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  • BioPython: extracting sequence IDs from a Blast output file

    - by Jon
    Hi, I have a BLAST output file in XML format. It is 22 query sequences with 50 hits reported from each sequence. And I want to extract all the 50x22 hits. This is the code I currently have, but it only extracts the 50 hits from the first query. from Bio.Blast import NCBIXM blast_records = NCBIXML.parse(result_handle) blast_record = blast_records.next() save_file = open("/Users/jonbra/Desktop/my_fasta_seq.fasta", 'w') for alignment in blast_record.alignments: for hsp in alignment.hsps: save_file.write('>%s\n' % (alignment.title,)) save_file.close() Somebody have any suggestions as to extract all the hits? I guess I have to use something else than alignments. Hope this was clear. Thanks! Jon

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  • Simple select not working on JDBC MSSQL ?

    - by Xinus
    I am trying to move project which was using MySQL database to the one that uses MSSQL 2008, But the select that was working in mysql is no longer working in MSSQL PreparedStatement statement = connection .prepareStatement("select u.user_firstname,u.user_lastname from user_details u, login l where l.username=? and l.login_user = u.user_id"); statement.setString(1, userName); ResultSet resultSet = (ResultSet) statement.executeQuery(); It always gives me empty resultset even when there are values corresponding to that username, When I run query using MSSQL management studio - query works properly i.e. it gives non-zero rows, Are there any MSSQL specific change I need to do ?

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  • postgres - ERROR: syntax error at or near "COST"

    - by cino21122
    EDIT Taking COST 100 out made the command go through, however, I'm still unable to run my query because it yields this error: ERROR: function group_concat(character) does not exist HINT: No function matches the given name and argument types. You may need to add explicit type casts. The query I'm running is this: select tpid, group_concat(z) as z, group_concat(cast(r as char(2))) as r, group_concat(to_char(datecreated,'DD-Mon-YYYY HH12:MI am')) as datecreated, group_concat(to_char(datemodified,'DD-Mon-YYYY HH12:MI am')) as datemodified from tpids group by tpid order by tpid, zip This function seems to work fine locally, but moving it online yields this error... Is there something I'm missing? CREATE OR REPLACE FUNCTION group_concat(text, text) RETURNS text AS $BODY$ SELECT CASE WHEN $2 IS NULL THEN $1 WHEN $1 IS NULL THEN $2 ELSE $1 operator(pg_catalog.||) ',' operator(pg_catalog.||) $2 END $BODY$ LANGUAGE 'sql' IMMUTABLE COST 100; ALTER FUNCTION group_concat(text, text) OWNER TO j76dd3;

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  • How to switch 'default' sound device controlled by hardware keys in Xubuntu?

    - by Ruth
    I installed xubuntu-desktop on a 12.04 Ubuntu upgrade after finding Gnome3 lacking. I've mostly been happy, but I've found an odd and frustrating bug. My laptop has two sound 'outputs' - an HDMI-out plug I never use, and the onboard speakers/headphones. For some reason, the hardware keys have been mapped to the HDMI output, even if I set it as 'fallback' in pavucontrol, and notify-osd only displays changes in the HDMI output (though the panel indicator volume control controls onboard sound). I'd ideally like both hardware keys and notify-osd to be looking at the onboard sound, though if I can't get notify-osd it's an acceptable loss. Having to click through a bunch of stuff to change volume is driving me crazy, though. Googling suggested that it /may/ be a Pulseaudio/ALSA conflict, but the hardware keys seem to change at least indicated volume in pavucontrol for HDMI as expected (I don't have an HDMI cable to test actual sound output)

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  • Pidgin doesn't show buddy list?

    - by Nicholas Flynt
    I like to use pidgin instead of Empathy because I'm used to it, and because I have to venture into windows for more development than I would prefer. In Ubuntu 11.10, I can't find any way to get to the buddy list. It opens, and just sits there in the messenger panel tray thing. From its previous behavior, I believe Pidgin usually starts up minimized-- you have to click on its system tray to show the buddy list. The messenger applet does not seem to support this functionality. Is this a bug, or am I just missing something obvious?

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  • Isn't INT more efficient than UNIQUEIDENTIFIER?

    - by ck
    I have a parent table and child table where the columns that join them together are the UNIQUEIDENTIFIER type. The child table has a clustered index on the column that joins it to the parent table (its PK, which is also clustered). I have created a copy of both of these tables but changed the relationship columns to be INTs instead, have rebuilt the indexes so that they are essentially the same structure and can be queried in the same way. When I query for a known 20 records from the parent table, pulling in all the related records from the child tables, I get identical query costs across both, i.e. 50/50 cost for the batches. If this is true, then my giant project to change all of the tables like this appears to be pointless, other than speeding up inserts. Can anyone provide any light on the situation?

