<mapID target="release" url="html/releases.html"/>
<mapID target="alannotation" url="html/features/annotation.html"/>
<mapID target="keys" url="html/keys.html"/>
+ <mapID target="newkeys" url="html/features/newkeystrokes.html"/>
<mapID target="cursor" url="html/features/cursorMode.html"/>
<mapID target="search" url="html/features/search.html"/>
<mapID target="webservice" url="html/webServices/index.html"/>
<mapID target="redundancy" url="html/calculations/redundancy.html"/>
<mapID target="hiddenRegions" url="html/features/hiddenRegions.html"/>
<mapID target="recoverInputdata" url="html/calculations/recoverInputdata.html"/>
- <mapID target="colours" url="html/colourSchemes/index.html" />
+ <mapID target="colours" url="html/colourSchemes/index.html"/>
+ <mapID target="backdeptextcol" url="html/colourSchemes/textcolour.html"/>
<mapID target="colours.clustal" url="html/colourSchemes/clustal.html"/>
<mapID target="colours.zappo" url="html/colourSchemes/zappo.html" />
<mapID target="colours.taylor" url="html/colourSchemes/taylor.html" />
<mapID target="alMenu" url="html/menus/alignmentMenu.html"/>
<mapID target="alwFile" url="html/menus/alwfile.html"/>
<mapID target="alwEdit" url="html/menus/alwedit.html"/>
+ <mapID target="alwSelect" url="html/menus/alwselect.html"/>
<mapID target="alwView" url="html/menus/alwview.html"/>
+ <mapID target="alwFormat" url="html/menus/alwformat.html"/>
<mapID target="alwColour" url="html/menus/alwcolour.html"/>
<mapID target="alwCalc" url="html/menus/alwcalculate.html"/>
<tocitem text="Jalview Documentation" target="home" expand="true" >
<tocitem text="What's new" target="new" expand="true">
<tocitem text="Multiple Views" target="multipleviews"/>
+ <tocitem text="New keystrokes and Menus" target="newkeys"/>
<tocitem text="Reload and Save" target="reloadsave"/>
<tocitem text="Creating Sequence Features" target="seqfeatcreat"/>
<tocitem text="Amending or Deleting Sequence Features" target="seqfeatedit"/>
- </tocitem>
+ <tocitem text="Background Dependent Text Colour" target="backdeptextcol"/>
+ </tocitem>
<tocitem text="Release History" target="release"/>
<tocitem text="Editing Alignments" target ="edit"/>
<tocitem text="Cursor Mode" target="cursor"/>
<tocitem text="Desktop Window" target="desktopMenu"/>
<tocitem text="Alignment Window" target="alMenu">
<tocitem text="File Menu" target="alwFile"/>
- <tocitem text="Edit Menu" target="alwEdit"/>
- <tocitem text="View Menu" target="alwView"/>
+ <tocitem text="Edit Menu" target="alwEdit"/>
+ <tocitem text="Select Menu" target="alwSelect"/>
+ <tocitem text="View Menu" target="alwView"/>
+ <tocitem text="Format Menu" target="alwFormat"/>
<tocitem text="Colour Menu" target="alwColour"/>
<tocitem text="Calculation Menu" target="alwCalc"/>
<tocitem text="Web Service Menu" target="wsMenu"/>
<html>
-<head><title>Principal Component Analysis</title></head>
+<head>
+<title>Principal Component Analysis</title>
+</head>
<body>
<p><strong>Principal Component Analysis</strong></p>
<p>This calculation creates a spatial representation of the
-similarities within a selected group, or all of the sequences in
-an alignment. After the calculation finishes, a 3D viewer displays the
-set of sequences as points in 'similarity space', and similar
-sequences tend to lie near each other in the space.</p>
-<p>Note: The calculation is computationally expensive, and may fail for very large sets of sequences -
- usually because the JVM has run out of memory. A future release of
- Jalview will be able to avoid this by executing the calculation via a web service.</p>
+similarities within a selected group, or all of the sequences in an
+alignment. After the calculation finishes, a 3D viewer displays the set
+of sequences as points in 'similarity space', and similar sequences tend
+to lie near each other in the space.</p>
+<p>Note: The calculation is computationally expensive, and may fail
+for very large sets of sequences - usually because the JVM has run out
+of memory. A future release of Jalview will be able to avoid this by
+executing the calculation via a web service.</p>
<p>Principal components analysis is a technique for examining the
structure of complex data sets. The components are a set of dimensions
formed from the measured values in the data set, and the principle
-component is the one with the greatest magnitude, or length. The
-sets of measurements that differ the most should lie at either end of
-this principle axis, and the other axes correspond to less extreme
-patterns of variation in the data set.
