<li><strong>File</strong></li>\r
<ul>\r
<li><strong>Save As<br>\r
- </strong><em>Save the alignment to local file. A file selection window will \r
- open, use the "Files of type:" selection box to determine which \r
+ </strong><em>Save the alignment to local file. A file selection window will\r
+ open, use the "Files of type:" selection box to determine which\r
<a href="../io/index.html">alignment format</a> to save as.<br>\r
</em></li>\r
<li><strong>Export</strong> <em><br>\r
- Creates an alignment output maintaining the alignment background colours \r
- and group colours. If the alignment is wrapped, the output will also be \r
- wrapped and will have the same visible residue width as the open alignment. \r
- </em> \r
+ Creates an alignment output maintaining the alignment background colours\r
+ and group colours. If the alignment is wrapped, the output will also be\r
+ wrapped and will have the same visible residue width as the open alignment.\r
+ </em>\r
<ul>\r
<li><strong>HTML<br>\r
- </strong><em>Create a <a href="../io/index.html#export">web page</a> \r
+ </strong><em>Create a <a href="../io/index.html#export">web page</a>\r
from your alignment.</em></li>\r
<li><strong>EPS<br>\r
- </strong><em>Create an <a href="../io/index.html#export">Encapsulated \r
+ </strong><em>Create an <a href="../io/index.html#export">Encapsulated\r
Postscript</a> file from your alignment.</em></li>\r
<li><strong>PNG<br>\r
- </strong><em>Create a <a href="../io/index.html#export">Portable Network \r
+ </strong><em>Create a <a href="../io/index.html#export">Portable Network\r
Graphics</a> file from your alignment.<br>\r
</em></li>\r
</ul>\r
</li>\r
<li><strong>Output to Textbox<br>\r
- </strong><em>The alignment will be displayed in plain text in a new window \r
- which you can "Copy and Paste" using the pull down menu, or your \r
+ </strong><em>The alignment will be displayed in plain text in a new window\r
+ which you can "Copy and Paste" using the pull down menu, or your\r
standard operating system copy and paste keys. <br>\r
- Select the format of the text by selecting one of the following menu items.</em> \r
+ Select the format of the text by selecting one of the following menu items.</em>\r
<ul>\r
<li><strong>FASTA</strong> <em></em></li>\r
<li><strong>MSF</strong></li>\r
</ul>\r
</li>\r
<li><strong>Print<br>\r
- </strong><em>Jalview will print the alignment using the current fonts and \r
- coloursof your alignment. If the alignment has annotations visible, these \r
- will be printed below the alignment. If the alignment is wrapped the number \r
- of residues per line of your alignment will depend on the paper width or \r
+ </strong><em>Jalview will print the alignment using the current fonts and\r
+ colours of your alignment. If the alignment has annotations visible, these\r
+ will be printed below the alignment. If the alignment is wrapped the number\r
+ of residues per line of your alignment will depend on the paper width or\r
your alignment window width, whichever is the smaller. <br>\r
</em></li>\r
<li><strong>Load Associated Tree<br>\r
- </strong><em>Jalview can load in trees which are in the Newick file format \r
- and associate them with a particular alignment. Note: the ids of the tree \r
+ </strong><em>Jalview can load in trees which are in the Newick file format\r
+ and associate them with a particular alignment. Note: the ids of the tree\r
file and your alignment MUST be the same.<br>\r
</em></li>\r
<li><strong>Close<br>\r
- </strong><em>Close the alignment window. Be aware that changes to your alignment \r
- will not be save unless specifically actioned from the "Save As" \r
+ </strong><em>Close the alignment window. Be aware that changes to your alignment\r
+ will not be save unless specifically actioned from the "Save As"\r
menu.<br>\r
</em></li>\r
</ul>\r
<li><strong>Edit</strong></li>\r
</ul>\r
-<blockquote> \r
+<blockquote>\r
<ul>\r
<li><strong>Undo</strong><em><br>\r
- This will undo any edits you make to the alignment. This applies to insertion \r
- or deletion of gaps, cutting residues or sequences from the alignment or \r
- pasting sequences to the current alignment or sorting the alignment. It \r
- DOES NOT undo colour changes or adjustments to group sizes affect the annotation \r
+ This will undo any edits you make to the alignment. This applies to insertion\r
+ or deletion of gaps, cutting residues or sequences from the alignment or\r
+ pasting sequences to the current alignment or sorting the alignment. It\r
+ DOES NOT undo colour changes or adjustments to group sizes affect the annotation\r