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  • PHP: Alternative to SESSIONS

    - by iamjonesy
    Hi, I have a PHP application that relies on session variables quite a lot. After login the user get redirected to a page that executes code to set up a load of session variables depending on who the user is. The application is using data from different sources and the sessions are used to store ID numbers to query the databases. So when the user goes to a page that will query their asset management system their ID for that particular database is called via the session. I've had a LOT of problems with session variables recently. Sometimes only one session file is created during the lifetime of the app, and sometimes each session request results in a new session id (still haven't managed to find out why!). My question is this. Is there an alternative to using session variables for this? Like globals or some other way? Any help most appreciated! Regards, Jonesy

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  • SQL DISTINCT Value Question

    - by CPOW
    How can I filter my results in a Query? example I have 5 Records John,Smith,apple Jane,Doe,apple Fred,James,apple Bill,evans,orange Willma,Jones,grape Now I want a query that would bring me back 3 records with the DISTINCT FRUIT, BUT... and here is the tricky part, I still want the columns for First Name , Last Name. PS I do not care which of the 3 it returns mind you, but I need it to only return 3 (or what ever how many DISTINCT fruit there are. ex return would be John,Smith,apple Bill,evans,orange Willma,Jones,grape Thanks in advance I've been banging my head on this all day.

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  • Chrome Web Store verification

    - by Vince V.
    A couple of days ago I created an extension for Chrome and added it to the store. Now I want it to get verified. I payed the 5 dollar and added my website to Webmaster Tools. The website is also verified on those Webmaster Tools. Today I wanted to add my URL to my extension (ultimately to do online installations) but it doesn't recognize the URL I put in those Webmaster Tools. I tried refreshing and clicking add site, but it just doesn't work. Is there some step that I am missing or is this a bug in the Chrome Web Store, because I don't see any option left.

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  • SQL Server: how to optimize "like" queries?

    - by duke84
    I have a query that searches for clients using "like" with wildcard. For example: SELECT TOP (10) [t0].[CLIENTNUMBER], [t0].[FIRSTNAME], [t0].[LASTNAME], [t0].[MI], [t0].[MDOCNUMBER] FROM [dbo].[CLIENT] AS [t0] WHERE (LTRIM(RTRIM([t0].[DOCREVNO])) = '0') AND ([t0].[FIRSTNAME] LIKE '%John%') AND ([t0].[LASTNAME] LIKE '%Smith%') AND ([t0].[SSN] LIKE '%123%') AND ([t0].[CLIENTNUMBER] LIKE '%123%') AND ([t0].[MDOCNUMBER] LIKE '%123%') AND ([t0].[CLIENTINDICATOR] = 'ON') It can also use less parameters in "where" clause, for example: SELECT TOP (10) [t0].[CLIENTNUMBER], [t0].[FIRSTNAME], [t0].[LASTNAME], [t0].[MI], [t0].[MDOCNUMBER] FROM [dbo].[CLIENT] AS [t0] WHERE (LTRIM(RTRIM([t0].[DOCREVNO])) = '0') AND ([t0].[FIRSTNAME] LIKE '%John%') AND ([t0].[CLIENTINDICATOR] = 'ON') Can anybody tell what is the best way to optimize performance of such query? Maybe I need to create an index? This table can have up to 1000K records in production.

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  • Decode json string returned from Flickr API using PHP, curl

    - by Globalz
    Im trying to decode a json string returned from flickr within my PHP code. Im using CURL but it keeps returning a string even when I wrap json_decode() around the json sring variable. Any ideas? $api_key = '####'; $photoset_id = '###'; $query = 'http://api.flickr.com/services/rest/?&method=flickr.photosets.getPhotos&api_key='.$api_key.'&photoset_id='.$photoset_id.'&extras=url_o,url_t&format=json&jsoncallback=1'; $ch = curl_init(); // open curl session // set curl options curl_setopt($ch, CURLOPT_URL, $query); curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1); $data = curl_exec($ch); // execute curl session curl_close($ch); // close curl session var_dump(json_decode($data));

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  • How do You Get a Specific Value From a System.Data.DataTable Object?

    - by Giffyguy
    I'm a low-level algorithm programmer, and databases are not really my thing - so this'll be a n00b question if ever there was one. I'm running a simple SELECT query through our development team's DAO. The DAO returns a System.Data.DataTable object containing the results of the query. This is all working fine so far. The problem I have run into now: I need to pull a value out of one of the fields of the first row in the resulting DataTable - and I have no idea where to even start. Microsoft is so confusing about this! Arrrg! Any advice would be appreciated. I'm not providing any code samples, because I believe that context is unnecessary here. I'm assuming that all DataTable objects work the same way, no matter how you run your queries - and therefore any additional information would just make this more confusing for everyone.

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  • Bing search API using Jsonp not working, invalid label

    - by Blankman
    Struggling with Bing's json request (bing search, not map), I am getting an error back that says 'Invalid Label' My query url is: var bingurl="http://api.search.live.net/json.aspx?Appid=##APIKEY##&query=Honda&sources=web"; $.ajax({ type: "GET", url: bingurl, data: "{}", contentType: "application/json; charset=utf-8", dataType: "jsonp", success: function(data) { $callBack(data); }, error: function(msg) { alert("error" + msg); } }); Firebug reports 'invalid label' and then dumps the json response. No idea what is wrong? help appreciated.

