-<html>\r
-<head>\r
-Alignment Window Menus\r
-</head>\r
-<body>\r
-<p><strong>Alignment Window Format Menu</strong></p>\r
-<ul>\r
- <li><strong>Font...<br>\r
- </strong><em>Opens the "Choose Font" dialog box, in order to\r
- change the font of the display and enable or disable 'smooth fonts'\r
- (anti-aliasing) for faster alignment rendering. </em></li>\r
- <li><strong>Wrap<br>\r
- </strong><em>When ticked, the alignment display is "<a\r
- href="../features/wrap.html">wrapped</a>" to the width of the\r
- alignment window. This is useful if your alignment has only a few\r
- sequences to view its full width at once.<br>\r
- Additional options for display of sequence numbering and scales are\r
- also visible in wrapped layout mode:<br>\r
- <ul>\r
- <li><strong>Scale Above</strong><br>Show the alignment column position scale.</li>\r
- <li><strong>Scale Left</strong><br>Show the sequence position for the first aligned residue in each row in the left column of the alignment.</li>\r
- <li><strong>Scale Right</strong><br>Show the sequence position for the last aligned residue in each row in the right-most column of the alignment.</li>\r
- </em></li>\r
- <li><strong>Show Sequence Limits<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\r
- NAME/START-END</em></li>\r
- <li><strong>Right Align Sequence ID<br>\r
- </strong><em>If this box is selected then the sequence names displayed in\r
- the sequence label area will be aligned against the left-hand edge of\r
- the alignment display, rather than the left-hand edge of the alignment\r
- window.</li>\r
- <li><strong>Show Hidden Markers<br>\r
- </strong><em>When this box is selected, positions in the alignment where\r
- rows and columns are hidden will be marked by blue arrows.</li>\r
- <li><strong>Boxes</strong><em><br>\r
- If this is selected the background of a residue will be coloured using\r
- the selected background colour. Useful if used in conjunction with\r
- "Colour 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\r
- slightly darker than background so the amino acid symbol remains\r
- 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\r
- appear as blank spaces. <br>\r
- You may set the default gap character in <a\r
- href="../features/preferences.html">preferences</a>.</em></li>\r
-</ul>\r
-</body>\r
-</html>\r
+<html>
+<head>
+Alignment Window Menus
+</head>
+<body>
+<p><strong>Alignment Window Format Menu</strong></p>
+<ul>
+ <li><strong>Font...<br>
+ </strong><em>Opens the "Choose Font" dialog box, in order to
+ change the font of the display and enable or disable 'smooth fonts'
+ (anti-aliasing) for faster alignment rendering. </em></li>
+ <li><strong>Wrap<br>
+ </strong><em>When ticked, the alignment display is "<a
+ href="../features/wrap.html">wrapped</a>" to the width of the
+ alignment window. This is useful if your alignment has only a few
+ sequences to view its full width at once.<br>
+ Additional options for display of sequence numbering and scales are
+ also visible in wrapped layout mode:<br>
+ <ul>
+ <li><strong>Scale Above</strong><br>Show the alignment column position scale.</li>
+ <li><strong>Scale Left</strong><br>Show the sequence position for the first aligned residue in each row in the left column of the alignment.</li>
+ <li><strong>Scale Right</strong><br>Show the sequence position for the last aligned residue in each row in the right-most column of the alignment.</li>
+ </em></li>
+ <li><strong>Show Sequence Limits<br>
+ </strong><em>If this box is selected the sequence name will have the start
+ and end position of the sequence appended to the name, in the format
+ NAME/START-END</em></li>
+ <li><strong>Right Align Sequence ID<br>
+ </strong><em>If this box is selected then the sequence names displayed in
+ the sequence label area will be aligned against the left-hand edge of
+ the alignment display, rather than the left-hand edge of the alignment