panel. <br>\r
</em></li>\r
<li><strong>Redo<br>\r
</strong><em>Any actions which you undo can be redone using redo. <br>\r
</em></li>\r
<li><strong>Cut<br>\r
- </strong><em>This will make a copy of the currently selected residues before \r
- removing them from your alignment. Click on a sequence name if you wish \r
+ </strong><em>This will make a copy of the currently selected residues before\r
+ removing them from your alignment. Click on a sequence name if you wish\r
to select a whole sequence. <br>\r
Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.<br>\r
</em></li>\r
<li><strong>Copy</strong><br>\r
- <em>Copies the currently selected residues to the system clipboard. The \r
- format of copied residues is NAME<tab>START_RES<tab>END_RES<tab>SEQUENCE \r
+ <em>Copies the currently selected residues to the system clipboard. The\r
+ format of copied residues is NAME<tab>START_RES<tab>END_RES<tab>SEQUENCE\r
<br>\r
Use <CTRL> and C (<APPLE> and C on MacOSX) to copy.<br>\r
</em></li>\r
- <li><strong>Paste </strong> \r
+ <li><strong>Paste </strong>\r
<ul>\r
<li><strong>To New Alignment<br>\r
- </strong><em>A new alignment window will be created from sequences previously \r
+ </strong><em>A new alignment window will be created from sequences previously\r
copied or cut to the system clipboard. <br>\r
Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.</em></li>\r
<li><strong>Add To This Alignment<br>\r
- </strong><em>Copied sequences from another alignment window can be added \r
+ </strong><em>Copied sequences from another alignment window can be added\r
to the current Jalview alignment. <br>\r
</em><strong> </strong></li>\r
</ul>\r
</li>\r
<li><strong>Delete<br>\r
- </strong><em>This will delete the currently selected residues without making \r
+ </strong><em>This will delete the currently selected residues without making\r
a copy of them first.<br>\r
</em></li>\r
<li><strong>Select All<br>\r
Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.<br>\r
</em></li>\r
<li><strong>Deselect All<br>\r
- </strong><em>Removes the current selection box (red dashed box) from the \r
- alignment window. All selected sequences, residues and marked columns will \r
+ </strong><em>Removes the current selection box (red dashed box) from the\r
+ alignment window. All selected sequences, residues and marked columns will\r
be deselected. </em><em> <br>\r
Use <ESCAPE> to deselect all.<br>\r
</em></li>\r
<li><strong>Invert Selection<br>\r
- </strong><em>Any sequence ids currently not selected will replace the current \r
+ </strong><em>Any sequence ids currently not selected will replace the current\r
selection. <br>\r
</em><strong> </strong></li>\r
<li><strong>Undefine Groups<br>\r
- </strong><em>The alignment will be reset with no defined groups. WARNING: \r
+ </strong><em>The alignment will be reset with no defined groups. WARNING:\r
This cannot be undone.<br>\r
</em></li>\r
<li><strong>Remove Left<br>\r
- </strong><em>If the alignment has marked columns, the alignment will be \r
- trimmed to the left of the leftmost marked column. To mark a column, mouse \r
- click the scale bar above the alignment. Click again to unmark a column, \r
+ </strong><em>If the alignment has marked columns, the alignment will be\r
+ trimmed to the left of the leftmost marked column. To mark a column, mouse\r
+ click the scale bar above the alignment. Click again to unmark a column,\r
or select "Deselect All" to deselect all columns.<br>\r
</em></li>\r
<li><strong>Remove Right<br>\r
- </strong><em>If the alignment has marked columns, the alignment will be \r
- trimmed to the left of the leftmost marked column. To mark a column, mouse \r
- click the scale bar above the alignment. Click again to unmark a column, \r
+ </strong><em>If the alignment has marked columns, the alignment will be\r
+ trimmed to the left of the leftmost marked column. To mark a column, mouse\r
+ click the scale bar above the alignment. Click again to unmark a column,\r
or select "Deselect All" to deselect all columns.<br>\r
</em></li>\r
<li><strong>Remove Empty Columns<br>\r
- </strong><em>All columns which contain purely gap characters ("-", \r
+ </strong><em>All columns which contain purely gap characters ("-",\r
".") will be deleted.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
+ You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
</em><em><br>\r
</em></li>\r
<li><strong>Remove All Gaps</strong><br>\r
- <em>All gap characters ("-", ".") will be deleted from \r
+ <em>All gap characters ("-", ".") will be deleted from\r