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  • Why Beta versions have so many bugs?

    - by Eugene
    When I worked in Microsoft on MSE antivirus, we had several stages of pre-release: Alpha, Beta, RC. The biggest difference between these stages were bug fixes. Each time we fixed more bugs, and usually updated some minor features. Apple works in the same way. Look here: http://www.techrepublic.com/article/pro-tip-how-to-create-a-bootable-usb-installer-for-os-x-yosemite/ They released a beta of Yosemite OS, but the beta is full of bugs. Why do these big companies work like this? Isn't it better to release a beta version that was tested very thoroughly but one that just doesn't provide all the features that the final version will provide?

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  • What's New In 11.1.2.1 (Talleyrand SP1)

    - by russ.bishop
    This release is primarily about bug fixes and that's what we spent the most time on, but we also addressed a number of other things: 1. Performance improvements We've done a lot of work to improve the performance of page load and execution times. For example, the View Compare page is about half the size it was previously! We've also done a lot of work on the server to improve performance of queries, exports, action scripts, etc. We implemented some finer-grained locking so fewer operations will block other users while they are in progress. We made some optimizations to improve performance when you have a lot of network or database latency as well. Just a few examples: An Import that previously took 8 GB of memory and hours to complete now runs in about 30 minutes and never takes more than 1 GB of RAM. Searching by exact Node Name now completes within 2 seconds even for a hierarchy with millions of nodes. Another search that was taking 30 seconds to run now completes in less than 5 seconds. 2. Upgrade support This release supports automatic upgrade from previous releases, built right into the console. 3. Console Improvements The Console has been reorganized and made easier to use. It is also much more multi-threaded so it responds quicker without freezing up when you save changes or when it needs to get status. 4. Property Namespaces Properties now have a concept called a Namespace. This is tied into the Application Templates to prevent conflicts with duplicate property names. Right now, if you have an AccountType and you pull in the HFM template, it also has AccountType so you end up creating properties with decorations on the name like "Account Type (HFM)". This is no longer necessary. In addition, properties within a namespace must have unique labels but they can be duplicated across namespaces. So in the Property Grid when you click on the HFM category, you just see "AccountType". When you click on MyCategory, you see "AccountType", but they are different properties with different values. Within formulas, the names are still unique (eg: Custom.AccountType vs HFM.AccountType). I'll write more about this one later. 5. Single Sign On DRM now supports Single Sign-On via HSS. For example, if you are using Oracle's OAM as your SSO solution then you configure HSS to use OAM just like you would before. You also configure DRM to use HSS, again just like before. Then you configure OAM to protect the DRM web app, like you would any other website. However once you do those things, users are no longer prompted to enter their username/password. They simply get redirected to OAM if they don't already have a login token, otherwise they pick their application and sail right into DRM. You can also avoid having to pick an application (see the next item) 6. URL-based navigation You can now specify the application you want to log into via the URL. Combined with SSO and your Intranet, it becomes easy to provide links on our intranet portal that take users directly into a specific DRM application. We also support specifying the Version, Hierarchy, and Node. Again, this can be used on your internal portal, but the scenarios get even more interesting when you are using workflow like Oracle BPEL you can automatically generate links within emails that will take users directly to a specific node in the UI. 7. Job status and cancellation A lot of the jobs now report their status and support true cancellation. Action Scripts also report a progress complete percentage since the amount of work is known ahead of time. 8. Action Script Options Action scripts support Option declarations at the top of the file so a script can self-describe (when specified in the file, the corresponding item in the file is ignored). For example: Option|DetectDelimiter Option|UsePropertyNames|true This will tell DRM to automatically detect the delimiter (a pipe symbol in this case) and that all references to properties are by Name, not by Label. Note that when you load a script in the UI, if you use Labels we automatically try to match them up if they are unique. Any duplicates are indicated and you are presented with a choice to pick which property you actually referred to. This is somewhat similar to Version substitution, but tailored for properties. There are other more minor changes and like I said earlier a lot of bug fixes and performance improvements. Hopefully I will get a chance to dig into some of these things in future blog posts.

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  • mySQL experts - need help with 'intersect'

    - by MTCreations
    I know that mySQL 5.x does not support INTERSECT, but that seems to be what I need. Table A: Products (p_id) Table B: Prod_cats (cat_id) - category info (name, description, etc) Table C: prod_2cats (p_id, cat_id) - many to many prod_2cats holds the many (1 or more) categories that have been assigned to Products (A). Doing a query/filter lookup, (user interactive) and need to be able to select across multiple categories the products that meet ALL the criteria. Ex: - 80 products assigned to Category X - 50 products assigned to Category Y - but only 10 products (intersect) are assigned to BOTH cat X AND cat Y This sql works for one category: SELECT * FROM products WHERE p_show='Y' AND p_id IN ( SELECT p_id FROM prods_2cats AS PC WHERE PC.cat_id =" . $cat_id ." <-$cat_id is sanitized var passed from query form . I can't seem to find the means to say ' give me the intersect of cat A and cat B' and get back the subset (10 records, from my example) Help!

