: org.hibernate.MappingException: Could not determine type for: com.realestate.details.Address, at table: Person, for columns: [org.hibernate.mapping.Column(address)] at org.hibernate.mapping.SimpleValue.getType(SimpleValue.java:269) at org.hibernate.mapping.SimpleValue.isValid(SimpleValue.java:253) at org.hibernate.mapping.Property.isValid(Property.java:185) at org.hibernate.mapping.PersistentClass.validate(PersistentClass.java:440) at org.hibernate.mapping.RootClass.validate(RootClass.java:192) at org.hibernate.cfg.Configuration.validate(Configuration.java:1108) at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1293)

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  • click on one column total row is highlate

    - by sairam333
    If i click a paricular column in a dispalying list dynamically at that time that particular row will be highlated ,In the sam etime if i click another value in that column that row will be highlated only and previous highlated row will be now in normal How can i do.Give me suggestions Thanks in advance

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  • how to invoke a webservice from one container in another container in glassfish

    - by vinny
    I have webservices deployed on two containers in two separate servers A and B. A webMethod in 'Server A' needs to invoke a webmethod in 'Server B'. I have created a client stub for Sever B. Im trying to make 'Server A' use this client stub and talk to Server B. I get an exception while trying to instantiate the port object specifically at : service.getABCBeanPort(); (using JAX-WS library) Is my approach correct? Is there any better way of invoking a webservice on a remote server?

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  • One DataGrid Item Renderer for multiple columns

    - by user329650
    Hey, I'm trying to create a Flex DataGrid where the firstname and lastname are shown under each other, but in the DataGridColumn Ideally I would want to do something like <mx:columns> <mx:DataGridColumn headerText="Column 2" dataField="time"/> <mx:DataGridColumn headerText="Column 2" dataField="firstname,lastname" itemRenderer="renderers.FirstNameLastName"/> so that both values get passed to the itemrenderer, is this possible? Dennis

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  • Django "Page not found" error page shows only one of two expected urls

    - by Frank V
    I'm working with Django, admittedly for the first time doing anything real. The URL config looks like the following: urlpatterns = patterns('my_site.core_prototype.views', (r'^newpost/$', 'newPost'), (r'^$', 'NewPostAndDisplayList'), # capture nothing... #more here... - perhaps the perma-links? ) This is in an app's url.py which is loaded from the project's url.py via: urlpatterns = patterns('', # only app for now. (r'^$', include('my_site.core_prototype.urls')), ) The problem is, when I receive a 404 attempting to utilize newpost, the error page only shows the ^$ -- it seems to ignore the newpost pattern... I'm sure the solution is probably stupid-simple but right now I'm missing it. Can someone help get me on the right track...

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  • Vim hanging after parsing .vimrc (even a blank one) file on Solaris 10

    - by Seamus
    Hello all, I am having a problem with vim 7.2 hanging (for about 10 seconds) after it parses the .vimrc file. I had a similar issue in the past with tcsh on linux, but it was resolved by setting TERM to xterm-color. The same does not resolve the issue here. Any idea what may be causing this? $ env USER=redacted LOGNAME=redacted HOME=/home/redacted PATH=redacted MAIL=/var/spool/mail/redacted SHELL=/bin/tcsh TZ=redacted LC_COLLATE=C SSH_CLIENT=redacted SSH_CONNECTION=redacted SSH_TTY=/dev/pts/11 TERM=dtterm HOSTTYPE=sun4 VENDOR=sun OSTYPE=solaris MACHTYPE=sparc SHLVL=1 PWD=/home/redacted GROUP=redacted HOST=redacted REMOTEHOST=redacted QUOTA_CHECKED=1 WHOAMI=redacted HOSTNAME=redacted EDITOR=vim PRINTER=redacted INFOPATH=/software/gnu/gcc/2.8.1/sun4os5.10/info:/software/gnu/sun4os5/info:/software/gnu/emacs/20.3.1/sun4os5/info:/software/gnuish/sun4os5/info:/usr/local/gnu/info MANPATH=/software/gnu/gcc/2.8.1/sun4os5.10/man:/software/gnu/sun4os5/man:/software/gnu/emacs/20.3.1/sun4os5/man:/opt/rational/clearcase/doc/man:/usr/openwin/man:/usr/share/man:/usr/local/man:/usr/dt/man:/software/gnuish/sun4os5/man H_ARCH=sun4 H_ARCHOS=sun4os5 H_ARCHOS_SUB=sun4os5.10 H_OSTYPE=SUNOS H_OSREV=51000 T_ARCH=sun4 T_ARCHOS=sun4os5 T_ARCHOS_SUB=sun4os5.10 T_OSTYPE=SUNOS T_OSREV=51000 X11HOME=/usr/local/x11/sun4os5 OPENWINHOME=/usr/openwin LD_LIBRARY_PATH=/usr/dt/lib:/usr/openwin/lib MOTIFHOME=/usr/dt XINITRC=/usr/openwin/lib/Xinitrc GCC_REV=281

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  • Make fully visible one element from overflow:hidden element

    - by Oleksandr Khavdiy
    Please check http://jsfiddle.net/mtN6R/5/ .tooltip{ color:red; } .wrapper { overflow:hidden; height:50px; border:1px solid black; width:50px; } <div class="wrapper"> <div class='tooltip'>A big tooltip which should be visible fully</div> A lot of text<br> A lot of text<br> </div> I need .tooltip make fully visible but I can't take it outside wrapper. Can we stylize that example so .tooltip will be shown above wrapper and the rest content will stay as is?

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