the alignment.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
+ You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
<br>\r
</em> </li>\r
<li><strong>Remove Redundancy<br>\r
- </strong><em>Selecting this option brings up a window asking you to select \r
- a threshold. If the percentage identity between two sequences exceeds this \r
- value one of the sequences (the shorter) is discarded. Press the "Apply" \r
- button to reomove redundant sequences.<br>\r
+ </strong><em>Selecting this option brings up a window asking you to select\r
+ a threshold. If the percentage identity between two sequences exceeds this\r
+ value one of the sequences (the shorter) is discarded. Press the "Apply"\r
+ button to remove redundant sequences.<br>\r
</em></li>\r
<li><strong>Pad Gaps<br>\r
- </strong><em>If the sequences in an alignment window are not all the same \r
- length they can all be set to the length of the longest sequence by selecting \r
- "Pad Gaps." Any sequences which are shorter than the longest sequence \r
- in an alignment will have gap characters ("-" or ".") \r
+ </strong><em>If the sequences in an alignment window are not all the same\r
+ length they can all be set to the length of the longest sequence by selecting\r
+ "Pad Gaps." Any sequences which are shorter than the longest sequence\r
+ in an alignment will have gap characters ("-" or ".")\r
appended to the beginning or end to make them equal length. <br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
+ You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
</em></li>\r
</ul>\r
</blockquote>\r
<ul>\r
<li><strong>Search</strong></li>\r
</ul>\r
-<blockquote> \r
+<blockquote>\r
<ul>\r
<li><strong>Find<br>\r
- </strong><em>Select this to <a href="../features/search.html">search</a> \r
+ </strong><em>Select this to <a href="../features/search.html">search</a>\r
for residues, sequence name or residue position within the alignment. </em></li>\r
</ul>\r
</blockquote>\r
<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. The default font can be set \r
- from the "Choose Font" window, which is shown when the "Font \r
+ </strong><em>Change the font of the display. The default font can be set\r
+ from the "Choose Font" window, which is shown when the "Font\r
Menu" is selected. <br>\r
</em></li>\r
<li><strong>Wrap<br>\r
- </strong><em>The default alignment display shows sequences in a single horizontal \r
- row. If your alignment has only a few sequences you may wish to "Wrap" \r
- the alignment so that the sequences are shown on multiple horizontal rows. \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>The default alignment display shows sequences in a single horizontal\r
+ row. If your alignment has only a few sequences you may wish to "Wrap"\r
+ the alignment so that the sequences are shown on multiple horizontal rows.\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
- NOTE: In the current version the wrap alignment should be used for viewing, \r
+ NOTE: In the current version the wrap alignment should be used for viewing,\r
not editing. <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 to enable the residue to be read. <br>\r
</em></li>\r
<li><strong>Show Gaps<br>\r
- </strong><em>If this is selected gap characters will be displayed as "." \r
- or "-". If unselected gap characters will appear as blank spaces. \r
+ </strong><em>If this is selected gap characters will be displayed as "."\r
+ or "-". If unselected gap characters will appear as blank spaces.\r
<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
- calulation, quality calculation and consensus values as bar charts. </em><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>Sequence Features<br>\r
- </strong><em>If the sequence names are Swissprot entries Jalview will use \r
- the names to retrieve sequence features 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
+ </strong><em>If the sequence names are Swissprot entries Jalview will use\r
+ the names to retrieve sequence features 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
+ Note: The retrieved information will update the sequence start and end labels\r
if they are incorrect. <br>\r
</em></li>\r
<li><strong>Overview Window<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
<ul>\r
<li><strong>Colour</strong></li>\r
</ul>\r
-<blockquote> \r
+<blockquote>\r
<ul>\r
<li><strong>Apply Colour To All Groups<br>\r
- </strong><em>If this is selected, any changes made to the background colour \r
+ </strong><em>If this is selected, any changes made to the background colour\r
will be applied to all currently defined groups.<br>\r