-</p>
+component is the one with the greatest magnitude, or length. The sets of
+measurements that differ the most should lie at either end of this
+principle axis, and the other axes correspond to less extreme patterns
+of variation in the data set.</p>
<p>In this case, the components are generated by an eigenvector
-decomposition of the matrix formed from the sum of BLOSUM scores at
-each aligned position between each pair of sequences. The basic method
-is described in the paper by G. Casari, C. Sander and
-A. Valencia. Structural Biology volume 2, no. 2, February 1995 (<a
-href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7749921">pubmed</a>)
- and implemented at the SeqSpace server at the EBI.
-</p>
+decomposition of the matrix formed from the sum of BLOSUM scores at each
+aligned position between each pair of sequences. The basic method is
+described in the paper by G. Casari, C. Sander and A. Valencia.
+Structural Biology volume 2, no. 2, February 1995 (<a
+ href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7749921">pubmed</a>)
+and implemented at the SeqSpace server at the EBI.</p>
<p><strong>The PCA Viewer</strong></p>
<p>This is an interactive display of the sequences positioned within
- the similarity space. The colour of each sequence point is the same
- as the sequence group colours, white if no colour has been
- defined for the sequence, and green if the sequence is part of a
- the currently selected group.
-</p>
- <p>The 3d view can be rotated by dragging the mouse with the
- <strong>left mouse button</strong> pressed. The view can also be
- zoomed in and out with the up and down <strong>arrow
- keys</strong> (and the roll bar of the mouse if present). Labels
- will be shown for each sequence if the entry in the View menu is
- checked, and the plot background colour changed from the
- View→Background Colour.. dialog box. The File menu allows the
- view to be saved (File→Save submenu) as an EPS or PNG image or
- printed, and the original alignment data and matrix resulting from
- its PCA analysis to be retrieved.
-</p>
- </p>
+the similarity space, as points in a rotateable 3D scatterplot. The
+colour of each sequence point is the same as the sequence group colours,
+white if no colour has been defined for the sequence, and green if the
+sequence is part of a the currently selected group.</p>
+<p>The 3d view can be rotated by dragging the mouse with the <strong>left
+mouse button</strong> pressed. The view can also be zoomed in and out with the up
+and down <strong>arrow keys</strong> (and the roll bar of the mouse if
+present). Labels will be shown for each sequence if the entry in the
+View menu is checked, and the plot background colour changed from the
+View→Background Colour.. dialog box. The File menu allows the view
+to be saved (<strong>File→Save</strong> submenu) as an EPS or PNG
+image or printed, and the original alignment data and matrix resulting
+from its PCA analysis to be retrieved.</p>
<p>A tool tip gives the sequence ID corresponding to a point in the
- space, and clicking a point toggles the selection of the
- corresponding sequence in the alignment window. Rectangular region
- based selection is also possible, by holding the 'S' key whilst
- left-clicking and dragging the mouse over the display.
-</p>
+space, and clicking a point toggles the selection of the corresponding
+sequence in the associated alignment window views. Rectangular region
+based selection is also possible, by holding the 'S' key whilst
+left-clicking and dragging the mouse over the display. By default,
+points are only associated with the alignment view from which the PCA
+was calculated, but this may be changed via the <strong>Associate
+Nodes</strong> sub-menu.</p>
<p>Initially, the display shows the first three components of the
- similarity space, but any eigenvector can be used by changing the selected
- dimension for the x, y, or z axis through each ones menu located
- below the 3d display.
