* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
-<title>Filter Columns by Annotation</title>
+<title>Select/Hide Columns by Annotation</title>
</head>
<body>
<p>
- <strong> Filter Columns by Annotation </strong>
+ <strong> Select/Hide Columns by Annotation </strong>
</p>
- <p>Jalview allows the columns of an alignment to be filtered using
+ <p>From Jalview-2.9 columns of an alignment can be filtered using
any annotation rows added to that alignment.</p>
- From "Select" menu
- <strong>→</strong> "Select by Annotation..." to bring
- up the Select by Annotation window. The filter options vary depending
+ 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
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.
+ figure on the right below, otherwise the dialog will exclude the threshold filter option as seen in the figure on the left.
<br>
<br>
<div> </div>
<ul>
- <li>Select which annotation to base the filtering on using the
- top-most selection box.</li>
+ <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 textfield on the search
- filter section, the "Display Label" and "Description"
- checkboxes becomes selectable.</li>
- <li>On selecting any of the checkboxes, a regular expresion
+ <li>When a text is entered in the text box within the Search
+ 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
annotation row selected, and the matching columns will be highlighted
in the alignment.</li>
<li><strong>Structure Filter</strong>
<ul>
<li>Alignment columns can also be filtered by the type of
- secondary structure present in a choosen annotation row.</li>
+ secondary structure present in a target annotation row.</li>
<li>This can be achieved by ticking the type of structure you
wish to filter by under the structures filter section.</li>
</ul>
<ul>
<li>This filter is only activated for annotation which contain
numeric values</li>
- <li>Select whether to Filter the alignment above or below an
+ <li>Select whether to filter the alignment above or below an
adjustable threshold with the selection box within the threshold
filter section.</li>
<li>Change the threshold value with the slider, or enter the
<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 the filtering when clicked.
+ <li>And finally, the "Cancel" button restores the alignment to its previous state before any filtering was applied.
</ul></li>
</ul>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>BioJSON-1.0</title>
+</head>
+<body>
+ <h1>BioJSON</h1>
+ BioJSON is a standardise JavaScript Object Notation (JSON) format for exchange of Bio-informatics Sequence Alignment data.
+ BioJSON-1.0 schema/documentation is available at <a href="#">http://www.jalview.org/builds/develop/examples/biojson-doc/</a>.
+ You can keep up to date with BioJSON development and latest news at <a href="#">https://github.com/jalview/biojson/wiki</a>.
+
+ <h2>Features supported</h2>
+ Export/Import of the following alignment elements are supported in BioJSON-1.0:
+ <ul>
+ <li>Alignment Annotations</li>
+ <li>Alignment Features</li>
+ <li>Alignment Sequences</li>
+ <li>Color Scheme</li>
+ <li>Hidden Columns</li>
+ <li>Hidden Sequences</li>
+ <li>Sequence Groups</li>
+ </ul>
+
+ <h2>Features not yet supported</h2>
+ Export/Import of the following alignment elements are not supported in BioJSON-1.0:
+ <ul>
+ <li>Reference sequence</li>
+ <li>Representative sequence</li>
+ <li>Trees</li>
+ <li>3D Structures</li>
+ </ul>
+</body>
+</html>
<td><div align="center">-blc FILE</div></td>
<td><div align="left">Create alignment file FILE in BLC format.</div></td>
</tr>
+ <tr>
+ <td><div align="center">-json FILE</div></td>
+ <td><div align="left">Create alignment file FILE in JSON format.</div></td>
+ </tr>
<tr>
<td><div align="center">-jalview FILE</div></td>
<body>
<strong>PDB Sequence Fetcher</strong>
- <p>From Jalview 2.x.x a speciliased 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 cross-reference other bioinformatics websites before retrieving
- a sequence data in jalview. The underlying technology is provided by
+ or to manually cross-reference other bioinformatics websites before retrieving
+ sequence data in Jalview. The underlying technology 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>
</p>
<p>
<img src="pdbseqfetcher.png" align="left"
- alt="PDB sequence fetcher (introduced in Jalview 2.x.x)">
+ alt="PDB sequence fetcher (introduced in Jalview 2.9)">
</p>
- <strong>Searching the PDB Database</strong>
- <br> Once the interface is opened, typing in the search text box
- will execute a live query to the PDB database and display the results
- on-the-fly as seen in the screen-shot above. Use the drop-down menu to
- select a specific field to search by in the PDB database, the default
- option is
- <strong>'ALL'</strong>. Furthermore, the PDB search interface also
- provides the following functionalities:
+ <p><strong>Searching the PDB Database</strong></p>
+ <p>When the interface is opened, a live query to the PDB database is
+ executed every time a character is typed into the search text box, and
+ 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>
+
+ <p> Furthermore, the PDB search interface also provides the following functionalities:</p>
<ul>
<li>Retrieving a unique chain for a PDB entry: <br>To
retrieve a specific chain for a PDB entry, append the PDB ID with a
<p>
<strong>Importing Sequence</strong><br> After querying the PDB
database, to import the found data into Jalview, select the entries
- you wish to import then click the ok button at the bottom of the
+ you wish to import then click the 'Ok' button at the bottom of the
interface.