</em></li>\r
- <li><strong>None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor, \r
- Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried \r
+ <li><strong>None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor,\r
+ Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried\r
Index, Nucleotide, User Defined<br>\r
- </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for \r
+ </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for\r
a description of all colour schemes.</em><br>\r
</li>\r
<li><strong>By Conservation<br>\r
- </strong><em>See <a href="../colourSchemes/conservation.html">Colouring \r
+ </strong><em>See <a href="../colourSchemes/conservation.html">Colouring\r
by Conservation</a>.</em><br>\r
</li>\r
<li><strong>Modify Conservation Threshold<br>\r
- </strong><em>Use this to display the conservation threshold slider window. \r
+ </strong><em>Use this to display the conservation threshold slider window.\r
Useful if the window has been closed. </em></li>\r
<li><strong>Above Identity Threshold<br>\r
- </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage \r
+ </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage\r
Identity</a></em><strong>.<br>\r
</strong></li>\r
<li><strong>Modify Identity Threshold<br>\r
- </strong><em>Use this to set the threshold value for colouring above Identity. \r
+ </strong><em>Use this to set the threshold value for colouring above Identity.\r
Useful if the window has been closed. </em></li>\r
</ul>\r
</blockquote>\r
<ul>\r
<li><strong>Calculate</strong></li>\r
</ul>\r
-<blockquote> \r
+<blockquote>\r
<ul>\r
- <li><strong>Sort </strong> \r
+ <li><strong>Sort </strong>\r
<ul>\r
<li><strong>by ID<br>\r
- </strong><em>This will sort the sequences according to sequence name. \r
- If the sort is repeated, the order of the sorted sequences will be inverted. \r
+ </strong><em>This will sort the sequences according to sequence name.\r
+ If the sort is repeated, the order of the sorted sequences will be inverted.\r
</em><strong><br>\r
</strong></li>\r
<li><strong>by Group</strong><strong><br>\r
- </strong><em>This will sort the sequences according to sequence name. \r
- If the sort is repeated, the order of the sorted sequences will be inverted. \r
+ </strong><em>This will sort the sequences according to sequence name.\r
+ If the sort is repeated, the order of the sorted sequences will be inverted.\r
</em><strong></strong><strong><br>\r
</strong></li>\r
<li><strong>by Pairwise Identity<br>\r
- </strong><em>This will sort the selected sequences by their percentage \r
- identity to the consensus sequence. The most similar sequence is put \r
+ </strong><em>This will sort the selected sequences by their percentage\r
+ identity to the consensus sequence. The most similar sequence is put\r
at the top. </em><strong><br>\r
</strong></li>\r
</ul>\r
</li>\r
- <li><strong>Calculate Tree </strong> \r
+ <li><strong>Calculate Tree </strong>\r
<ul>\r
<li><strong>Average Distance Using % Identity</strong></li>\r
<li><strong>Neighbour Joining Using % Identity</strong></li>\r
<li><strong>Average Distance Using Blosum62</strong></li>\r
<li><strong>Neighbour Joining Using Blosum62<br>\r
- </strong><em>See <a href="../calculations/tree.html">calculating trees</a>.</em><strong> \r
+ </strong><em>See <a href="../calculations/tree.html">calculating trees</a>.</em><strong>\r
<br>\r
</strong></li>\r
</ul>\r
</li>\r
- <li><strong>Paiwise Alignments</strong><br>\r
+ <li><strong>Pairwise Alignments</strong><br>\r
<em>See <a href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>\r
</li>\r
<li><strong>Principal Component Analysis</strong><br>\r
- <em>See <a href="../calculations/pca.html">Principal Component Analysis</a>.</em> \r
+ <em>See <a href="../calculations/pca.html">Principal Component Analysis</a>.</em>\r
<br>\r
</li>\r
<li><strong>Web Service <br>\r
- </strong> \r
+ </strong>\r
<ul>\r
- <em>Selecting one of the following menu items will start a remote service \r
- on the high powered computing faciltiy at the University of Dundee. You \r
- will need a continuous network connection in order to use these services. \r
- </em> \r
+ <em>Selecting one of the following menu items will start a remote service\r
+ on the high powered computing facility at the University of Dundee. You\r
+ will need a continuous network connection in order to use these services.\r
+ </em>\r
<li><strong>Clustal Alignment</strong></li>\r
<li><strong>Clustal Realign</strong></li>\r
<li><strong>JPred</strong></li>\r
git://source.jalview.org / jalview.git / commitdiff