--- /dev/null
+<html>\r
+<head><title>Alignment Window Menus</title></head>\r
+\r
+<body>\r
+<p><strong>Alignment Window Calculate Menu</strong></p>\r
+<ul>\r
+ <li><strong>Calculate</strong></li>\r
+</ul>\r
+<blockquote>\r
+ <ul>\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
+ </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
+ </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
+ at the top. </em><strong><br>\r
+ </strong></li>\r
+ </ul>\r
+ <em>The <a href="../calculations/sorting.html">Sort menu</a> will\r
+ have some additional options if you have just done a multiple\r
+ alignment calculation, or opened a tree viewer window.</em><br>\r
+ </li>\r
+ <li><strong>Calculate Tree </strong>\r
+ <br><em>Functions for calculating trees on the alignment or the\r
+ currently selected region. See <a\r
+ href="../calculations/tree.html">calculating trees</a>.</em>\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></strong></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Pairwise Alignments</strong><br>\r
+ <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>\r
+ </li>\r
+ <li><strong>Principal Component Analysis</strong><br>\r
+ <em>Shows a spatial clustering of the sequences based on the\r
+ BLOSUM62 scores in the alignment. See <a href="../calculations/pca.html">Principal Component Analysis</a>.</em>\r
+ <br>\r
+ </li>\r
+ <li><strong>Web Service<br>\r
+ </strong>\r
+ <em>Selecting one of the following menu items starts a remote service\r
+ on compute facilities at the University of Dundee. You need a\r
+ continuous network connection in order to use these services\r
+ through Jalview.\r
+ </em>\r
+ <ul>\r
+ <li><strong>Clustal Alignment</strong><br><em>\r
+ Submits all, or just the currently selected sequences for alignment with clustal W.</em><br></li>\r
+ <li><strong>Clustal Realign</strong><br><em>\r
+ Submits the alignment or currently selected region for\r
+ re-alignment with clustal W. Use this if you have added some\r
+ new sequences to an existing alignment.</em><br></li>\r
+ <li><strong>Muscle Alignment</strong><br><em>\r
+ Submits all, or jut the currently selected sequences for\r
+ alignment using Muscle. Do not use this if you are working with\r
+ nucleic acid sequences.</em><br>\r
+ <li><strong>JNet</strong><br><em>\r
+ Secondary structure prediction by network consensus. The\r
+ behaviour of this calculation depends on the current selection:\r
+ <ul>\r
+ <li>If nothing is selected, and the displayed sequences appear to\r
+ be aligned, then a JNet prediction will be run for the first\r
+ sequence in the alignment, using the current\r
+ alignment. Otherwise the first sequence will be submitted for prediction.\r
+ </li>\r
+ <li>If\r
+ just one sequence (or a region on one sequence) has been selected,\r
+ it will be submitted to the automatic JNet prediction server\r
+ for homolog detection and prediction.\r
+ </li>\r
+ <li>If a set of sequences are selected, and they appear to be aligned,\r
+ then the alignment will be used for a Jnet prediction on the\r
+ <strong>first</strong> sequence selected in the set (that is, the one\r
+ that was first clicked on).\r
+ </li>\r
+ </ul>\r
+ </li>\r
+ <p> </p>\r
+</ul>\r
+</blockquote>\r
+\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head><title>Alignment Window Menus</title></head>\r
+\r
+<body>\r
+<p><strong>Alignment Window Colour Menu</strong></p>\r
+<ul>\r
+ <li><strong>Colour</strong></li>\r
+</ul>\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
+ will be applied to all currently defined groups.<br>\r
+ </em></li>\r
+ <li>Colour Scheme options: <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
+ 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
+ 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
+ Useful if the window has been closed, or if the 'by\r
+ conservation' option appears to be doing nothing!</em><br></li>\r
+ <li><strong>Above Identity Threshold<br>\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
+ Useful if the window has been closed. </em></li>\r
+ </ul>\r
+</blockquote>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head><title>Alignment Window Menus</title></head>\r
+\r
+<body>\r
+<p><strong>Alignment Window Edit Menu</strong></p>\r
+<ul>\r
+ <li><strong>Edit</strong></li>\r
+</ul>\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\r
+ alignment. <strong>NOTE:</strong> It DOES NOT undo colour\r
+ changes, adjustments to group sizes, or changes to the annotation 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
+ 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\r
+ clipboard - you can also do this by pressing <CTRL> and C\r
+ (<APPLE> and C on MacOSX). <br>\r
+ If you try to paste the clipboard contents to a text editor, you will see\r
+ the format of the copied residues is a tab separated list:<br>\r
+<pre>\r
+NAME START_RES END_RES SEQUENCE\r
+</pre><br>\r
+ </em></li>\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
+ 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
+ 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\r
+ without copying them to the clipboard. Like the other edit\r
+ operations, this can be undone with <strong>Undo</strong>.<br>\r
+ </em></li>\r
+ <li><strong>Select All<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.<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
+ 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
+ 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.<br> <strong>WARNING</strong>:\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
+ 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
+ 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 only contain gap characters ("-",\r
+ ".") will be deleted.<br>\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><strong>All</strong> 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
+ <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 any two sequences\r
+ (under the current alignment) exceeds this\r
+ value then one of the sequences (the shorter) is discarded. Press the "Apply"\r
+ button to remove redundant sequences. The "Undo" button will undo the last\r
+ redundancy deletion.<br>\r
+ </em></li>\r
+ <li><strong>Pad Gaps<br>\r
+ </strong><em>Adds gaps to the end of all the sequences so they\r
+ are all the same length. This is useful for making a tree using\r
+ unaligned sequences.<br>\r
+ You may set the default gap character in <a href="../features/preferences.html">preferences</a>.\r
+ </em></li>\r
+ </ul>\r
+</blockquote>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head><title>Alignment Window Menus</title></head>\r
+\r
+<body>\r
+<p><strong>Alignment Window File Menu</strong></p>\r
+<ul>\r
+ <li><strong>File</strong></li>\r
+</ul>\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
+ <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 graphic with the current annotation,\r
+ alignment background colours and group colours. If the alignment is <a\r
+ href="../features/wrap.html">wrapped</a>, the output will also\r
+ be wrapped and will have the same visible residue width as the\r
+ 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
+ from your alignment.</em></li>\r
+ <li><strong>EPS<br>\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
+ 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
+ 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
+ <ul>\r
+ <li><strong>FASTA</strong> <em></em></li>\r
+ <li><strong>MSF</strong></li>\r
+ <li><strong>CLUSTAL</strong></li>\r
+ <li><strong>BLC</strong></li>\r
+ <li><strong>PIR</strong></li>\r
+ <li><strong>PFAM</strong><br></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Print<br>\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 <a\r
+ href="../calculations/treeviewer.html">view trees</a> stored in\r
+ the Newick file format, and associate them with the\r
+ alignment. Note: the ids of the tree file and your alignment\r
+ MUST be the same.<br>\r
+ </em></li>\r
+ <li><strong>Close<br>\r
+ </strong><em>Close the alignment window. Make sure you have\r
+ saved your alignment before you close - either as a Jalview\r
+ project or by using the <strong>Save As</strong> menu.<br>\r
+ </em></li>\r
+ </ul>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head><title>Alignment Window Menus</title></head>\r
+\r
+<body>\r
+<p><strong>Alignment Window View Menu</strong></p>\r
+<ul>\r
+ <li><strong>View</strong></li>\r
+</ul>\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
+ </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
+ 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
+ </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 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
+ 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
+ </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
+</body>\r
+</html>\r
git://source.jalview.org / jalview.git / commitdiff