+ window.</li>
+ <li><strong>Show Hidden Markers<br>
+ </strong><em>When this box is selected, positions in the alignment where
+ rows and columns are hidden will be marked by blue arrows.</li>
+ <li><strong>Boxes</strong><em><br>
+ If this is selected the background of a residue will be coloured using
+ the selected background colour. Useful if used in conjunction with
+ "Colour Text." </em></li>
+ <li><strong>Text<br>
+ </strong><em>If this is selected the residues will be displayed using the
+ standard 1 character amino acid alphabet.</em></li>
+ <li><strong>Colour Text<br>
+ </strong><em>If this is selected the residues will be coloured according to
+ the background colour associated with that residue. The colour is
+ slightly darker than background so the amino acid symbol remains
+ visible. </em></li>
+ <li><strong>Show Gaps<br>
+ </strong><em>When this is selected, gap characters will be displayed as
+ "." or "-". If unselected, then gap characters will
+ appear as blank spaces. <br>
+ You may set the default gap character in <a
+ href="../features/preferences.html">preferences</a>.</em></li>
+</ul>
+</body>
+</html>
-<html>\r
-<head>\r
-Alignment Window Menus\r
-</head>\r
-<body>\r
-<p><strong>Alignment Window Select Menu</strong></p>\r
-<ul>\r
- <li><strong><a href="../features/search.html">Find...\r
- (Control F)</a></strong><em><br>\r
- Opens the Find dialog box to perform regular expression searches on the\r
- aligned sequences and their IDs and create new features.\r
- <li><strong>Select All (Control A)<br>\r
- </strong><em>Selects all the sequences and residues in the alignment. <br>\r
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.</em></li>\r
- <li><strong>Deselect All (Escape)<br>\r
- </strong><em>Removes the current selection box (red dashed box) from the\r
- alignment window. All selected sequences, residues and marked columns\r
- will be deselected. </em><em> <br>\r
- Use <ESCAPE> to deselect all.</em></li>\r
- <li><strong>Invert Sequence Selection (Control I)<br>\r
- </strong><em>Any sequence ids currently not selected will replace the\r
- current selection. </em></li>\r
- <li><strong>Invert Column Selection (Control Alt I)<br>\r
- </strong><em>Any columns currently not selected will replace the current\r
- column selection. </em></li>\r
- <li><strong>Undefine Groups (Control U)<br>\r
- </strong><em>The alignment will be reset with no defined groups.<br>\r
- <strong>WARNING</strong>: This cannot be undone.</em></li>\r
-</ul>\r
-</body>\r
-</html>\r
+<html>
+<head>
+Alignment Window Menus
+</head>
+<body>
+<p><strong>Alignment Window Select Menu</strong></p>
+<ul>
+ <li><strong><a href="../features/search.html">Find...
+ (Control F)</a></strong><em><br>
+ Opens the Find dialog box to perform regular expression searches on the
+ aligned sequences and their IDs and create new features.
+ <li><strong>Select All (Control A)<br>
+ </strong><em>Selects all the sequences and residues in the alignment. <br>
+ Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.</em></li>
+ <li><strong>Deselect All (Escape)<br>
+ </strong><em>Removes the current selection box (red dashed box) from the
+ alignment window. All selected sequences, residues and marked columns
+ will be deselected. </em><em> <br>
+ Use <ESCAPE> to deselect all.</em></li>
+ <li><strong>Invert Sequence Selection (Control I)<br>
+ </strong><em>Any sequence ids currently not selected will replace the
+ current selection. </em></li>
+ <li><strong>Invert Column Selection (Control Alt I)<br>
+ </strong><em>Any columns currently not selected will replace the current
+ column selection. </em></li>
+ <li><strong>Undefine Groups (Control U)<br>
+ </strong><em>The alignment will be reset with no defined groups.<br>
+ <strong>WARNING</strong>: This cannot be undone.</em></li>
+</ul>
+</body>
+</html>
git://source.jalview.org / jalview.git / commitdiff