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  • Web Services: more frequent "small" calls, or less frequent "big" calls

    - by Klay
    In general, is it better to have a web application make lots of calls to a web service getting smaller chunks of data back, or to have the web app make fewer calls and get larger chunks of data? In particular, I'm building a Silverlight app that needs to get large amounts of data back from the server in response to a query created by a user. Each query could return anywhere from a few hundred records to a few thousand. Each record has around thirty fields of mostly decimal-type data. I've run into the situation before where the payload size of the response exceeded the maximum allowed by the service. I'm wondering whether it's better (more efficient for the server/client/web service) to cut this payload vertically--getting all values for a single field with each call--or horizontally--getting batches of complete records with each call. Or does it matter?

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  • Cannot populate form with ajax and populate jquery plugin

    - by Azriel_
    I'm trying to populate a form with jquery's populate plugin, but using $.ajax The idea is to retrieve data from my database according to the id in the links (ex of link: get_result_edit.php?id=34), reformulate it to json, return it to my page and fill up the form up with the populate plugin. But somehow i cannot get it to work. Any ideas: here's the code: $('a').click(function(){ $('#updatediv').hide('slow'); $.ajax({ type: "GET", url: "get_result_edit.php", success: function(data) { var $response=$(data); $('#form1').populate($response); } }); $('#updatediv').fadeIn('slow'); return false; whilst the php file states as follow: <?php $conn = new mysqli('localhost', 'XXXX', 'XXXXX', 'XXXXX'); @$query = 'Select * FROM news WHERE id ="'.$_GET['id'].'"'; $stmt = $conn->query($query) or die ($mysql->error()); if ($stmt) { $results = $stmt->fetch_object(); // get database data $json = json_encode($results); // convert to JSON format echo $json; } ?> Now first thing is that the mysql returns a null in this way: is there something wrong with he declaration of the sql statement in the $_GET part? Second is that even if i put a specific record to bring up, populate doesn't populate. Update: I changed the populate library with the one called "PHP jQuery helper functions" and the difference is that finally it says something. finally i get an error saying NO SUCH ELEMENT AS i wen into the library to have a look and up comes the following function function populateFormElement(form, name, value) { // check that the named element exists in the form var name = name; // handle non-php naming var element = form[name]; if(element == undefined) { debug('No such element as ' + name); return false; } // debug options if(options.debug) { _populate.elements.push(element); } } Now looking at it one can see that it should print out also the name, but its not printing it out. so i'm guessing that retrieving the name form the json is not working correctly. Link is at http://www.ocdmonline.org/michael/edit%5Fnews.php with username: Testing and pass:test123 Any ideas?

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  • SQL to retrieve the latest records, grouping by unique foreign keys

    - by jbox
    I'm creating query to retrieve the latest posts in a forum using a SQL DB. I've got a table called "Post". Each post has a foreign key relation to a "Thread" and a "User" as well as a creation date. The trick is I don't want to show two posts by the same user or two posts in the same thread. Is it possible to create a query that contains all this logic? # Grab the last 10 posts. SELECT id, user_id, thread_id FROM posts ORDER BY created_at DESC LIMIT 10; # Grab the last 10 posts, max one post per user SELECT id, user_id, thread_id FROM post GROUP BY user_id ORDER BY date DESC LIMIT 10; # Grab the last 10 posts, max one post per user, max one post per thread???

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  • MS SQL Server: how to optimize "like" queries?

    - by duke84
    I have a query that searches for clients using "like" with wildcard. For example: SELECT TOP (10) [t0].[CLIENTNUMBER], [t0].[FIRSTNAME], [t0].[LASTNAME], [t0].[MI], [t0].[MDOCNUMBER] FROM [dbo].[CLIENT] AS [t0] WHERE (LTRIM(RTRIM([t0].[DOCREVNO])) = '0') AND ([t0].[FIRSTNAME] LIKE '%John%') AND ([t0].[LASTNAME] LIKE '%Smith%') AND ([t0].[SSN] LIKE '%123%') AND ([t0].[CLIENTNUMBER] LIKE '%123%') AND ([t0].[MDOCNUMBER] LIKE '%123%') AND ([t0].[CLIENTINDICATOR] = 'ON') It can also use less parameters in "where" clause, for example: SELECT TOP (10) [t0].[CLIENTNUMBER], [t0].[FIRSTNAME], [t0].[LASTNAME], [t0].[MI], [t0].[MDOCNUMBER] FROM [dbo].[CLIENT] AS [t0] WHERE (LTRIM(RTRIM([t0].[DOCREVNO])) = '0') AND ([t0].[FIRSTNAME] LIKE '%John%') AND ([t0].[CLIENTINDICATOR] = 'ON') Can anybody tell what is the best way to optimize performance of such query? Maybe I need to create an index? This table can have up to 1000K records in production.

