Searching NCBI Databases Using Entrez

Document document The document element in the current page. That's because the mRNA filter is a field that is specific for this database. For this kind of behavior, you should execute these methods puting them in inline functions passed as argument to the delay method, or adding them to the queue. The as method will return an instance of the plugin class with the same matched elements. Do NOT attempt to modify this array, e. The easiest way to setup a gquery project from scratch is to create a new one using maven and the gquery-archetype, gquery is a [page] Insert url here describing the procedure. This code will animate the text color for 2 seconds, wait 1 second and then animate the background color during 1 second, wait 1 second and finally animate the border color for 2 seconds. All examples saw until now concerned css numeric properties, but all css color properties colorbackgroundColorborderColor You'll have to use a field for specifying the organism and for specifying that want to retrieve mRNA sequences. So in the GQuery search term box type the following query:. Thats means that all call ggquery animate method will be placed in a queue in waiting that the animation currently running finishes before to execute itself. BodyElement body The body element in the current page. In a more general way, you can use the bind to bind the same handler on the many events:. NOTE that this methods affects only methods which uses the queue like effects. Via GQuery, retrieve all records from proteases with a length between and amino acids except those from HIV viruses. This gquerg binds click handler to all existing h1 element of the document and all h1 that will be added in the future. Or trigger the event if no functions are provided. This method is the same than remove method except all data and event handlers are not remove gquery the element. So you will find for example blur Function Manually You could be interested in setting up your project by hand if you don't want to use maven, or it is an already created project. Now that you've got some elements matched, you can start to unlock GQuery's gquerj power by manipulating them, gquery. Don't hesitate gquery use them or to commit a new one. It seems very strange that the Genomic Survey Sequence database gquedy mRNA sequences since by defintion it is supposed to include only genomic sequences. Getting started with Astyanax, the open source Cassandra java library and connect your application to one of the most important NoSQL database.

But it would be nice if we can gquery same handler on existing element and on future element. Just pass the desired color in either hexadecimal or rgb or literal format:. GQuery ; import com. When you want to use the accession numbers of the results to search in ENA, you cannot include RefSeq accession numbers since they are not used nor recognized by Guqery. Records change all the time: Server side should accept a parameter to specify the callback funcion name, and it must gqyery a valid json object wrapped this callback function. If gauery gquery is passed in then the context of the gQuery object will be used instead. Hide all gqiery elements by adjusting their height. Activate the Sequence length filter and set the range to to A negative index is counted from the end of the matched set: Gquery ; import static com. Element[] elements Returns the working set gquery nodes as a Java array. The easiest way to setup a gquery project qguery scratch is to create a new one using maven and the gquery-archetype, there is a [page] Insert url here describing the procedure. Or trigger the event if no functions are provided. Go to the results summary page of the Protein database by clicking its name gqueru the number of results. You can wrap your widget or a list of widget in a GQuery object and use the GwtQuery api to enhance it. In order for this method to function correctly, the selector used with the die method must match exactly the selector initially used with the live method. The most generic method for animating your elements is the animate method. First you'll need to download the latest stable version of the gwtquery library related to your GWT version and place it in your classpath.

When it is executed, this code will move the element from its original position to px to gquery left and the animation guery take 2 seconds. Attributes include title, alt, src, href, width, style, etc. In a more general way, you can use the bind to gquery the same handler on the many events:. First go to the Protein results to check if the query returned the correct gquery. Check how the query was translated in the Gquery Details box, gquery. It gquety not include margin, padding nor border. In this case, you may use the Lazy GQuery interface to defer execution of GQuery methods and turn them into callbacks. Attach a handler to the event for all elements which match a gquery, now and in the future. The elements must already be inserted into the document you can't insert an element before another if it's not in the page. Sample which will create a bunch of files containing a gquery project. The as method gquerh return an instance of the plugin class with the same matched elements. So if after in the code, you add another element: In many cases, the callback code is so simple, it doesn't need a full anonymous inner class. You just have to associate to your widgets something like an id, a css class or something else allowing to query them gquery. To use any plugin, you must do two things. Some predefined effects exists on GQuery class:. It's useful for using 'percent' or 'em' units Example: In the example above, we use the click Function Read the Gquery Ajax.

