-<html>\r
-<head>\r
-<title>Creating Sequence Features</title>\r
-</head>\r
-<body>\r
-<strong>Creating Sequence Features</strong>\r
-<p>Jalview can create sequence features from the matches of a <a\r
- href="search.html">regular expression search</a>, or from the currently\r
-selected area via the <strong>"selection→Create\r
-sequence feature"</strong> entry in the selection area popup menu. In both\r
-cases, the <strong>Create Features</strong> dialog box will then be\r
-opened:</p>\r
-<img src="crnewfeature.gif">\r
-<p>Select or enter the attributes for the features being created,\r
-and then press OK to create the new features.</p>\r
-<p>Each attribute is described below:\r
-<ul>\r
- <li><strong>Sequence Feature Name</strong>\r
- <p>Either give the new features a new name or use the menu to\r
- re-use an existing feature name.</p>\r
- </li>\r
- <li><strong>Feature group</strong>\r
- <p>Enter a new group name, or re-use an existing group from the\r
- pull-down menu.</p>\r
- </li>\r
- <li><strong>Feature Colour</strong>\r
- <p>Keep the existing colour for this feature's name and group, or\r
- select the colour box to open a colour chooser to pick a different one.</p>\r
- </li>\r
- <li><strong>Description</strong>\r
- <p>Enter a description for all the features being created. Each\r
- feature defined on a sequence may have its own description that will be\r
- displayed in the tooltip for the feature in that region.</p>\r
- </li>\r
-</ul>\r
-</p><p><em>Sequence Feature Creation was introduced in Jalview Version 2.2</em></p>\r
-</body>\r
+<html>
+<head>
+<title>Creating Sequence Features</title>
+</head>
+<body>
+<strong>Creating Sequence Features</strong>
+<p>Jalview can create sequence features from the matches of a <a
+ href="search.html">regular expression search</a>, or from the currently
+selected area via the <strong>"selection→Create
+sequence feature"</strong> entry in the selection area popup menu. In both
+cases, the <strong>Create Features</strong> dialog box will then be
+opened:</p>
+<img src="crnewfeature.gif">
+<p>Select or enter the attributes for the features being created,
+and then press OK to create the new features.</p>
+<p>Each attribute is described below:
+<ul>
+ <li><strong>Sequence Feature Name</strong>
+ <p>Either give the new features a new name or use the menu to
+ re-use an existing feature name.</p>
+ </li>
+ <li><strong>Feature group</strong>
+ <p>Enter a new group name, or re-use an existing group from the
+ pull-down menu.</p>
+ </li>
+ <li><strong>Feature Colour</strong>
+ <p>Keep the existing colour for this feature's name and group, or
+ select the colour box to open a colour chooser to pick a different one.</p>
+ </li>
+ <li><strong>Description</strong>
+ <p>Enter a description for all the features being created. Each
+ feature defined on a sequence may have its own description that will be
+ displayed in the tooltip for the feature in that region.</p>
+ </li>
+</ul>
+</p><p><em>Sequence Feature Creation was introduced in Jalview Version 2.2</em></p>
+</body>
</html>
\ No newline at end of file
-<html>\r
-<head>\r
-<title>Amending or Deleting Sequence Features</title>\r
-</head>\r
-<body>\r
-<strong>Amending or Deleting Sequence Features</strong>\r
-<p>Double clicking a position in the alignment with one or more\r
-displayed sequence features opens the <strong>"Amend/Delete\r
-Features"</strong> dialog box.</p>\r
-<p><img src="amendfeature.gif"></p>\r
-<p>The dialog box only allows one of the features at the\r
-double-clicked position to be edited or deleted at a time, and it will\r
-also be highlighted in black in the alignment window.</p>\r
-<p>Choose which feature is to be modified by selecting it from the <strong>Sequence\r
-Feature Name</strong> <!-- and <strong>Feature Group</strong> --> pull down\r
-menu. In addition to the Name, group, colour and description attributes\r
-described for the <a href="creatinFeatures.html">new feature dialog\r
-box</a>, a feature's start and end position can be changed either by\r
-entering a new position directly or by using the adjacent up and down\r
-buttons.</p>\r
-<p>Select <strong>Amend</strong> to update the feature, <strong>Delete</strong>\r
-to remove the selected feature, or <strong>Cancel</strong> to leave the\r
-feature unchanged.</p>\r
-<p><em>Sequence feature editing was implemented in Jalview 2.2</em></p>\r
-</body>\r
-</html>\r
+<html>
+<head>
+<title>Amending or Deleting Sequence Features</title>
+</head>
+<body>
+<strong>Amending or Deleting Sequence Features</strong>
+<p>Double clicking a position in the alignment with one or more
+displayed sequence features opens the <strong>"Amend/Delete
+Features"</strong> dialog box.</p>
+<p><img src="amendfeature.gif"></p>
+<p>The dialog box only allows one of the features at the
+double-clicked position to be edited or deleted at a time, and it will
+also be highlighted in black in the alignment window.</p>
+<p>Choose which feature is to be modified by selecting it from the <strong>Sequence
+Feature Name</strong> <!-- and <strong>Feature Group</strong> --> pull down
+menu. In addition to the Name, group, colour and description attributes
+described for the <a href="creatinFeatures.html">new feature dialog
+box</a>, a feature's start and end position can be changed either by
+entering a new position directly or by using the adjacent up and down
+buttons.</p>
+<p>Select <strong>Amend</strong> to update the feature, <strong>Delete</strong>
+to remove the selected feature, or <strong>Cancel</strong> to leave the
+feature unchanged.</p>
+<p><em>Sequence feature editing was implemented in Jalview 2.2</em></p>
+</body>
+</html>
-<html>\r
-<head>\r
-<title>Multiple Alignment Views</title>\r
-</head>\r