-</p>
+similarity space, but any eigenvector can be used by changing the
+selected dimension for the x, y, or z axis through each ones menu
+located below the 3d display.</p>
<p>
-
</body>
</html>
--- /dev/null
+<html>\r
+<head>\r
+Background Dependent Text Colour\r
+</head>\r
+<body>\r
+<strong>Background Dependent Text Colour</strong>\r
+<p>The <strong>Colour→Text Colour</strong> menu entry opens\r
+the <strong>Text Colour</strong> dialog box. This contains a slider, and\r
+two colour icons showing the text colour for dark backgrounds (left hand\r
+end of slider), and light backgrounds (right hand end of slider). Drag\r
+the slider to change the threshold for transitioning between dark and\r
+light background colours, and select either of the colour boxes to open\r
+a colour chooser to select a different text colour.\r
+</p>\r
+</body>\r
+</html>\r
</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>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
+<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><strong>Tree Viewers, PCA 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
+ 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>The results of a <a href="../calculations/pca.html">PCA calculation</a> on a particular view
+may also be associated with other views, using the <strong>"Associate
+Nodes"</strong> submenu.</p>
+<p><em>Multiple Views were introduced in Jalview 2.2</em></p>
+</body>
+</html>
--- /dev/null
+<html>
+<title>New Key Strokes and Menus</title>
+<body>
+<strong>New Key Strokes and Menus</strong>
+<p>Many new <a href="../keys.html">keyboard shortcuts</a> have been
+added in Jalview 2.2 to make editing, selecting and navigating an
+alignment even easier. Some of the commands in the <strong>Edit</strong>
+and <strong>View</strong> menus present in earlier releases have also
+been moved into their own <strong>Select</strong> and <strong>Format</strong>
+menus. Some of the important new keystrokes are shown below :
+<ul>
+ <li><strong>Page Up</strong> and <strong>Page Down</strong>
+ scrolls through the alignment view.</li>
+ <li><strong>Control I</strong> inverts the currently selected
+ sequence set, and <strong>Control Alt I</strong> will invert the
+ currently selected set of columns.
+ <li><strong>Control+V</strong> will paste the contents of the
+ clipboard to the current alignment window, and <strong>Control
+ Shift V</strong> pastes the data to a new window.</li>
+</ul>
+</p>
+</body>
+</html>
--- /dev/null
+<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
--- /dev/null
+<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>\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 \r
- Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity, \r
- Turn Propensity, Buried 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 conservation' option \r
- appears to be doing nothing!</em><br>\r
- </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.<br>\r
- </em></li>\r
- <li><strong>By Annotation</strong><br>\r
- <em>Colours the alignment on a per-column value from a specified annotation. \r
- See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>\r
- </li>\r
- </ul>\r
-</blockquote>\r
-</body>\r
-</html>\r
+<html>
+<head><title>Alignment Window Menus</title></head>
+
+<body>
+<p><strong>Alignment Window Colour Menu</strong></p>
+ <ul>
+ <li><strong>Apply Colour To All Groups<br>
+ </strong><em>If this is selected, any changes made to the background colour
+ will be applied to all currently defined groups.<br>
+ </em></li>
+ <li><strong><a href="../colourSchemes/textcolour.html">Colour Text...</a></strong><em><br>
+ Opens the Colour Text dialog box to set a different text colour for light and dark background, and the intensity threshold for transition between them.
+ </em></li>
+ <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage
+ Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
+ Turn Propensity, Buried Index, Nucleotide, User Defined<br>
+ </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
+ a description of all colour schemes.</em><br>
+ </li>
+ <li><strong>By Conservation<br>
+ </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
+ by Conservation</a>.</em><br>
+ </li>
+ <li><strong>Modify Conservation Threshold<br>
+ </strong><em>Use this to display the conservation threshold slider window.
+ Useful if the window has been closed, or if the 'by conservation' option
+ appears to be doing nothing!</em><br>
+ </li>
+ <li><strong>Above Identity Threshold<br>
+ </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage
+ Identity</a></em><strong>.<br>
+ </strong></li>
+ <li><strong>Modify Identity Threshold<br>
+ </strong><em>Use this to set the threshold value for colouring above Identity.