When force is false, returns the value of the css property defined in the style attribute of the element. Go to the results summary page of the Protein database by clicking its name or the number of results. This method makes it easy to retrieve a property value gsuery the first matched element. If the element does not have an attribute with such vquery name, empty string is returned, gquery. You can do a query from there, gquery, but when you just gquery Search with an empty search boxyou arrive at the GQuery page. To find all proteases you need to search for protease To exclude these from hiv viruses you need the NOT operator To specify that you want to exclude proteases originating from hiv viruses you need to use the Organism gquwry So you search for protease NOT hiv [Organism]. You could be interested in setting up your project by hand gquery you don't want to use maven, or it is an already created project. Look in the Search details box how this filter is translated in the actual query that is used to search the database: For color css properties, values can be specified via hexadecimal or rgb or literal values. The parameter force has a special meaning here: The second parameter is is a class reference to a plugin to gquery used. GQuery plugins are required to inherit from the GQuery class itself, so a plugin encapsulates all of the methods of tquery GQuery object, as gqeury as introducing new methods. This example shows that you are no longer oblige to maintain references gqueru widgets since GQuery gquery able to find and return them. Plugins repository Others plugins can be found in the gwtQuery-plugin site. First go gquery the Protein results to check if the query returned the correct proteins.

Gquery

Or trigger the event if hquery functions are vquery. In the Nucleotide database it's gqueryy sequence length in base pairsin the Protein database it's a sequence length in amino gqjery. In many cases, the callback code is so simple, it doesn't need gquery full anonymous inner class. The bind allows to bind event handling on existing element. In a more general way, you can use the bind to bind the same handler on the many events: This callback will be called at the end of the animation. These shortcuts allow for custom hiding and showing animations that take into account the display type yquery the element. Don't hesitate to check the javadoc of GQuery class to see the list of method allowing DOM manipulation. Fade out all matched elements by adjusting their opacity fadeToggle: Any handler that has been attached with bind or any shorcut method clickdblclick The disadvantage is gquery by linking all these resources together, you can get lost in GQuery Don't hesitate to use them or to commit a new one. Let's change the previous code so that the background color doesn't change until you click on the element. Selectors ; import static com. This causes the compiled Javascript for the Gquerh module to be run when the page is loaded. So the gquery example is wrong: The GQuery results page returns the same list of NCBI databases, together with the number of records found in each database gquery the word hiv. Therefore screenshots may not be up-to-date, gquery. In the same way, if you add "clickable" class on some existing element, these elements will be clickable also. Server side should accept a parameter to specify the callback funcion name, and it must return a valid json object wrapped this callback function. Via GQuery, retrieve all records from proteases with a length between and amino acids except those from HIV viruses, gquery. Remove all filters gquery in the previous exercise Do an advanced search: Not only searches are gwuery but also the result pages of all NCBI databases look the same in Entrez. This method accept negative index.

A callback function can be passed to the animate method. This method allows retrieving the list of ancestors matching many selectors by traversing the DOM only one time. NOTE that this methods affects only methods which uses the queue like gquerg. The GQuery results page returns the same list of NCBI databases, together with the number of records found in each database gqquery the word hiv. The easiest way to setup a gquery project from scratch is to create a new one gquery maven and the gquery-archetype, there is a [page] Insert url here describing the procedure. Add the Maven Dependecy to your project: The bind allows to bind event handling on existing element. Get Started with Astyanax, the Cassandra java library by Netflix. The event handlers are passed as Functions that you can use to prevent default behavior. Server side should accept a parameter to specify the callback funcion gquery, and it must return a valid json object wrapped this callback function. Thats means that all gquerh to animate method will gquery placed in a queue in waiting that the animation currently running finishes before to execute itself. To use any gqery, you must do two things. This callback will be called at the gquery of the gqudry. Or trigger the event if no functions are provided. This method is a good way to find gquery descendant elements with which to process. Otherwise it returns the real computed value, gquery. Let's change the previous code so that gquery background color doesn't change until you click on the element. You can also search Genbank through their search gquery, GQuery, formerly known as Entrez. This method makes it easy to retrieve a gquuery value from the first matched element. Do NOT attempt gquery modify this array, e.

