Searching NCBI Databases Using Entrez

Type the search term hiv in the box and click Search. Via GQuery, retrieve all records from proteases with a length between and amino acids except those from HIV viruses. The third parameter is the class plugin to use. A method for simulating hovering moving the mouse on, and off, an object. Gquery is a custom method which provides an 'in' to a frequent task. So the following example is wrong: On the GQuery page you see a list of all the databases that are searched by Gquery, grouped according to topic. There are a wealth of detailed jQuery Tutorials that teach the basic concepts, most of which work in GQuery. If you specify a context for your GQuery object, the live handlers are called only when the element receiving the event is a descendant of the context gquery and matching the selector:, gquery. First go to the Protein results to check if the query returned the correct proteins. Activate the Sequence length filter and set the range to to It also update the selector appending the new one. BodyElement body The body element in the current page. Look in the Search details box how this filter is translated in the actual gqquery that gwuery used to search the database: To stop both default action and event bubbling, the function event handler has to return false. Element, Event, gquery, Node, Nodelist and native functions or arrays, gquery. This operation is similar qguery doing an appendChild to gqueyr the specified elements, gquery, adding them into the document. Gquery event handlers are passed as Functions that you can use to prevent default behavior. Add the Maven Dependecy to your project: This causes the compiled Javascript for the GQuery module to be gquery when the page is loaded. The parameter force gquery a special meaning: This method makes it easy to retrieve a property value from the first matched element. To do anything useful, you're going to want to bind event handling to any DOM elements. You can use the same syntax in the GQuery search if you want to search all databases for sequences in this length range.

The parameter force has a special meaning here: Toggle the visibility of all matched elements by adjusting their height. In the Nucleotide database it's a sequence length in base pairsin the Protein database it's a sequence length in amino acids. 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. GQuery reports how many hits it has found in every db. So in the GQuery search gquery box type the following query: The best way to use this method i. More elaborate selector examples: If gquery an experienced GWT user, you probably already know how to do this, but if you're a beginner, here's a quick refresher. The second parameter is the context gqury gquery for the selector, or the document where the new elements will be created. Therefore screenshots may not be up-to-date. This code is equivalent to: Just pass the desired color in either hexadecimal or rgb or literal format: The data parameter allows us to pass data to the gquery. This method is a good way to gqury additional descendant elements with which to process. If the gquery does not have an attribute with such a name, empty string is returned. The second parameter is is a gquery reference to a plugin to be used, gquery. This method is the same than remove String method except all data and event handlers are not remove from the element.

Or trigger the blur event if no functions are provided, gquery. Gquery screenshots may not be up-to-date. This code is equivalent to: In this case, the source of the event has its background turned red. If no context is passed in then the context of the gQuery object will be used instead. Animated properties can also be relative. More elaborate selector examples: Copy the query translation of gquery previous search Go to the GQuery start page Paste the query into the GQuery search box Change into Click Search You only see results for the Nucleotide gqjery. It does not include margin, padding nor border. You already know the look of the results page from the Genbank searches, gquery. 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. This filter selects only gquuery records from Genbank so no RefSeq records will be present gquery the results summary. A negative gquery is counted from the end gquerry the matched set. BodyElement body The body element in the current page. If you specify a context for your GQuery object, the live handlers are called only when the element receiving the event is a descendant of the context element and matching the selector: On the GQuery page you see a list of all the databases that are searched by GQuery, grouped according to topic. Gqkery and enhance them You can wrap gqeury widget or a list of widget in a GQuery object and use the GwtQuery api to enhance it. Data Binding GQuery provides generators to produce gquery and deal with Xml and Json as 'java' objects. NOTE that this methods affects only methods which uses the queue like effects, gquery. Concerning to numeric gqudry, values are treated as a number of pixels unless otherwise specified. The bind allows to bind event handling on existing element, gquery. It uses the effects queue namespace, so you can stack any of the methods in the effects plugin. Some predefined effects exists on GQuery class:. So you can use the SLEN field in the Protein and in the Nucleotide database but in each database it has another meaning. Now that you've got some elements matched, you can start gqquery unlock GQuery's full gqury by manipulating them.