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  • Sound Juicer doesn't respect Lame's codec settings when ripping CDs

    - by Takkat
    Using Sound Juicer I am able to rip CDs very conveniently. I would like to rip them in about 256 kbit/s variable bitrate. To accomplish this I have defined the settings for mp3 in gnome-audio-profiles-properties as follows: audio/x-raw-int,rate=44100,channels=2 ! lame name=enc mode=0 vbr-quality=0 ! id3v2mux where vbr-quality=0 should give me a variable bitrate averaging 245 kbit/s. The resulting files however always say they are in 128 kbit/s. Is this only a tagging bug or is indeed the bitrate that low? How could I find out?

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  • Glib.h error while trying to compile an application

    - by user91125
    I've been trying to compile this app from source https://code.launchpad.net/gala and i keep getting this message when i run MAKE: Scanning dependencies of target gala [ 11%] Building C object CMakeFiles/gala.dir/src/DBus.c.o /home/camilo/notifications/build/src/DBus.c:21:18: fatal error: glib.h: No such file or directory compilation terminated. make[2]: *** [CMakeFiles/gala.dir/src/DBus.c.o] Error 1 make[1]: *** [CMakeFiles/gala.dir/all] Error 2 make: *** [all] Error 2 Even though I' have installed glib and there is the glib.h file camilo@ian:~$ find /usr -iname glib.h /usr/include/glib-2.0/glib.h Is it a bug form the application or is it something wrong with my system?

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  • XAML2CPP 1.0.1.0

    - by Valter Minute
    I upgraded XAML2CPP to fix some bugs and support some new features that will be used in my next tutorial step (that I hope to publish very soon!). Bug fixed: the listbox selection changed event was generated with an incorrect prototype events generated by the XAML tree root element (UserControl) were not handled. New features: XAML2CPP generates panels (dynamically generated XAML subtrees that may be added to a page) and user controls (those will be the object of my next post, stay tuned!). XAML2CPPXRValue class has been added to XAML2CPPbase.h. This class will allow single-line declaration of XRValue objects (I’m lazy!) and destroys automatically objects and string XRValues when the object itself is destroyed. You can download the latest XAML2CPP release here: http://cid-9b7b0aefe3514dc5.skydrive.live.com/self.aspx/.Public/XAML2CPP.zip

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  • NullPointerException when linking to Service that uses ContentProvider