+ Useful if the window has been closed.<br>
+ </em></li>
+ <li><strong>By Annotation</strong><br>
+ <em>Colours the alignment on a per-column value from a specified annotation.
+ See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>
+ </li>
+ </ul>
+</body>
+</html>
-<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>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 pasting \r
- sequences to the current alignment or sorting the alignment. <strong>NOTE:</strong> \r
- It DOES NOT undo colour changes, adjustments to group sizes, or changes to \r
- the annotation panel. </em></li>\r
- <li><strong>Redo<br>\r
- </strong><em>Any actions which you undo can be redone using redo. </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 to \r
- select a whole sequence. <br>\r
- Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>\r
- <li><strong>Copy</strong><br>\r
- <em>Copies the currently selected residues to the system clipboard - you can \r
- also do this by pressing <CTRL> and C (<APPLE> and C on MacOSX). \r
- <br>\r
- If you try to paste the clipboard contents to a text editor, you will see \r
- the format of the copied residues FASTA.</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. </em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Delete<br>\r
- </strong><em>This will delete the currently selected residues without copying \r
- them to the clipboard. Like the other edit operations, this can be undone \r
- with <strong>Undo</strong>.</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.</em></li>\r
- <li><strong>Deselect All<br>\r
- </strong><em>Removes the current selection box (red dashed box) from the alignment \r
- window. All selected sequences, residues and marked columns will be deselected. \r
- </em><em> <br>\r
- Use <ESCAPE> to deselect all.</em></li>\r
- <li><strong>Invert Sequence Selection<br>\r
- </strong><em>Any sequence ids currently not selected will replace the current \r
- selection. </em></li>\r
- <li><strong>Invert Column Selection<br>\r
- </strong><em>Any columns currently not selected will replace the current column \r
- selection. </em></li>\r
- <li><strong>Undefine Groups<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
- <li><strong>Remove Left<br>\r
- </strong><em>If the alignment has marked columns, the alignment will be trimmed \r
- to the left of the leftmost marked column. To mark a column, mouse click the \r
- scale bar above the alignment. Click again to unmark a column, or select "Deselect \r
- All" to deselect all columns.</em></li>\r
- <li><strong>Remove Right<br>\r
- </strong><em>If the alignment has marked columns, the alignment will be trimmed \r
- to the left of the leftmost marked column. To mark a column, mouse click the \r
- scale bar above the alignment. Click again to unmark a column, or select "Deselect \r
- All" to deselect all columns.</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></li>\r
- <li><strong>Remove All Gaps</strong><br>\r
- <em>Gap characters ("-", ".") will be deleted from the \r
- selected area of the alignment. If no selection is made, ALL the gaps in the \r
- alignment will be removed.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \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 (under the \r
- current alignment) exceeds this value then one of the sequences (the shorter) \r
- is discarded. Press the "Apply" button to remove redundant sequences. \r
- The "Undo" button will undo the last redundancy deletion.</em></li>\r
- <li><strong>Pad Gaps<br>\r
- </strong><em>When selected, the alignment will be kept at minimal width (so \r
- there no empty columns before or after the first or last aligned residue) \r
- and all sequences will be padded with gap characters to the before and after \r
- their terminating residues.<br>\r
- This switch is useful when making a tree using unaligned sequences and when \r
- working with alignment analysis programs which require 'properly aligned sequences' \r
- to be all the same length.<br>\r
- You may set the default for <strong>Pad Gaps</strong> in the <a href="../features/preferences.html">preferences</a>. \r
- </em></li>\r
-</ul>\r
- </body>\r
-</html>\r
+<html>
+<head>
+<title>Alignment Window Menus</title>
+</head>
+
+<body>
+<p><strong>Alignment Window Edit Menu</strong></p>
+<ul>