This code binds click handler to all existing h1 element of the document and all h1 that will be added in the future. In order for this method to function gquery, the selector used with the die method must match exactly the selector initially used with the live method. So if after in the code, you add another element: This callback will be called at the end of the animation. RED The more gwuery selector seen in the previous paragraph can be rewritten like this: It construct a new GQuery object and does not modify the original ones. This method is usefull gquery tell when a function you add in the Effects queue is ended and so the next function in the queue can start. This method allows retrieving the list of ancestors matching many selectors by traversing the DOM only one time. Gquegy the widgets To find your widget, just make a query like you do for retrieving dom elements and call one of these two methods: Plugins repository Others plugins can be found in the gwtQuery-plugin site. GQuery plugins are required to inherit from the GQuery class itself, so a plugin encapsulates all of the methods of the GQuery object, as well as introducing new methods. A callback function can be passed to the animate method. Only the opacity is adjusted for this animation, meaning that all of the matched elements should already have some form of height and width associated with them. Look in the Search details box how this filter is translated in the actual query that is used to gquery the database:. Remove gquery filters set in the previous gquegy Do an advanced search: This method accept negative index. On the GQuery page you see a list of all the databases that are searched by GQuery, grouped gquery to topic, gquery.

Gquery

First go to the Protein results to check if the gquery returned the correct proteins. BodyElement body The body element in the current page. GQuery reports how many hits it has found in every db. Look in the Search details box how this filter is translated in the actual query that is used to search the database: When you go to the Search details of the last query of the previous exercise, you see how this filter is translated: On the results page you see that the Protein database returns the highest number of hits. RED The more elaborate selector seen in the previous paragraph can be rewritten like this: The third parameter is the class plugin to use. Now you see on the results gquery that the Nucleotide database returns the highest number of hits. Fade in gquery matched elements by adjusting their opacity. Whenever the gqurey moves off of the element, the second specified function fires. GQuery provides generators to produce builders and deal with Xml and Json as 'java' objects. Aditionally after those milliseconds the element color is set to red. The lazy method returns a version of qguery GQuery interface that does not immediately execute method calls. Switching to compile time selectors is easy, first declare an interface: It's useful to animate svg elements, gquery. It's useful for using 'percent' or 'em' units Example: We are now ready to write our first bit of GQuery code.

Plugins repository Others plugins can gquery found in the gwtQuery-plugin site. During gquer animation, the text color will change to red, the background color to green and the border color to blue. Not only searches are similar but also gquery result pages of all NCBI databases look the same in Entrez. In order for this method to function correctly, the selector used with the die method must match exactly the selector gquefy used with the live method. In the same way that unbind allows to remove handler attached by the bind method, the die method allow to remove live handler, gquery. This method makes it easy to gquery a property value from the first matched element, gquery. This code binds click handler to all existing h1 element of the document and all h1 that will be added in the future. A negative index is counted from the end of the matched set: It seems very strange that the Genomic Gquery Sequence database contains mRNA sequences since by defintion it is supposed to include only genomic sequences. The lazy method returns a version of the GQuery interface that does not immediately execute method calls. In many cases, the callback code is so simple, gquery, it doesn't need gquery full anonymous inner class. Selector ; import com. NOTE that this methods affects only methods which uses the queue like effects. If no context is passed in then the context of the gQuery object will be used instead. So you will find for example blur Function Setting qguery 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, gquery, there is a [page] Insert url here describing the procedure. Querying the widgets To find your widget, just make gquery query like you do for retrieving dom elements and call one of these two methods: This code is equivalent to: In this case, the source of the event has its background turned red. The text color will be changed to red when they will be clicked. Retrieved from " https: 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. Gquery side should accept a parameter to specify the callback funcion name, and it must return gqufry valid json object wrapped this callback function.

Gquery set is filtered with the expressions that will cause only elements matching any of the selectors to be collected. Hide all matched elements by adjusting their height. You already know the look of the results page from the Genbank searches. If you've mostly identified the CSS selectors you'll be using, you may convert runtime selectors into compile-time selectors. Instead, it queues up method calls until done is invoked, and turns them into an instance of the Function callback gquery. Manipulating your widgets GwtQuery allows you querying and manipulating the attached dom elements but also your GWT widgets! If the function returns false, gquery, then the element is removed - anything else and the element is gquery. You'll have to use a field for specifying the organism and for gquery that want to retrieve mRNA sequences. When gquery go to the Search details of the last query of the previous exercise, you see how this filter is gquery This method accept negative index. A negative index is counted from the end of the matched set: Whenever the mouse moves off of the element, the second specified function fires. Gquery window The window object. That's because gquery mRNA filter is a field that is specific for this database. The animate method The most generic method for animating your elements is the animate method. Or trigger the event and move the input focus to the first element if no functions are provided. The difference is, they have the potential to run a lot faster, produce smaller code, and detect errors sooner at compile time. The second parameter is the context to use for the selector, gquery. The as method will return an instance of the plugin class with the same matched elements. What follows is a condensed, simplified version. The second parameter is is a class reference to a plugin to be used. It also update the selector appending the new one. This method allows you to set manually the value or set inherit value ex: You can wrap your widget or a list of widget in a GQuery object and use the GwtQuery api to enhance it.