</p>
<p>
<em>The PDB Sequence Fetcher interface was introduced in Jalview
- 2.x.x.</em>
+ 2.9</em>
</p>
</body>
</html>
\ No newline at end of file
one or more accession ids (as a semi-colon separated list), or press the
"Example" button to paste the example accession for the currently selected database into the retrieval box.
Finally, press "OK" to initiate the retrieval.</p>
- <p>Since Jalview 2.x.x if PDB is selected as the sequence database, a specialised interface - <a href="pdbsequencefetcher.html">PDB Sequence Fetcher</a> is used for discovering and retrieving the sequenec data. </p>
+ <p>Since Jalview 2.9 if PDB is selected as the sequence database, a specialised interface - <a href="pdbsequencefetcher.html">PDB Sequence Fetcher</a> is used for discovering and retrieving the sequenec data. </p>
<p><strong>Specifying chains for PDB IDs</strong>
If you are retrieving sequences from the PDB, you can retrieve
specific chains by appending a colon and the chain id to the PDB
</ul>
<p>
- <em>The Structure Chooser interface was introduced in Jalview 2.x.x.
+ <em>The Structure Chooser interface was introduced in Jalview 2.9.
</em>
</p>
</body>
<em>...</em><br>//</td>
<td width="23%">.phy</td>
</tr>
+<tr>
+<td width="17%">JSON</td>
+<td width="60%">Data starts with '{' <br>Data ends with '}' <br><br>See <a href="../features/bioJsonFormat.html">BioJson</a> for more info about Jalview JSON format <br></td>
+<td width="23%">.json</td>
+</tr>
</table>
<p>The file extensions are used to associate jalview alignment icons
with alignment files: <img src="file.png" width=12 height=12 >
<li><strong>AMSA</strong></li>
<li><strong>STH</strong></li>
<li><strong>Phylip</strong></li>
+ <li><strong>JSON</strong></li>
</ul></li>
<li><strong>Print (Control P)<br> </strong><em>Jalview
will print the alignment using the current fonts and colours of
+ "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
+ "-pir FILE\tCreate alignment file FILE in PIR format.\n"
+ "-blc FILE\tCreate alignment file FILE in BLC format.\n"
+ + "-json FILE\tCreate alignment file FILE in JSON format.\n"
+ "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+ "-png FILE\tCreate PNG image FILE from alignment.\n"
+ "-svg FILE\tCreate SVG image FILE from alignment.\n"
public class AnnotationRenderer
{
+ private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
+
+ private static final int CHAR_A = 'A'; // 65
+
+ private static final int CHAR_Z = 'Z'; // 90
+
/**
* flag indicating if timing and redraw parameter info should be output
*/
}
}
- if (ss >= 65)
+ if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
{
// distinguish between forward/backward base-pairing
- if (displayChar.indexOf(ss + 32) > -1)
+ int ssLowerCase = ss + UPPER_TO_LOWER;
+ // TODO would .equals() be safer here? or charAt(0)?
+ if (displayChar.indexOf(ssLowerCase) > -1)
{
-
- ss = (char) (ss + 32);
-
+ ss = (char) ssLowerCase;
}
}
{
String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
+ "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
- + "-features uniref50_test_features -annotations uniref50_test_annot -tree uniref50_test_tree";
+ + "-features examples/uniref50_test_features -annotations examples/uniref50_test_annot -tree examples/uniref50_test_tree";
Worker worker = jalviewDesktopRunner(true, cmds, 9000);
String ln = null;
while ((ln = worker.getOutputReader().readLine()) != null)
"Failed command : -nosortbytree" },
{ "CMD [-dasserver nickname=www.test.com] executed successfully!",
"Failed command : -dasserver nickname=www.test.com" },
- { "CMD [-features uniref50_test_features] executed successfully!",
- "Failed command : -features uniref50_test_features" },
- { "CMD [-annotations uniref50_test_annot] executed successfully!",
- "Failed command : -annotations uniref50_test_annot" },
- { "CMD [-tree uniref50_test_tree] executed successfully!",
- "Failed command : -tree uniref50_test_tree" },
+ {
+ "CMD [-features examples/uniref50_test_features] executed successfully!",
+ "Failed command : -features examples/uniref50_test_features" },
+ {
+ "CMD [-annotations examples/uniref50_test_annot] executed successfully!",
+ "Failed command : -annotations examples/uniref50_test_annot" },
+ { "CMD [-tree examples/uniref50_test_tree] executed successfully!",
+ "Failed command : -tree examples/uniref50_test_tree" },
// non headless mode input operations
{ "CMD [-nousagestats] executed successfully!",
"Failed command : -nousagestats" },
git://source.jalview.org / jalview.git / commitdiff