    - by Danny Chia
    H.i everyone, this is my first post here! Anyways, I'm trying to write a "todo list" application. It stores the data in a ContentProvider, which is accessed via a Service. However, my app crashes at launch. My code is below: Manifest file: <?xml version="1.0" encoding="utf-8"?> <manifest xmlns:android="http://schemas.android.com/apk/res/android" package="com.examples.todolist" android:versionCode="1" android:versionName="1.0"> <application android:icon="@drawable/icon" android:label="@string/app_name" android:debuggable="True"> <activity android:name=".ToDoList" android:label="@string/app_name" android:theme="@style/ToDoTheme"> <intent-filter> <action android:name="android.intent.action.MAIN" /> <category android:name="android.intent.category.LAUNCHER" /> </intent-filter> </activity> <service android:name="TodoService"/> <provider android:name="TodoProvider" android:authorities="com.examples.provider.todolist" /> </application> <uses-sdk android:minSdkVersion="7" /> </manifest> ToDoList.java: package com.examples.todolist; import com.examples.todolist.TodoService.LocalBinder; import java.util.ArrayList; import java.util.Date; import android.app.Activity; import android.content.SharedPreferences; import android.database.Cursor; import android.os.AsyncTask; import android.os.Bundle; import android.view.ContextMenu; import android.content.ComponentName; import android.content.Context; import android.content.Intent; import android.content.ServiceConnection; import android.os.IBinder; import android.view.KeyEvent; import android.view.Menu; import android.view.MenuItem; import android.view.View; import android.view.View.OnKeyListener; import android.widget.AdapterView; import android.widget.EditText; import android.widget.ListView; import android.widget.Toast; public class ToDoList extends Activity { static final private int ADD_NEW_TODO = Menu.FIRST; static final private int REMOVE_TODO = Menu.FIRST + 1; private static final String TEXT_ENTRY_KEY = "TEXT_ENTRY_KEY"; private static final String ADDING_ITEM_KEY = "ADDING_ITEM_KEY"; private static final String SELECTED_INDEX_KEY = "SELECTED_INDEX_KEY"; private boolean addingNew = false; private ArrayList<ToDoItem> todoItems; private ListView myListView; private EditText myEditText; private ToDoItemAdapter aa; int entries = 0; int notifs = 0; //ToDoDBAdapter toDoDBAdapter; Cursor toDoListCursor; TodoService mService; boolean mBound = false; /** Called when the activity is first created. */ public void onCreate(Bundle icicle) { super.onCreate(icicle); setContentView(R.layout.main); myListView = (ListView)findViewById(R.id.myListView); myEditText = (EditText)findViewById(R.id.myEditText); todoItems = new ArrayList<ToDoItem>(); int resID = R.layout.todolist_item; aa = new ToDoItemAdapter(this, resID, todoItems); myListView.setAdapter(aa); myEditText.setOnKeyListener(new OnKeyListener() { public boolean onKey(View v, int keyCode, KeyEvent event) { if (event.getAction() == KeyEvent.ACTION_DOWN) if (keyCode == KeyEvent.KEYCODE_DPAD_CENTER) { ToDoItem newItem = new ToDoItem(myEditText.getText().toString(), 0); mService.insertTask(newItem); updateArray(); myEditText.setText(""); entries++; Toast.makeText(ToDoList.this, "Entry added", Toast.LENGTH_SHORT).show(); aa.notifyDataSetChanged(); cancelAdd(); return true; } return false; } }); registerForContextMenu(myListView); restoreUIState(); populateTodoList(); } private void populateTodoList() { // Get all the todo list items from the database. toDoListCursor = mService. getAllToDoItemsCursor(); startManagingCursor(toDoListCursor); // Update the array. updateArray(); Toast.makeText(this, "Todo list retrieved", Toast.LENGTH_SHORT).show(); } private void updateArray() { toDoListCursor.requery(); todoItems.clear(); if (toDoListCursor.moveToFirst()) do { String task = toDoListCursor.getString(toDoListCursor.getColumnIndex(ToDoDBAdapter.KEY_TASK)); long created = toDoListCursor.getLong(toDoListCursor.getColumnIndex(ToDoDBAdapter.KEY_CREATION_DATE)); int taskid = toDoListCursor.getInt(toDoListCursor.getColumnIndex(ToDoDBAdapter.KEY_ID)); ToDoItem newItem = new ToDoItem(task, new Date(created), taskid); todoItems.add(0, newItem); } while(toDoListCursor.moveToNext()); aa.notifyDataSetChanged(); } private void restoreUIState() { // Get the activity preferences object. SharedPreferences settings = getPreferences(0); // Read the UI state values, specifying default values. String text = settings.getString(TEXT_ENTRY_KEY, ""); Boolean adding = settings.getBoolean(ADDING_ITEM_KEY, false); // Restore the UI to the previous state. if (adding) { addNewItem(); myEditText.setText(text); } } @Override public void onSaveInstanceState(Bundle outState) { outState.putInt(SELECTED_INDEX_KEY, myListView.getSelectedItemPosition()); super.onSaveInstanceState(outState); } @Override public void onRestoreInstanceState(Bundle savedInstanceState) { int pos = -1; if (savedInstanceState != null) if (savedInstanceState.containsKey(SELECTED_INDEX_KEY)) pos = savedInstanceState.getInt(SELECTED_INDEX_KEY, -1); myListView.setSelection(pos); } @Override protected void onPause() { super.onPause(); // Get the activity preferences object. SharedPreferences uiState = getPreferences(0); // Get the preferences editor. SharedPreferences.Editor editor = uiState.edit(); // Add the UI state preference values. editor.putString(TEXT_ENTRY_KEY, myEditText.getText().toString()); editor.putBoolean(ADDING_ITEM_KEY, addingNew); // Commit the preferences. editor.commit(); } @Override public boolean onCreateOptionsMenu(Menu menu) { super.onCreateOptionsMenu(menu); // Create