<p>
<strong> Select/Hide Columns by Annotation </strong>
</p>
- <p>From Jalview-2.9 columns of an alignment can be filtered using
- any annotation rows added to that alignment.</p>
- To carry out this operation, navigate to "Select" menu
- <strong>→</strong> "Select/Hide Columns by Annotation..." to bring
- up the Select/Hide by Annotation window. The filter options vary depending
+ <p>From Jalview 2.9 columns of an alignment can be filtered using
+ any annotation row added to that alignment.</p>
+ To carry out this operation, navigate to "<b>Select</b><strong><b>→</b></strong><b>Select/Hide Columns by Annotation...</b>" to bring
+ up the 'Select/Hide by Annotation' window. The filter options vary depending
on the type of annotation selected. If an annotation that has a numeric
values is selected, the threshold filter option is activated as seen in the
figure on the right below, otherwise the dialog will exclude the threshold filter option as seen in the figure on the left.
<br>
- <br>
+ <br>
+ <table>
+ <tr>
+ <td><img src="annotationColumnSelectionWithoutSM.gif"></td>
+ <td><img src="annotationColumnSelectionWithSM.gif"></td>
+ </tr>
+ </table>
- <div style="width: 48%; float: left; margin-left: 4%">
- <img src="annotationColumnSelectionWithoutSM.gif">
- </div>
- <div style="width: 48%; float: right">
- <img src="annotationColumnSelectionWithSM.gif">
- </div>
- <div> </div>
<ul>
<li>The target annotation row can be selected using the drop-down option menu in the top-most part of the window.</li>
<li><strong>Search Filter</strong>
<ul>
<li>When a text is entered in the text box within the Search
- Filter section, the "Display Label" and "Description"
+ Filter section, the 'Display Label' and 'Description'
options becomes enabled for selection. </li>
<li>On selecting any of the options, a regular expression
search (RegEx) is executed on the specified field of the current
</ul>
<li><strong>Actions</strong>
<ul>
- <li>The "Select" and "Hide" radio buttons
+ <li>The 'Select' and 'Hide' radio buttons
determines the action that will be carried out on the matching
columns in the alignment during the filtering process.</li>
- <li>The default option is "Select" and this simply
+ <li>The default option is 'Select' and this simply
enables column selection on the matching alignment column.</li>
- <li>While the "Hide" option enables the matching columns to
+ <li>While the 'Hide' option enables the matching columns to
be hidden automatically during the filtering process.</li>
- <li>The "Ok" button applies the filter when clicked.</li>
- <li>And finally, the "Cancel" button restores the alignment to its previous state before any filtering was applied.
+ <li>The 'Ok' button applies the filter when clicked.</li>
+ <li>And finally, the 'Cancel' button restores the alignment to its previous state before any filtering was applied.
</ul></li>
</ul>
<body>
<strong>PDB Sequence Fetcher</strong>
- <p>From Jalview 2.9 a specialised interface was introduced for
+ <p>From Jalview 2.9, a specialised interface was introduced for
fast and efficient discovery/retrieval of sequence data from the PDB
database. The introduced interface enables live querying of PDB data
on-the-fly thereby eliminating the need to memorise database accession
or to manually cross-reference other bioinformatics websites before retrieving
- sequence data in Jalview. The underlying technology is provided by
+ sequence data in Jalview. The underlying infrastructure is provided by
EBI and is based on Apache Solr which is a text based search engine.</p>
<p>
- The PDB Sequence Fetcher interface can be opened by selecting <strong>PDB</strong>
- as the choice database from the <strong>'Select Database
- Retrieval Source'</strong> interface of <a href="seqfetch.html">Sequence
- Fetcher</a>.
+ The PDB Sequence Fetcher interface can be accessed from <b>"File →Fetch Sequence(s) →Select Database →PDB"</b> click the ok button after selecting PDB from the 'Select Database
+ Retrieval Source' interface.
</p>
<p>
<img src="pdbseqfetcher.png" align="left"
a result is displayed on-the-fly as seen in the screenshot above.</p>
<p>Use the drop-down menu to select a specific field to search by in the PDB database, the default
- option is <strong>'ALL'</strong>.</p>
+ option is 'ALL'.</p>
<p> Furthermore, the PDB search interface also provides the following functionalities:</p>
<ul>
</ul>
<p>
<strong>Customising displayed meta-data</strong> <br>To change
- the displayed meta-data in the search result, click the <strong>'Configure
- Displayed Columns'</strong> tab, then tick off the options wanted.
+ the displayed meta-data in the search result, click the 'Configure
+ Displayed Columns' tab, then tick off the options wanted.
</p>
<p>
<strong>Importing Sequence</strong><br> After querying the PDB
<strong>Associating PDB files with Sequences</strong><br>
- Discovery/Association of PDB entries to a sequence happens
+ Discovery/Association of PDB entries to a sequence now happens
automatically during the initialisation of the Structure Chooser
- Interface. Jalview uses the sequence's ID to query the PDB Rest API,
+ Interface. Jalview uses the sequence's ID to query the PDB Rest API
provided by the EBI to discover PDB Ids associated with the sequence.
<br><br>
<strong>Configuring displayed meta-data for Structures</strong><br>
- To configure the visible meta-data displayed for the discovered structures, click the <strong>'Configure Displayed Columns'</strong> tab, then tick the options which you intend to make visible.
+ To configure the visible meta-data displayed for the discovered structures, click the 'Configure Displayed Columns' tab, then tick the options which you intend to make visible.
<br><br>
<strong>Auto-selection of best Structures</strong>
<br> Jalview can automatically filter and select the best structures using various metric categories avaialble from the meta-data
of the structures. To perform this simply select any of the following options from the drop-down menu in the Structure
Chooser interface: Best Uniprot coverage, Higest Resolution,
-
- Best Quality, Highest Protein Chain etc. When the <strong>'Invert'</strong> option is selected, Jalview returns an inverse result for the current selected option in the drop-down menu.<p>
+ Best Quality, Highest Protein Chain etc. When the 'Invert' option is selected, Jalview returns an inverse result for the current selected option in the drop-down menu.<p>
+
<img src="schooser_main.png" style="width: 464px; height: 369px;">
<!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
<p><img src="schooser_drop-down.png" style="width: 464px; height: 368px; ">
git://source.jalview.org / jalview.git / commitdiff