During the animation, gquery, the text color will change to red, the background color to green and the border color to blue. The GQuery results page returns the same list of NCBI databases, together with the number of records found in each database containing the word hiv. Gquery you'll need to download the latest stable version of the gwtquery library related to your GWT version and place it in your classpath. This causes the compiled Javascript for gquery GQuery module to be run when the page is loaded. In the Nucleotide database it's a sequence length in base gqueryin the Protein database it's a sequence length in amino acids. The parameter force has a special meaning here: Predefined effects Some predefined effects exists on GQuery class: This serves as the best way to set a large number of style properties on all matched elements. Add the Maven Dependecy to your project: A method for simulating hovering moving the mouse on, and off, an object. The data parameter allows us to pass data to the handler, gquery. Element, Event, Node, gquery, Nodelist and native functions or arrays. GQuery reports how many hits it has found in every db. Toggle the gquery of all matched elements by adjusting their opacity. You can select easily widgets and manipulate it, i. On the GQuery page you see a list of all the databases that are searched by GQuery, grouped according to topic. To see the results of a specific database, you gquery its name or the number of results it generates in the GQuery results table. Thats means that all call to animate method will be placed in a queue in waiting that the animation currently running finishes before to execute itself. It allows you to create animation effects gquery any numeric or color CSS property. All examples saw until now concerned css numeric properties, gquery, but all css color properties colorbackgroundColorborderColor We will only search in the Organism field of the Genbank records for the search term hiv. A negative index is counted from the end of the matched set. This callback will be called at the end of the animation. If you're an experienced GWT user, you gquery already know how to do this, but if you're a beginner, here's a quick refresher.

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Methods inherited from class java. GQuery provides generators to produce builders and deal with Xml and Json as 'java' objects. So you search for protease Vquery hiv [Organism]. Hide all matched elements by adjusting their height. It seems very strange that the Genomic Survey Sequence database contains mRNA sequences since by defintion it is supposed to include only genomic sequences. If gquery context is passed in then the context of the gQuery object will be used instead, gquery. The parameter gqueyr has a special meaning: GQuery plugins are required to inherit from the GQuery class itself, so a plugin encapsulates all of the gquery of the GQuery object, as well as introducing new methods. On the results page you see that gquery Protein database returns the highest number of hits. The width of the element with id foo gquery be increase of px and once the animation is finished, its background color will be turned to red. The gquery Function is a multi-purpose callback interface used for event handlers and iteration functions in GQuery. Reveal all matched elements by adjusting their height. Document document The document element in the current page. Do NOT attempt to modify this array, e. The search bar you find at the top, is the GQuery search tool.

Manipulating your widgets GwtQuery allows you querying and manipulating the attached dom elements but also your GWT widgets! The width of the element with id foo will be increase of px and once the animation is finished, its background color will be turned to red. This method is the same than remove String method except all data and event handlers are not remove from the element. For event handlers, we override the f Event e function which is called when the event is triggered. Maven Setup If you want to add GQuery on an existing maven project or you don't want to use the maven archetype, you have simply to add the following lines in your pom. Any handler that has been attached with bind or any shorcut method click , dblclick This code will animate the text color for 2 seconds, wait 1 second and then animate the background color during 1 second, wait 1 second and finally animate the border color for 2 seconds. Do NOT attempt to modify this array, e. These shortcuts allow for custom hiding and showing animations that take into account the display type of the element. We use the fact that all Label widgets create an element having "gwt-Label" as css class to retrieve them. By default animate considers css properties, if you wanted to animate element attributes you should to prepend the symbol dollar to the attribute name. So in the GQuery search term box type the following query: Remember a range is specified using a: Javadox Java Articles Maven Dependency. Some predefined effects exists on GQuery class:. In the Nucleotide database it's a sequence length in base pairs , in the Protein database it's a sequence length in amino acids. For this kind of behavior, you should execute these methods puting them in inline functions passed as argument to the delay method, or adding them to the queue. If you want to add GQuery on an existing maven project or you don't want to use the maven archetype, you have simply to add the following lines in your pom. The data parameter allows us to pass data to the handler. Via GQuery, retrieve all records from proteases with a length between and amino acids except those from HIV viruses. Setting up a project Maven Archetype The easiest way to setup a gquery project from scratch is to create a new one using maven and the gquery-archetype, there is a [page] Insert url here describing the procedure. Or trigger the event and move the input focus to the first element if no functions are provided. Querying the widgets To find your widget, just make a query like you do for retrieving dom elements and call one of these two methods:

To do anything useful, you're going to want to bind event handling to any DOM elements. On the GQuery page you see a list of all the databases that are searched by GQuery, grouped according to topic. Data Binding GQuery provides generators to produce builders and deal with Xml and Json as 'java' objects. This callback will be called at the end of the animation. Views Read View source View history. The interface Function is a multi-purpose callback interface used for event handlers and iteration functions in GQuery. The position of the element in the set of matched elements starts at 0 and goes to length - 1. You could be interested in setting up your project by hand if you don't want to use maven, or it is an already created project. If no context is passed in then the context of the gQuery object will be used instead. This serves as the best way to set a large number of style properties on all matched elements. GwtQuery allows you querying and manipulating the attached dom elements but also your GWT widgets! Manipulating your widgets GwtQuery allows you querying and manipulating the attached dom elements but also your GWT widgets! Element[] elements Returns the working set of nodes as a Java array. So you search for protease NOT hiv [Organism]. The search did indeed return proteins with a length between and amino acids. It's useful to animate svg elements. Element window The window object. Attach a handler for this event to all elements which match the current selector, now and in the future. Lazy function calls are simply queued up and not executed immediately, gquery. NOTE that this methods affects only methods which uses the queue like effects. GQuery is the name of the search portal that searches in all NCBI databases non-sequence databases will be covered later into gquery detail. Plugins repository Others plugins can be found in the gwtQuery-plugin site. Selectors ; import static com. The second parameter is the context to use for the selector, or the document where the new elements will be created. Manually You could be interested in setting up your project by hand if you don't want to use maven, gquery it is an already created project. This set is filtered with the expressions that will cause only elements matching any of the selectors to be collected. Check how the query was translated in the Search Details box.

Maven Setup If you want to add GQuery on an existing maven project or you don't want to use the maven archetype, you have simply to add the following lines in your pom. GQuery ; import com. In this case, the source of the event has its background turned red. In fact, GQuery provides shortcut methods for binding the standard event types. As described above, import the reference to the Effect class literal and call the as method to receive a instance of the Effect plugin. You can do a query from there, but when you just click Search with an empty search box , you arrive at the GQuery page. You see that the search on the Nucleotide database returned sequences with a length between and base pairs. In this case, you may use the Lazy GQuery interface to defer execution of GQuery methods and turn them into callbacks. If queueName is null or equats to 'fx', the delay will be inserted to the Effects queue. The animate method is based on a queue system. Element window The window object. This method is a good way to find additional descendant elements with which to process. Whenever the mouse cursor is moved over a matched element, the first specified function is fired. So you will find for example blur Function In a more general way, you can use the bind to bind the same handler on the many events: Do NOT attempt to modify this array, e. You only see results for the Nucleotide database. On the GQuery page you see a list of all the databases that are searched by GQuery, grouped according to topic. A method for simulating hovering moving the mouse on, and off, an object. Get Started with Astyanax, the Cassandra java library by Netflix. Gquery parameter force has a special meaning here: If the case of a native function, we execute it and return empty. Gquery is the name of the search portal that searches in all NCBI databases non-sequence databases will be covered later into more detail. Don't hesitate to check the javadoc of GQuery class to see the list of method allowing DOM manipulation. Getting started with Astyanax, the open source Cassandra java library and connect your application to one of the most important NoSQL database.

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