+ <li><strong>Undo (Control Z)</strong><em><br>
+ This will undo any edits you make to the alignment. This applies to
+ insertion or deletion of gaps, cutting residues or sequences from the
+ alignment or pasting sequences to the current alignment or sorting the
+ alignment. <strong>NOTE:</strong> It DOES NOT undo colour changes,
+ adjustments to group sizes, or changes to the annotation panel. </em></li>
+ <li><strong>Redo (Control Y)<br>
+ </strong><em>Any actions which you undo can be redone using redo. </em></li>
+ <li><strong>Cut (Control X)<br>
+ </strong><em>This will make a copy of the currently selected residues
+ before removing them from your alignment. Click on a sequence name if
+ you wish to select a whole sequence. <br>
+ Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>
+ <li><strong>Copy (Control C)</strong><br>
+ <em>Copies the currently selected residues to the system clipboard
+ - you can also do this by pressing <CTRL> and C (<APPLE>
+ and C on MacOSX). <br>
+ If you try to paste the clipboard contents to a text editor, you will
+ see the format of the copied residues FASTA.</em></li>
+ <li><strong>Paste </strong>
+ <ul>
+ <li><strong>To New Alignment (Control Shift V)<br>
+ </strong><em>A new alignment window will be created from sequences
+ previously copied or cut to the system clipboard. <br>
+ Use <CTRL> and <SHIFT> and V(<APPLE> and
+ <SHIFT;> and and V on MacOSX) to paste.</em></li>
+ <li><strong>Add To This Alignment (Control V)<br>
+ </strong><em>Copied sequences from another alignment window can be added
+ to the current Jalview alignment. </em></li>
+ </ul>
+ </li>
+ <li><strong>Delete (Backspace)<br>
+ </strong><em>This will delete the currently selected residues without
+ copying them to the clipboard. Like the other edit operations, this can
+ be undone with <strong>Undo</strong>.</em></li>
+ <li><strong>Remove Left (Control L)<br>
+ </strong><em>If the alignment has marked columns, the alignment will be
+ trimmed to the left of the leftmost marked column. To mark a column,
+ mouse click the scale bar above the alignment. Click again to unmark a
+ column, or select "Deselect All" to deselect all columns.</em></li>
+ <li><strong>Remove Right (Control R)<br>
+ </strong><em>If the alignment has marked columns, the alignment will be
+ trimmed to the left of the leftmost marked column. To mark a column,
+ mouse click the scale bar above the alignment. Click again to unmark a
+ column, or select "Deselect All" to deselect all columns.</em></li>
+ <li><strong>Remove Empty Columns (Control E)<br>
+ </strong><em>All columns which only contain gap characters ("-",
+ ".") will be deleted.<br>
+ You may set the default gap character in <a
+ href="../features/preferences.html">preferences</a>. </em></li>
+ <li><strong>Remove All Gaps (Control Shift E)</strong><br>
+ <em>Gap characters ("-", ".") will be deleted
+ from the selected area of the alignment. If no selection is made, ALL
+ the gaps in the alignment will be removed.<br>
+ You may set the default gap character in <a
+ href="../features/preferences.html">preferences</a>. </em></li>
+ <li><strong>Remove Redundancy (Control D)<br>
+ </strong><em>Selecting this option brings up a window asking you to select
+ a threshold. If the percentage identity between any two sequences
+ (under the current alignment) exceeds this value then one of the
+ sequences (the shorter) is discarded. Press the "Apply"
+ button to remove redundant sequences. The "Undo" button will
+ undo the last redundancy deletion.</em></li>
+ <li><strong>Pad Gaps<br>
+ </strong><em>When selected, the alignment will be kept at minimal width (so
+ there no empty columns before or after the first or last aligned
+ residue) and all sequences will be padded with gap characters to the
+ before and after their terminating residues.<br>
+ This switch is useful when making a tree using unaligned sequences and
+ when working with alignment analysis programs which require 'properly
+ aligned sequences' to be all the same length.<br>
+ You may set the default for <strong>Pad Gaps</strong> in the <a
+ href="../features/preferences.html">preferences</a>. </em></li>
+</ul>
+</body>
+</html>
-<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>Add Sequences</strong><em><br>\r
- Add sequences to the visible alignment from file, URL, or cut & paste \r