-<body>\r
-<p><strong>Multiple Alignment Views<strong></p>\r
-<p>Multiple alignment views allow's the same alignment to be viewed in\r
-many different ways, either as multiple alignment tabs, or simultaneously in\r
-linked alignment windows. A view is an independent visualization of\r
-the same alignment, so each may have a different ordering, colouring,\r
-row and column hiding and seuqence feature and annotation display\r
-setting, but alignment, feature and annotation edits are common to\r
-all, since this affects the underlying data.\r
-</p>\r
-<p>\r
-A new view is created using the <strong>"View→New View"</strong> menu item, or by pressing\r
-<strong>Control+T</strong>. A newly created view will be identical to\r
-the view it was created from, but any changes to the way the alignment\r
-is coloured or displayed will only affect the new view.\r
-</p>\r
-<p>A particular view may focus on some specific aspect of an alignment -\r
-for example, hiding all but the region of an alignment containing a\r
-particular domain. <strong>Right-clicking</strong> a view's tab opens\r
-the View Name dialog box, allowing it to be renamed to something more\r
-meaningful.\r
-</p>\r
-<p><strong>Viewing Multiple Views Simultaneously</strong></p>\r
-<p>Multiple views of an alignment are, by default, gathered together as tabs\r
-within a single alignment window. They can be viewed simultanously by\r
-pressing <strong>X</strong> (or via\r
-<strong>"View→Expand"</strong>) to expand each view\r
-into its own linked alignment window. Expanded views are gathered\r
-back into into a single tabbed alignment window by pressing\r
-<strong>G</strong>, or by selecting <strong>"View→Gather"</strong>).\r
-</p>\r
-<p><strong>Tree Viewers and Multiple Views</strong></p>\r
-<p>A tree calculated on a particular view, or loaded onto it, is by\r
-default associated with just that view. However, the <a\r
-href="../calculations/treeviewer.html">Tree Viewer's</a> \r
-<strong>"View→Associate leaves"</strong> submenu\r
-allows a tree's view association to be changed to to any or all other\r
-views.</p>\r
-<p><em>Multiple Views were introduced in Jalview 2.2</em></p></body>\r
+<html>
+<head>
+<title>Multiple Alignment Views</title>
+</head>
+<body>
+<p><strong>Multiple Alignment Views<strong></p>
+<p>Multiple alignment views allow's the same alignment to be viewed in
+many different ways, either as multiple alignment tabs, or simultaneously in
+linked alignment windows. A view is an independent visualization of
+the same alignment, so each may have a different ordering, colouring,
+row and column hiding and seuqence feature and annotation display
+setting, but alignment, feature and annotation edits are common to
+all, since this affects the underlying data.
+</p>
+<p>
+A new view is created using the <strong>"View→New View"</strong> menu item, or by pressing
+<strong>Control+T</strong>. A newly created view will be identical to
+the view it was created from, but any changes to the way the alignment
+is coloured or displayed will only affect the new view.
+</p>
+<p>A particular view may focus on some specific aspect of an alignment -
+for example, hiding all but the region of an alignment containing a
+particular domain. <strong>Right-clicking</strong> a view's tab opens
+the View Name dialog box, allowing it to be renamed to something more
+meaningful.
+</p>
+<p><strong>Viewing Multiple Views Simultaneously</strong></p>
+<p>Multiple views of an alignment are, by default, gathered together as tabs
+within a single alignment window. They can be viewed simultanously by
+pressing <strong>X</strong> (or via
+<strong>"View→Expand"</strong>) to expand each view
+into its own linked alignment window. Expanded views are gathered
+back into into a single tabbed alignment window by pressing
+<strong>G</strong>, or by selecting <strong>"View→Gather"</strong>).
+</p>
+<p><strong>Tree Viewers and Multiple Views</strong></p>
+<p>A tree calculated on a particular view, or loaded onto it, is by
+default associated with just that view. However, the <a
+href="../calculations/treeviewer.html">Tree Viewer's</a>
+<strong>"View→Associate leaves"</strong> submenu
+allows a tree's view association to be changed to to any or all other
+views.</p>
+<p><em>Multiple Views were introduced in Jalview 2.2</em></p></body>
</html>
\ No newline at end of file
-<html>\r
-<head>\r
-<title>Reload and Save Alignment</title>\r
-</head>\r
-<body>\r
-<p><strong>Reload and Save Alignment</strong></p>\r
-<p>Jalview remembers the original source of an alignment if it has\r
-been loaded from a file or\r
-URL.<ul>\r
-<li><strong>"File→Reload"</strong> will reload the\r
-alignment from its original source, discarding any edits or applied\r
-colouring and features since the last save.</li>\r
-<li><strong>"File→Save"</strong> will save the\r
-alignment back to the same filename, with the same format, easing the\r
-the process of editing and updating an alignment file <em>in\r
-place</em>.\r
-</li>\r
-</ul>\r
-</body>\r
+<html>
+<head>
+<title>Reload and Save Alignment</title>
+</head>
+<body>
+<p><strong>Reload and Save Alignment</strong></p>
+<p>Jalview remembers the original source of an alignment if it has
+been loaded from a file or
+URL.<ul>
+<li><strong>"File→Reload"</strong> will reload the
+alignment from its original source, discarding any edits or applied
+colouring and features since the last save.</li>
+<li><strong>"File→Save"</strong> will save the
+alignment back to the same filename, with the same format, easing the
+the process of editing and updating an alignment file <em>in
+place</em>.
+</li>
+</ul>
+</body>
</html>
\ No newline at end of file
git://source.jalview.org / jalview.git / commitdiff