<mapID target="clustal" url="html/webServices/clustalw.html"/>\r
<mapID target="muscle" url="html/webServices/muscle.html"/>\r
<mapID target="jnet" url="html/webServices/jnet.html"/>\r
- \r
- <mapID target="io" url="html/io/index.html"/>\r
+ <mapID target="seqfetch" url="html/features/seqfetch.html"/>\r
+ <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>\r
+ <mapID target="pdbviewer" url="html/features/pdbviewer.html"/>\r
+ <mapID target="preferences" url="html/features/preferences.html"/> \r
+ <mapID target="io" url="html/io/index.html"/>\r
<mapID target="export" url="html/io/export.html"/>\r
<mapID target="alformats" url="html/io/fileformats.html"/>\r
<mapID target="edit" url="html/editing/index.html"/>\r
\r
<body>\r
<p><strong>Preferences</strong></p>\r
-<p> The <strong>"Visual" </strong>tab on the preferences window allows \r
- you to configure the default display for a new alignment window. </p>\r
+<p>There are three tabs in the Preferences dialog box:\r
+<ul><li>The <a href="#visual"><strong>"Visual"</strong>\r
+ Preferences</a> tab allows \r
+ you to configure the default display for a new alignment\r
+ window. </li>\r
+<li>The <a\r
+ href="#connections"><strong>"Connections"</strong>\r
+ Preferences</a> tab allows you to change the links \r
+ made from Jalview to your default web browser.\r
+</li>\r
+<li>The <a href="#output"><strong>"Output"</strong>\r
+ Preferences</a> tab contains settings affecting the export of sequence\r
+alignments and EPS files.\r
+</li>\r
+</ul></p>\r
+<p><strong><a name="visual">Visual</a> Preferences tab</strong></p>\r
<p><em>Maximise Window</em> - If this is selected, a new alignment window will stretch \r
to fit the available space.</p>\r
<p><em>Show Annotations</em> - If this is selected the new window will display an annotation \r
be opened when Jalview is started. You can change the default file by clicking \r
on file name and either typing in the file path or selecting it from the file \r
chooser window. </p>\r
-<p>The <strong>"Connections"</strong> tab allows you to change the links \r
- made from Jalview to your default web browser.</p>\r
+<p><a name="connections"><strong>"Connections" Preferences tab</strong></a></p>\r
<p><em>URL Link From Sequence ID</em><br>\r
Right click a sequence id to see a popup menu with "Link" as one of \r
the items. By default the item "SRS" is added to this link menu. This \r
box "Use a Proxy Server" and enter the address and port details as \r
necessary. Web Services will not work if you are using a proxy server and do \r
not enter the settings here.</p>\r
-<p>The "<strong>Output</strong>" tab has a selection box allowing the \r
- user to set a default rendering style for EPS export. "Lineart" will \r
- produce an accurate representation of the visible alignment in Jalview, all \r
- the characters will be graphics objects. "Text" will produce a much \r
- smaller file and will rely on the software you use to view the EPS file, such \r
- as Adobe Illustrator, having the same font as the file was created with. You \r
- will only be able to edit text in an EPS file if you select the "Text" \r
- option.<br>\r
- Choose "Prompt each time" to select between Lineart and Text each \r
- time you make an EPS file.</p>\r
-<p>The output tab also has a group of checkboxes for each file format. If these \r
+<p><a name="output"><strong>Output Preferences tab</strong></a></p>\r
+<p><em>EPS Rendering Style</em><br>\r
+This is a selection box which allows the \r
+ user to set a default rendering style for EPS export: \r
+<ul><li>"Lineart"<br>EPS files will accurately\r
+reproduce the alignment view in Jalview and all characters will be\r
+converted into line art. Files generated in this way are large and are\r
+not easily editable, but have no font table dependencies.</li>\r
+<li>"Text"<br>EPS files will be a mixture of text and\r
+lineart. This produces compact files that can be edited easily in\r
+programs like Microsoft Word and Adobe Illustrator, but can be\r
+problematic if the fonts available to jalview are not accessible by\r
+the program reading the EPS file.\r
+<li>"Prompt each time"<br>Choose this to be asked select between Lineart and Text each time you make an EPS file.</li>\r
+</ul>\r
+</p>\r
+<p><em>Sequence//Start-End Numbering</em><br>\r
+The output tab also has a group of checkboxes for each file format. If these \r
are ticked, then Jalview will write files with the start and end sequence positions \r
- appended to each sequence id. If the boxes are left unchecked for a paritcular \r
+ appended to each sequence id:<br>\r
+<pre>\r
+ >ID//1-10\r
+ AACDEAAFEA\r
+</pre>\r
+<br>If the boxes are left unchecked for a particular \r
format, the sequence limits will not be appended to the sequence id. </p>\r
<p> </p>\r
<p> </p>\r
<head><title>Sequence Fetcher</title></head>\r
<body>\r
<p><strong>Sequence Fetcher</strong></p>\r
-<p>The Sequence Fetcher can be started from the main desktop "File" \r
- menu or from a particular alignment window.</p>\r
-<p>Select which database to fetch your sequence from and enter the sequence id. \r
- If you are retrieving sequences from PDB database and you know which chain you \r
- would like to retrieve, append the chain id after colon to the PDB id. eg 1GAQ:A</p>\r
-<p>The Sequence Fetcher uses WSDBFetch provided by the European Bioinformatics \r
- Institute. If you use this service please quote:</p>\r
+<p>Jalview can retrieve sequences from certain databases via the\r
+WSDBFetch service provided by the European Bioinformatics Institute.</p>\r
+<p>A Sequence Fetcher dialog box can be opened via the "File" \r
+ menu on the main desktop in order to retrieve sequences as a new\r
+ alignment, or opened via the "File" menu of an existing alignment\r
+ to import additional sequences.\r
+</p>\r
+<p>Select the database you want to retrieve sequences from, and enter a\r
+ the database id (or a semi-colon separated list of several ids) in\r
+ the text box. Finally, press OK to initiate the retrieval.</p>\r
+<p>\r
+ If you are retrieving sequences from the PDB, you can retrieve\r
+ specific chains by appending a colon and the chain id to the PDB\r
+ id. For example :<br><pre> 1GAQ:A</pre></p>\r
+<p>If you use the sequence fetcher in work for publication, then please cite:</p>\r
<p>Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar \r
S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R. <br>\r
SOAP-based services provided by the European Bioinformatics Institute.<br>\r
git://source.jalview.org / jalview.git / commitdiff