- window </em></li>\r
- <li><strong>Fetch Sequence</strong><br>\r
- <em>Shows a dialog window in which you can select known ids from Uniprot, \r
- EMBL, EMBLCDS or PDB database using Web Services provided by the European \r
- Bioinformatics Institute. See <a href="../features/seqfetch.html">Sequence \r
- Fetcher</a></em>.</li>\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.</em></li>\r
- <li><strong>Export</strong> <em><br>\r
- Creates an alignment graphic with the current annotation, alignment background \r
- colours and group colours. If the alignment is <a\r
- href="../features/wrap.html">wrapped</a>, the output will also be wrapped \r
- and will have the same visible residue width as the open alignment. </em> \r
- <ul>\r
- <li><strong>HTML<br>\r
- </strong><em>Create a <a href="../io/export.html">web page</a> from your \r
- alignment.</em></li>\r
- <li><strong>EPS<br>\r
- </strong><em>Create an <a href="../io/export.html">Encapsulated Postscript</a> \r
- file from your alignment.</em></li>\r
- <li><strong>PNG<br>\r
- </strong><em>Create a <a href="../io/export.html">Portable Network Graphics</a> \r
- file from your alignment.</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></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 your \r
- alignment window width, whichever is the smaller. </em></li>\r
- <li><strong>Export Features</strong><em><br>\r
- All features visible on the alignment can be saved to file or displayed in \r
- a textbox in either Jalview or GFF format</em></li>\r
- <li><strong>Export Annotations</strong><em><br>\r
- All annotations visible on the alignment can be saved to file or displayed \r
- in a textbox in Jalview annotations format. </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 the Newick \r
- file format, and associate them with the alignment. Note: the ids of the tree \r
- file and your alignment MUST be the same.</em></li>\r
- <li><strong>Load Features / Annotations<br>\r
- </strong><em>Load files describing precalculated <a href="../features/featuresFormat.html">sequence \r
- features</a> or <a href="../features/annotationsFormat.html">alignment annotations</a>.</em></li>\r
- <li><strong>Close</strong><br>\r
- <em>Close the alignment window. Make sure you have saved your alignment before \r
- you close - either as a Jalview project or by using the <strong>Save As</strong> \r
- menu.</em></li>\r
-</ul>\r
-</body>\r
-</html>\r
+<html>
+<head>
+<title>Alignment Window Menus</title>
+</head>
+
+<body>
+<p><strong>Alignment Window File Menu</strong></p>
+<ul>
+ <li><strong>Fetch Sequence</strong><br>
+ <em>Shows a dialog window in which you can select known ids from
+ Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by
+ the European Bioinformatics Institute. See <a
+ href="../features/seqfetch.html">Sequence Fetcher</a></em>.</li>
+ <li><strong>Add Sequences</strong><em><br>
+ Add sequences to the visible alignment from file, URL, or cut &
+ paste window </em></li>
+ <li><strong>Reload</strong><em><br>
+ Reloads the alignment from the original file, if available.<br><strong>Warning:
+ This will delete any edits, analyses and colourings applied since the
+ alignment was last saved, and cannot be undone.</strong></em></li>
+ <li><strong>Save (Control S)</strong><em><br>
+ Saves the alignment to the file it was loaded from (if available), in
+ the same format, updating the original in place. </em></li>
+ <li><strong>Save As (Control Shift S)<br>
+ </strong><em>Save the alignment to local file. A file selection window will
+ open, use the "Files of type:" selection box to determine
+ which <a href="../io/index.html">alignment format</a> to save as.</em></li>
+ <li><strong>Output to Textbox<br>
+ </strong><em>The alignment will be displayed in plain text in a new window
+ which you can "Copy and Paste" using the pull down menu, or
+ your standard operating system copy and paste keys. <br>
+ Select the format of the text by selecting one of the following menu
+ items.</em>
+ <ul>
+ <li><strong>FASTA</strong> <em></em></li>
+ <li><strong>MSF</strong></li>
+ <li><strong>CLUSTAL</strong></li>
+ <li><strong>BLC</strong></li>
+ <li><strong>PIR</strong></li>
+ <li><strong>PFAM</strong></li>
+ </ul>
+ </li>
+ <li><strong>Print (Control P)<br>
+ </strong><em>Jalview will print the alignment using the current fonts and
