<body>\r
<p><strong>Alignment Window View Menu</strong></p>\r
<ul>\r
- <li><strong>View</strong></li>\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. </em></li>\r
+ <li><strong>Show (all Columns / Sequences)</strong><em><br>\r
+ All hidden Columns / Sequences will be revealed. </em></li>\r
+ <li><strong>Hide (all Columns / Sequences)</strong><em><br>\r
+ Hides the all the currently selected Columns / Sequences</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 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 end \r
+ of an alignment as well as showing the alignment position above each sequence \r
+ row. <br>\r
+ <strong>NOTE</strong>: When in wrapped alignment view, the alignment cannot \r
+ be edited or have regions selected on it. </em></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
+ and end position of the sequence appended to the name, in the format NAME/START-END</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
+ Text." </em></li>\r
+ <li><strong>Text<br>\r
+ </strong><em>If this is selected the residues will be displayed using the \r
+ standard 1 character amino acid alphabet.</em></li>\r
+ <li><strong>Colour Text<br>\r
+ </strong><em>If this is selected the residues will be coloured according to \r
+ the background colour associated with that residue. The colour is slightly \r
+ darker than background so the amino acid symbol remains visible. </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 \r
+ spaces. <br>\r
+ You may set the default gap character in <a href="../features/preferences.html">preferences</a>.</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
+ calculation, quality calculation and consensus values as bar charts. </em></li>\r
+ <li><strong>Fetch 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> \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 feature \r
+ 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></li>\r
+ <li><strong>Show Sequence Features</strong><br>\r
+ <em>Show or 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 alignment. \r
+ See <a\r
+ href="../features/featuresettings.html">Sequence Feature Settings</a>.</em></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
+ Move the visible region using the mouse. </em></li>\r
+ <strong> </strong>\r
</ul>\r
-<blockquote> \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. Select a "Monospaced" \r
- font for fast rendering of your alignment. The checkbox labelled "Monospaced" \r
- indicates whether the chosen font uses characters all of the same width.<br>\r
- </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.<br>\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 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 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
- 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
- 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
- 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
- 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 \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
- calculation, quality calculation and consensus values as bar charts. </em><br>\r
- </li>\r
- <li><strong>Fetch 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> \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>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 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
+<p> </p>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / commitdiff