<ul>\r
<li><strong>File</strong> \r
<ul>\r
+ <li><strong>Fetch Sequence</strong><br>\r
+ <em>Shows a dialog window in which you can select known ids from Uniprot, \r
+ EMBL, EMBLCDS or PDB database using Web Services provided by the European \r
+ Bioinformatics Institute. See <a href="../features/seqfetch.html">Sequence \r
+ Fetcher</a></em>.</li>\r
<li><strong>Save As<br>\r
</strong><em>Save the alignment to local file. A file selection window \r
will open, use the "Files of type:" selection box to determine \r
href="../calculations/treeviewer.html">view trees</a> stored in the Newick \r
file format, and associate them with the alignment. Note: the ids of the \r
tree file and your alignment MUST be the same.</em></li>\r
+ <li><strong>Load Features / Annotations<br>\r
+ </strong><em>Jalview load precalculated <a href="../features/featuresFormat.html">sequence \r
+ features</a> or <a href="../features/annotationsFormat.html">alignment \r
+ annotations</a>.</em></li>\r
<li><strong>Close<br>\r
</strong><em>Close the alignment window. Make sure you have saved your \r
alignment before you close - either as a Jalview project or by using the \r
can also do this by pressing <CTRL> and C (<APPLE> and C on \r
MacOSX). <br>\r
If you try to paste the clipboard contents to a text editor, you will \r
- see the format of the copied residues is a tab separated list</em><br>\r
- NAME START_RES END_RES SEQUENCE </li>\r
+ see the format of the copied residues FASTA.</em></li>\r
<li><strong>Paste </strong> \r
<ul>\r
<li><strong>To New Alignment<br>\r
the current alignment) exceeds this value then one of the sequences (the \r
shorter) is discarded. Press the "Apply" button to remove redundant \r
sequences. The "Undo" button will undo the last redundancy deletion.</em></li>\r
- <li><strong>Pad Gaps<br>\r
- </strong><em>Adds gaps to the end of all the sequences so they are all \r
- the same length. This is useful for making a tree using unaligned sequences.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
+ <li><strong>Pad Gaps<br>\r
+ </strong><em>When selected, the alignment will be kept at minimal\r
+ width (so there no empty columns before or after the first or last aligned\r
+ residue) and all sequences will be padded with gap characters to\r
+ the before and after their terminating residues.<br>\r
+ This switch is useful when making a tree using unaligned\r
+ sequences and when working with alignment analysis programs which\r
+ require 'properly aligned sequences' to be all the same length.<br>\r
+ You may set the default for <strong>Pad Gaps</strong> in the <a href="../features/preferences.html">preferences</a>. \r
+ </em></li>\r
</em><br>\r
</li>\r
</ul>\r
<ul>\r
<li><strong>Find<br>\r
</strong><em>Select this to <a href="../features/search.html">search</a> \r
- for residues, sequence name or residue position within the alignment. \r
+ for residues, sequence name or residue position within the\r
+ alignment and create new sequence features from the queries. \r
<br>\r
</em></li>\r
</ul>\r
<li><strong>Font<br>\r
</strong><em>Change the font of the display from the "Choose Font" \r
dialog box, which is shown when this item is selected. </em></li>\r
+ <li><strong>Smooth Fonts</strong><em><br>\r
+ If selected, the alignment will be drawn with anti-aliasing on which looks \r
+ better, but performace is reduced.\r
+ </em></li>\r
<li><strong>Wrap<br>\r
</strong><em>When ticked, the alignment display is "<a href="../features/wrap.html">wrapped</a>" \r
to the width of the alignment window. This is useful if your alignment \r
be displayed below the alignment. The default setting is to display the \r
conservation calculation, quality calculation and consensus values as \r
bar charts. </em></li>\r
- <li><strong>Sequence Features<br>\r
+ <li><strong>Fetch Sequence Features<br>\r
</strong><em>If the sequence names are Swissprot entries Jalview will \r
use the names to retrieve <a href="../features/seqfeatures.html">sequence \r
features</a> from the EBI. Features which are 1 residue in length are \r
<br>\r
Note: The retrieved information will update the sequence start and end \r
labels if they are incorrect. </em></li>\r
+ <li><strong>Show Sequence Features</strong><br><em>Show or\r
+ hide sequence features on this alignment.</em></li>\r
+ <li><strong>Seqence Feature Settings...</strong><em><br>\r
+ <em>Control the colour and display of sequence features on the\r
+ alignment. See <a\r
+ href="../features/featuresettings.html">Sequence Feature Settings</a>.</em><br>\r
+ </em></li>\r
<li><strong><a href="../features/overview.html">Overview Window</a><br>\r
</strong><em>A scaled version of the alignment will be displayed in a \r
small window. A red box will indicate the currently visible area of the \r
</strong><em>Use this to set the threshold value for colouring above Identity. \r
Useful if the window has been closed. <br>\r
</em></li>\r
+ <li><strong>By Annotation</strong><br>\r
+ <em>Colours the alignment on a per-column value from a specified annotation. \r
+ See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>\r
+ </li>\r
</ul>\r
</li>\r
<li><strong>Calculate</strong> \r
<li><strong>Principal Component Analysis</strong><br>\r
<em>Shows a spatial clustering of the sequences based on the BLOSUM62 \r
scores in the alignment. See <a href="../calculations/pca.html">Principal \r
- Component Analysis</a>.</em> <br>\r
+ Component Analysis</a>.</em> </li>\r
+ <li><strong>Translate cDNA</strong><br>\r
+ <em>If you are viewing a cDNA alignment a very simple translation service \r
+ is available. The translation ignores all gaps in the cDNA sequences. \r
+ </em> <br>\r
</li>\r
</ul>\r
</li>\r
sequences.</em></li>\r
</ul>\r
</li>\r
- <li><strong>Secondary Structure Prediction</strong>\r
+ <li><strong>Secondary Structure Prediction</strong> \r
<ul>\r
<li><strong>JPred Secondary Structure Prediction</strong><br>\r
<em>Secondary structure prediction by network consensus. The behaviour \r
git://source.jalview.org / jalview.git / blobdiff