+ colours of your alignment. If the alignment has annotations visible,
+ these will be printed below the alignment. If the alignment is wrapped
+ the number of residues per line of your alignment will depend on the
+ paper width or your alignment window width, whichever is the smaller. </em></li>
+ <li><strong>Export Image</strong> <em><br>
+ Creates an alignment graphic with the current view's annotation, alignment
+ background colours and group colours. If the alignment is <a
+ href="../features/wrap.html">wrapped</a>, the output will also be
+ wrapped and will have the same visible residue width as the open
+ alignment. </em>
+ <ul>
+ <li><strong>HTML<br>
+ </strong><em>Create a <a href="../io/export.html">web page</a> from your
+ alignment.</em></li>
+ <li><strong>EPS<br>
+ </strong><em>Create an <a href="../io/export.html">Encapsulated
+ Postscript</a> file from your alignment.</em></li>
+ <li><strong>PNG<br>
+ </strong><em>Create a <a href="../io/export.html">Portable Network
+ Graphics</a> file from your alignment.</em></li>
+ </ul>
+ </li>
+ <li><strong>Export Features</strong><em><br>
+ All features visible on the alignment can be saved to file or displayed
+ in a textbox in either Jalview or GFF format</em></li>
+ <li><strong>Export Annotations</strong><em><br>
+ All annotations visible on the alignment can be saved to file or
+ displayed in a textbox in Jalview annotations format. </em></li>
+ <li><strong>Load Associated Tree<br>
+ </strong><em>Jalview can <a href="../calculations/treeviewer.html">view
+ trees</a> stored in the Newick file format, and associate them with the
+ alignment. Note: the ids of the tree file and your alignment MUST be
+ the same.</em></li>
+ <li><strong>Load Features / Annotations<br>
+ </strong><em>Load files describing precalculated <a
+ href="../features/featuresFormat.html">sequence features</a> or <a
+ href="../features/annotationsFormat.html">alignment annotations</a>.</em></li>
+ <li><strong>Close (Control W)</strong><br>
+ <em>Close the alignment window. Make sure you have saved your
+ alignment before you close - either as a Jalview project or by using
+ the <strong>Save As</strong> menu.</em></li>
+</ul>
+</body>
+</html>
-<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>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
-<p> </p>\r
-</body>\r
-</html>\r
+<html>
+<head>
+<title>Alignment Window Menus</title>
+</head>
+
+<body>
+<p><strong>Alignment Window View Menu</strong></p>
+<ul>
+ <li><strong>New View (Control T)</strong><em><br>
+ Creates a new view from the current alignment view. </em></li>
+ <li><strong>Expand Views (X)</strong><em><br>
+ Display each view associated with the alignment in its own alignment
+ window, allowing several views to be displayed simultaneously. </em></li>
+ <li><strong>Gather Views (G)</strong><em><br>
+ Each view associated with the alignment will be displayed within its
+ own tab on the current alignment window. </em></li>
+ <li><strong>Show→(all Columns / Sequences)</strong><em><br>
+ All hidden Columns / Sequences will be revealed. </em></li>
+ <li><strong>Hide→(all Columns / Sequences)</strong><em><br>
+ Hides the all the currently selected Columns / Sequences</em></li>
+ <li><strong>Show Annotations<br>
+ </strong><em>If this is selected the "Annotation Panel" will be
+ displayed below the alignment. The default setting is to display the
+ conservation calculation, quality calculation and consensus values as
+ bar charts. </em></li>
+ <li><strong>Show Sequence Features</strong><br>
+ <em>Show or hide sequence features on this alignment.</em></li>
+ <li><strong><a href="../features/featuresettings.html">Seqence Feature Settings...</a></strong><em><br>
+ <em>Opens the Sequence
+ Feature Settings dialog box to control the colour and display of
+ sequence features on the alignment, and configure and retrieve features
+ from DAS annotation servers.</em></li>
+ <li><strong><a href="../features/overview.html">Overview
+ Window</a><br>
+ </strong><em>A scaled version of the alignment will be displayed in a small
+ window. A red box will indicate the currently visible area of the
+ alignment. Move the visible region using the mouse. </em></li>
+ <strong> </strong>
+</ul>
+<p> </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / commitdiff