Welcome to the GenomeQuest Documentation Wiki
The filtering widget is available at the top of the GenomeQuest page when browsing results of sequence or keyword search. To access it, simply click the Filtering button.
The filtering widget is useful for removing from your view, results that you don't wish to see. For example, you can specify that you wish to see "only human" sequences. Or only those sequences whose feature table contains a specific keyword.
Basic Operation of the Filtering Widget
Filtering widget allows you to filter your results based on alignment and/or annotation properties.
For each filtering condition
- Choose the parameter to filter on.
- To add one more filtering condition, click the big + button at the right.
- To remove a filtering condition, click the big - button to its right.
- To apply the conditions you entered, click the Apply button.
- To delete all conditions and return to the full list, click the Reset button.
In the picture below, when the [Apply] button is clicked, GenomeQuest will only display stronger alignments (percent identity > 50) from human sequences whose description has the word receptor in it.
Details of Filtering
The filtering widget can be used to apply a single filter or multiple filters. To start filtering, click the Filtering button.
When you enter multiple conditions, you can specify whether you want
- all your filtering conditions to be satisfied i.e. apply an AND between the conditions or
- any one of them to be satisfied i.e. apply an OR between the conditions.
Make this choice through the drop-down menu at the top of the filtering area. Click the Apply button in order for the filters to be applied. To remove all filters, click the Reset button.
To Add A New Filter
Define each of your filtering conditions by specifying three things:
- Field. Which annotation or other field should be matched.
- E.g. You can ask to find Arabidopsis in the Organism field.
- For text fields, you can try to "match" a keyword. Or flip the condition to "doesn't match". Match refers to full words but you can specify partial words as described in advanced syntax.
- For fields that have numbers (e.g. percent identity) the usual numeric comparators (=, >, <, <=, >=) are available.
- For Date fields the comparators provided are "earlier than" and "later than".
- Value. Type in the key words or numeric values as appropriate.
- For date fields, year date month drop downs are provided to easily specify the value of the date.
- If necessary, you can use advanced syntax in specifying the value.
- For most text fields, the value can be specified in a multi-line format. To get to the multi-line format, click the little "[+]" link to the right of the filtering condition.
Syntax for Text Filters
- Terms are case insensitive. E.g. Kinase is the same as kiNase
- Terms are considered to be full words unless modified by wildcards. E.g. Antibod does not match antibody
- An asterisk, *, is a wild card which stands for any number of any characters. E.g.antibod* matches antibody as well as antibodies.
- Terms on the same line, separated by spaces are considered ANDed. E.g. human kinase means human AND kinase.
- Terms on the different lines are considered ORed. E.g.
means kinase OR phosphatase.
- To retrieve the whole database, enter no terms i.e. leave the text box blank.
Advanced syntax allows you to do complicated wild cards, boolean logic and phrase searching.
Add a Canned Filter
Several common and useful filters are included in the Database browser page. To use these, click the Filter button at the top right of the filtering area. Under the Apply item, you will see the canned filters. Clicking one of them, adds one more filtering condition with the appropriate value filled in.
If you like a specific set of filters and are likely to use them again, it makes sense to save them. To do this, click the "Save" button on the Filter menu. On the pop-us dialog, you can create a new filter or replace an existing filter.
To create a new saved filter
- Choose "Create new filter"
- Give the filter set a name. The name may contain alphanumberic characters or spaces or underscores.
- Click Save.
Later, when you want to recall filters saved previously
- Click the Filter button, choose Apply filter and select the saved filter to add.
- This adds the filters from the saved set to any that you may already have in the filtering widget.
- You have to click Apply in order for all the filters to take effect.
You can modify an existing (saved) filter. To do this,
- Click the reset button to remove all existing filters.
- Click the Filter button, choose Apply filter and select the saved filter you want to modify.
- This will pull in all the filters from the saved set into the filtering widget.
- Now modify the filters, using the normal operation as described above.
- Click the Filter button and choose Save.
- In the pop-up dialog, select "Replace existing filter" and choose the filter you want to modify.
To delete a saved filter,
- Click the Filter button and choose Delete.
- In the pop-up dialog, select the filter to delete and click Delete.