and add new menu items. MenuItem itemAdd = menu.add(0, ADD_NEW_TODO, Menu.NONE, R.string.add_new); MenuItem itemRem = menu.add(0, REMOVE_TODO, Menu.NONE, R.string.remove); // Assign icons itemAdd.setIcon(R.drawable.add_new_item); itemRem.setIcon(R.drawable.remove_item); // Allocate shortcuts to each of them. itemAdd.setShortcut('0', 'a'); itemRem.setShortcut('1', 'r'); return true; } @Override public boolean onPrepareOptionsMenu(Menu menu) { super.onPrepareOptionsMenu(menu); int idx = myListView.getSelectedItemPosition(); String removeTitle = getString(addingNew ? R.string.cancel : R.string.remove); MenuItem removeItem = menu.findItem(REMOVE_TODO); removeItem.setTitle(removeTitle); removeItem.setVisible(addingNew || idx > -1); return true; } @Override public void onCreateContextMenu(ContextMenu menu, View v, ContextMenu.ContextMenuInfo menuInfo) { super.onCreateContextMenu(menu, v, menuInfo); menu.setHeaderTitle("Selected To Do Item"); menu.add(0, REMOVE_TODO, Menu.NONE, R.string.remove); } @Override public boolean onOptionsItemSelected(MenuItem item) { super.onOptionsItemSelected(item); int index = myListView.getSelectedItemPosition(); switch (item.getItemId()) { case (REMOVE_TODO): { if (addingNew) { cancelAdd(); } else { removeItem(index); } return true; } case (ADD_NEW_TODO): { addNewItem(); return true; } } return false; } @Override public boolean onContextItemSelected(MenuItem item) { super.onContextItemSelected(item); switch (item.getItemId()) { case (REMOVE_TODO): { AdapterView.AdapterContextMenuInfo menuInfo; menuInfo =(AdapterView.AdapterContextMenuInfo)item.getMenuInfo(); int index = menuInfo.position; removeItem(index); return true; } } return false; } @Override public void onDestroy() { super.onDestroy(); } private void cancelAdd() { addingNew = false; myEditText.setVisibility(View.GONE); } private void addNewItem() { addingNew = true; myEditText.setVisibility(View.VISIBLE); myEditText.requestFocus(); } private void removeItem(int _index) { // Items are added to the listview in reverse order, so invert the index. //toDoDBAdapter.removeTask(todoItems.size()-_index); ToDoItem item = todoItems.get(_index); final long selectedId = item.getTaskId(); mService.removeTask(selectedId); entries--; Toast.makeText(this, "Entry deleted", Toast.LENGTH_SHORT).show(); updateArray(); } @Override protected void onStart() { super.onStart(); Intent intent = new Intent(this, TodoService.class); bindService(intent, mConnection, Context.BIND_AUTO_CREATE); } @Override protected void onStop() { super.onStop(); // Unbind from the service if (mBound) { unbindService(mConnection); mBound = false; } } private ServiceConnection mConnection = new ServiceConnection() { public void onServiceConnected(ComponentName className, IBinder service) { LocalBinder binder = (LocalBinder) service; mService = binder.getService(); mBound = true; } public void onServiceDisconnected(ComponentName arg0) { mBound = false; } }; public class TimedToast extends AsyncTask<Long, Integer, Integer> { @Override protected Integer doInBackground(Long... arg0) { if (notifs < 15) { try { Toast.makeText(ToDoList.this, entries + " entries left", Toast.LENGTH_SHORT).show(); notifs++; Thread.sleep(20000); } catch (InterruptedException e) { } } return 0; } } } TodoService.java: package com.examples.todolist; import android.app.Service; import android.content.ContentResolver; import android.content.ContentValues; import android.content.Intent; import android.database.Cursor; import android.os.Binder; import android.os.IBinder; public class TodoService extends Service { private final IBinder mBinder = new LocalBinder(); @Override public IBinder onBind(Intent arg0) { return mBinder; } public class LocalBinder extends Binder { TodoService getService() { return TodoService.this; } } public void insertTask(ToDoItem _task) { ContentResolver cr = getContentResolver(); ContentValues values = new ContentValues(); values.put(TodoProvider.KEY_CREATION_DATE, _task.getCreated().getTime()); values.put(TodoProvider.KEY_TASK, _task.getTask()); cr.insert(TodoProvider.CONTENT_URI, values); } public void updateTask(ToDoItem _task) { long tid = _task.getTaskId(); ContentResolver cr = getContentResolver(); ContentValues values = new ContentValues(); values.put(TodoProvider.KEY_TASK, _task.getTask()); cr.update(TodoProvider.CONTENT_URI, values, TodoProvider.KEY_ID + "=" + tid, null); } public void removeTask(long tid) { ContentResolver cr = getContentResolver(); cr.delete(TodoProvider.CONTENT_URI, TodoProvider.KEY_ID + "=" + tid, null); } public Cursor getAllToDoItemsCursor() { ContentResolver cr = getContentResolver(); return cr.query(TodoProvider.CONTENT_URI, null, null, null, null); } } TodoProvider.java: package com.examples.todolist; import android.content.