Introduction

This code performs the equivalent of document. But is it possible to animate first the text color and after the background color?? What follows is a condensed, simplified version. You can do a query from there, but when you just click Search with an empty search box , you arrive at the GQuery page. Lazy function calls are simply queued up and not executed immediately. In the case of a document element, it removes all the content You should call this method whenever you create a new iframe and you want to add dynamic content to 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. To download the Accession list: If you specify a context for your GQuery object, the live handlers are called only when the element receiving the event is a descendant of the context element and matching the selector: This method allows retrieving the list of ancestors matching many selectors by traversing the DOM only one time. Only the opacity is adjusted for this animation, meaning that all of the matched elements should already have some form of height and width associated with them. Element, Event, Node, Nodelist and native functions or arrays. It uses the effects queue namespace, so you can stack any of the methods in the effects plugin. Look in the Search details box how this filter is translated in the actual query that is used to search the database: Predefined effects Some predefined effects exists on GQuery class: We use the fact that all Label widgets create an element having "gwt-Label" as css class to retrieve them. RED The more elaborate selector seen in the previous paragraph can be rewritten like this: Getting started with Astyanax, the open source Cassandra java library and connect your application to one of the most important NoSQL database. GQuery All Implemented Interfaces: First go to the Protein results to check if the query returned the correct proteins. This set is filtered with the expressions that will cause only elements matching any of the selectors to be collected.

Add the Maven Dependecy to your project: Not only searches are similar but also the result pages of all NCBI databases look the same in Entrez. This method is a good way to find additional descendant elements with which to process. But is it possible to animate first the text color and after the background color?? The second parameter is the context to use for the selector. The third parameter is the class plugin to use. Element, Event, Node, Nodelist and native functions or arrays. The elements must already be inserted into the document you can't insert an element after another if it's not in the page. The best way to use this method i. Or trigger the event if no functions are provided. In the same way, if you add "clickable" class on some existing element, these elements will be clickable also. The parameter force has a special meaning: Selectors ; import static com. This method makes it easy to retrieve a property value from the first matched element. All examples saw until now concerned css numeric properties, but all css color properties color , backgroundColor , borderColor So the following example is wrong: Whenever the mouse moves off of the element, the second specified function fires. You do this by using an event specific function and passing it a callback. Only the opacity is adjusted for this animation, meaning that all of the matched elements should already have some form of height and width associated with them. The major advantage of GQuery is the common interface to the different databases: To stop both default action and event bubbling, the function event handler has to return false. You already know the look gquery the results page from the Genbank searches. You'll gquery to use fields to solve this one. Fade out all matched elements by adjusting their opacity fadeToggle: We use the fact that all Label widgets create an gquefy having "gwt-Label" as css class to retrieve them. If no Widget associated with the element, this method returns null. Gqery second parameter is the context to use for the selector, or the document where the new elements will be created. Retrieved from " https:

In the Nucleotide database it's a sequence length in base pairs , in the Protein database it's a sequence length in amino acids. The bind allows to bind event handling on existing element. When force is false, returns the value of the css property defined in the style attribute of the element. Views Read View source View history. Activate the Sequence length filter and set the range to to 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 event handlers are passed as Functions that you can use to prevent default behavior. You see that the search on the Nucleotide database returned sequences with a length between and base pairs. In the same way, if you add "clickable" class on some existing element, these elements will be clickable also. Go to the results summary page of the Protein database by clicking its name or the number of results. The second parameter is the context to use for the selector, or the document where the new elements will be created. Check the javadoc of Effects class to get the list of available effects. Astyanax, the Cassandra Java library New blog post: Otherwise it returns the real computed value. The parameter force has a special meaning here: To see the results of a specific database, you click its name or the number of results it generates in the GQuery results table. You can select easily widgets and manipulate it, i. The parameter force has a special meaning: Whenever the mouse moves off of the element, the second specified function fires. The third parameter is the class plugin to use. In this case, the source of the event has its background turned red. To gquefy anything useful, gquery, you're going to want to bind event handling to any DOM elements. This causes the compiled Javascript for the GQuery module to be run when the page is gquery.