<ul>\r
<li><strong>View</strong></li>\r
</ul>\r
-<blockquote>\r
+<blockquote> \r
<ul>\r
<li><strong>Font<br>\r
- </strong><em>Change the font of the display from the\r
- "Choose Font" dialog box, which is shown when this\r
- item is selected. <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. <br>\r
</em></li>\r
<li><strong>Wrap<br>\r
- </strong><em>When ticked, the alignment display is\r
- "<a href="../features/wrap.html">wrapped</a>" to the\r
- width of the alignment window. This is useful if your alignment\r
- has only a few sequences to view its full width at once.<br>\r
- Options are available to show the residue numbering at the start and/or\r
- end of an alignment as well as showing the alignment position above each\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 has \r
+ only a few sequences to view its full width at once.<br>\r
+ Options are available to show the residue numbering at the start and/or \r
+ end of an alignment as well as showing the alignment position above each \r
sequence row. <br>\r
- <strong>NOTE</strong>: When in wrapped alignment view, the\r
- alignment cannot be edited or have regions selected on it. <br>\r
+ <strong>NOTE</strong>: When in wrapped alignment view, the alignment cannot \r
+ be edited or have regions selected on it. <br>\r
</em><strong> </strong></li>\r
<li><strong>Show Full Sequence ID<br>\r
- </strong><em>If this box is selected the sequence name will have the start\r
+ </strong><em>If this box is selected the sequence name will have the start \r
and end position of the sequence appended to the name, in the format NAME/START-END<br>\r
</em></li>\r
<li><strong>Boxes</strong><em><br>\r
- If this is selected the background of a residue will be coloured using the\r
- selected background colour. Useful if used in conjunction with "Colour\r
+ If this is selected the background of a residue will be coloured using the \r
+ selected background colour. Useful if used in conjunction with "Colour \r
Text." <br>\r
</em></li>\r
<li><strong>Text<br>\r
- </strong><em>If this is selected the residues will be displayed using the\r
+ </strong><em>If this is selected the residues will be displayed using the \r
standard 1 character amino acid alphabet.<br>\r
</em></li>\r
<li><strong>Colour Text<br>\r
- </strong><em>If this is selected the residues will be coloured according\r
- to the background colour associated with that residue. The colour is slightly\r
+ </strong><em>If this is selected the residues will be coloured according \r
+ to the background colour associated with that residue. The colour is slightly \r
darker than background so the amino acid symbol remains visible. <br>\r
</em></li>\r
<li><strong>Show Gaps<br>\r
- </strong><em>When this is selected, gap characters will be displayed as "."\r
- or "-". If unselected, then gap characters will appear as blank spaces.\r
- <br>\r
+ </strong><em>When this is selected, gap characters will be displayed as \r
+ "." or "-". If unselected, then gap characters will \r
+ appear as blank spaces. <br>\r
You may set the default gap character in <a href="../features/preferences.html">preferences</a>.<br>\r
</em></li>\r
<li><strong>Show Annotations<br>\r
- </strong><em>If this is selected the "Annotation Panel" will be\r
- displayed below the alignment. The default setting is to display the conservation\r
+ </strong><em>If this is selected the "Annotation Panel" will be \r
+ displayed below the alignment. The default setting is to display the conservation \r
calculation, quality calculation and consensus values as bar charts. </em><br>\r
</li>\r
<li><strong>Sequence Features<br>\r
- </strong><em>If the sequence names are Swissprot entries Jalview will use\r
- the names to retrieve <a href="../features/seqfeatures.html">sequence features</a> from the EBI. Features which are\r
- 1 residue in length are coloured red, sequences longer than 1 residue are\r
- coloured blue. Move the mouse over a coloured feature to display the details\r
- of the feature. <br>\r
- Note: The retrieved information will update the sequence start and end labels\r
- if they are incorrect. <br>\r
+ </strong><em>If the sequence names are Swissprot entries Jalview will use \r
+ the names to retrieve <a href="../features/seqfeatures.html">sequence features</a> \r
+ from the EBI. Features which are 1 residue in length are coloured red, sequences \r
+ longer than 1 residue are coloured blue. Move the mouse over a coloured \r
+ feature to display the details of the feature. <br>\r
+ Note: The retrieved information will update the sequence start and end labels \r
+ if they are incorrect. </em><br>\r
+ </li>\r
+ <li><strong>Seqence Settings </strong><em><br>\r
+ <em>If features have been added to the alignment then the priority of rendering \r
+ the features can be altered so that overlapping features can be displayed \r
+ or hidden. See <a href="features/seqfeatures.html">Sequence Features</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 small\r
- window. A red box will indicate the currently visible area of the alignment.\r
+ </strong><em>A scaled version of the alignment will be displayed in a small \r
+ window. A red box will indicate the currently visible area of the alignment. \r
Move the visible region using the mouse. </em><strong> </strong></li>\r
</ul>\r
</blockquote>\r
git://source.jalview.org / jalview.git / blobdiff