*; import android.database.Cursor; import android.database.SQLException; import android.database.sqlite.SQLiteOpenHelper; import android.database.sqlite.SQLiteDatabase; import android.database.sqlite.SQLiteQueryBuilder; import android.database.sqlite.SQLiteDatabase.CursorFactory; import android.net.Uri; import android.text.TextUtils; import android.util.Log; public class TodoProvider extends ContentProvider { public static final Uri CONTENT_URI = Uri.parse("content://com.examples.provider.todolist/todo"); @Override public boolean onCreate() { Context context = getContext(); todoHelper dbHelper = new todoHelper(context, DATABASE_NAME, null, DATABASE_VERSION); todoDB = dbHelper.getWritableDatabase(); return (todoDB == null) ? false : true; } @Override public Cursor query(Uri uri, String[] projection, String selection, String[] selectionArgs, String sort) { SQLiteQueryBuilder tb = new SQLiteQueryBuilder(); tb.setTables(TODO_TABLE); // If this is a row query, limit the result set to the passed in row. switch (uriMatcher.match(uri)) { case TASK_ID: tb.appendWhere(KEY_ID + "=" + uri.getPathSegments().get(1)); break; default: break; } // If no sort order is specified sort by date / time String orderBy; if (TextUtils.isEmpty(sort)) { orderBy = KEY_ID; } else { orderBy = sort; } // Apply the query to the underlying database. Cursor c = tb.query(todoDB, projection, selection, selectionArgs, null, null, orderBy); // Register the contexts ContentResolver to be notified if // the cursor result set changes. c.setNotificationUri(getContext().getContentResolver(), uri); // Return a cursor to the query result. return c; } @Override public Uri insert(Uri _uri, ContentValues _initialValues) { // Insert the new row, will return the row number if // successful. long rowID = todoDB.insert(TODO_TABLE, "task", _initialValues); // Return a URI to the newly inserted row on success. if (rowID > 0) { Uri uri = ContentUris.withAppendedId(CONTENT_URI, rowID); getContext().getContentResolver().notifyChange(uri, null); return uri; } throw new SQLException("Failed to insert row into " + _uri); } @Override public int delete(Uri uri, String where, String[] whereArgs) { int count; switch (uriMatcher.match(uri)) { case TASKS: count = todoDB.delete(TODO_TABLE, where, whereArgs); break; case TASK_ID: String segment = uri.getPathSegments().get(1); count = todoDB.delete(TODO_TABLE, KEY_ID + "=" + segment + (!TextUtils.isEmpty(where) ? " AND (" + where + ')' : ""), whereArgs); break; default: throw new IllegalArgumentException("Unsupported URI: " + uri); } getContext().getContentResolver().notifyChange(uri, null); return count; } @Override public int update(Uri uri, ContentValues values, String where, String[] whereArgs) { int count; switch (uriMatcher.match(uri)) { case TASKS: count = todoDB.update(TODO_TABLE, values, where, whereArgs); break; case TASK_ID: String segment = uri.getPathSegments().get(1); count = todoDB.update(TODO_TABLE, values, KEY_ID + "=" + segment + (!TextUtils.isEmpty(where) ? " AND (" + where + ')' : ""), whereArgs); break; default: throw new IllegalArgumentException("Unknown URI " + uri); } getContext().getContentResolver().notifyChange(uri, null); return count; } @Override public String getType(Uri uri) { switch (uriMatcher.match(uri)) { case TASKS: return "vnd.android.cursor.dir/vnd.examples.task"; case TASK_ID: return "vnd.android.cursor.item/vnd.examples.task"; default: throw new IllegalArgumentException("Unsupported URI: " + uri); } } // Create the constants used to differentiate between the different URI // requests. private static final int TASKS = 1; private static final int TASK_ID = 2; private static final UriMatcher uriMatcher; // Allocate the UriMatcher object, where a URI ending in 'tasks' will // correspond to a request for all tasks, and 'tasks' with a // trailing '/[rowID]' will represent a single task row. static { uriMatcher = new UriMatcher(UriMatcher.NO_MATCH); uriMatcher.addURI("com.examples.provider.Todolist", "tasks", TASKS); uriMatcher.addURI("com.examples.provider.Todolist", "tasks/#", TASK_ID); } //The underlying database private SQLiteDatabase todoDB; private static final String TAG = "TodoProvider"; private static final String DATABASE_NAME = "todolist.db"; private static final int DATABASE_VERSION = 1; private static final String TODO_TABLE = "todolist"; // Column Names public static final String KEY_ID = "_id"; public static final String KEY_TASK = "task"; public static final String KEY_CREATION_DATE = "date"; public long insertTask(ToDoItem _task) { // Create a new row of values to insert. ContentValues newTaskValues = new ContentValues(); // Assign values for each row. newTaskValues.put(KEY_TASK, _task.getTask()); newTaskValues.put(KEY_CREATION_DATE, _task.getCreated().getTime()); // Insert the row. return todoDB.insert(TODO_TABLE, null, newTaskValues); } public boolean updateTask(long _rowIndex, String _task) { ContentValues newValue = new ContentValues(); newValue.put(KEY_TASK, _task); return todoDB.update(TODO_TABLE, newValue, KEY_ID + "=" + _rowIndex, null) > 0; } public boolean removeTask(long _rowIndex) { return todoDB.delete(TODO_TABLE, KEY_ID + "=" + _rowIndex, null) > 0; } // Helper class for opening, creating, and managing database version control private static class todoHelper extends SQLiteOpenHelper { private static final String DATABASE_CREATE = "create table " + TODO_TABLE + " (" + KEY_ID + " integer primary key autoincrement, " + KEY_TASK + " TEXT, " + KEY_CREATION_DATE + " INTEGER);"; public todoHelper(Context cn, String name, CursorFactory cf, int ver) { super(cn, name, cf, ver); } @Override public void onCreate(SQLiteDatabase db) { db.execSQL(DATABASE_CREATE); } @Override public void onUpgrade(SQLiteDatabase db, int oldVersion, int newVersion) { Log.w(TAG, "Upgrading database from version " + oldVersion + " to " + newVersion + ", which will destroy all old data"); db.execSQL("DROP TABLE IF EXISTS " + TODO_TABLE); onCreate(db); } } } I've omitted the other files as I'm sure they are correct. When I run the program, LogCat shows that the NullPointerException occurs in populateTodoList(), at toDoListCursor = mService.getAllToDoItemsCursor(). mService is the Cursor object returned by TodoService. I've added the service to the Manifest file, but I still cannot find out why it's causing an exception. Thanks in advance.

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