Principal Component Analysis

From 96b6991703b70a1bbb0491f9946d397c9fcf5a38 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 27 Nov 2006 11:57:17 +0000 Subject: [PATCH] 2.2 documentation --- help/help.jhm | 6 +- help/helpTOC.xml | 10 +- help/html/calculations/pca.html | 91 ++++++++-------- help/html/colourSchemes/textcolour.html | 16 +++ help/html/features/multipleViews.html | 65 ++++++----- help/html/features/newkeystrokes.html | 23 ++++ help/html/menus/alwFormat.html | 56 ++++++++++ help/html/menus/alwSelect.html | 31 ++++++ help/html/menus/alwcolour.html | 88 ++++++++------- help/html/menus/alwedit.html | 181 ++++++++++++++----------------- help/html/menus/alwfile.html | 164 +++++++++++++++------------- help/html/menus/alwview.html | 113 +++++++------------ 12 files changed, 471 insertions(+), 373 deletions(-) create mode 100644 help/html/colourSchemes/textcolour.html create mode 100644 help/html/features/newkeystrokes.html create mode 100644 help/html/menus/alwFormat.html create mode 100644 help/html/menus/alwSelect.html diff --git a/help/help.jhm b/help/help.jhm index 729cff4..176569b 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -7,6 +7,7 @@ + @@ -41,7 +42,8 @@ - + + @@ -67,7 +69,9 @@ + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 6152307..5252a30 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -4,10 +4,12 @@ + - + + @@ -68,8 +70,10 @@ - - + + + + diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index af6550e..8cbf0ca 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -1,64 +1,61 @@ -Principal Component Analysis + +Principal Component Analysis +

Principal Component Analysis

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.

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.

+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.

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.

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. -

+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.

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 (pubmed) - and implemented at the SeqSpace server at the EBI. -

+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 (pubmed) +and implemented at the SeqSpace server at the EBI.

The PCA Viewer

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. -

The 3d view can be rotated by dragging the mouse with the - left mouse button pressed. The view can also be - zoomed in and out with the up and down arrow - keys (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. -

+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.

The 3d view can be rotated by dragging the mouse with the left +mouse button pressed. The view can also be zoomed in and out with the up +and down arrow keys (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.

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. -

+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 Associate +Nodes sub-menu.

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. -

+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.

- diff --git a/help/html/colourSchemes/textcolour.html b/help/html/colourSchemes/textcolour.html new file mode 100644 index 0000000..c5e18ed --- /dev/null +++ b/help/html/colourSchemes/textcolour.html @@ -0,0 +1,16 @@ + + +Background Dependent Text Colour + + +Background Dependent Text Colour +

The Colour→Text Colour menu entry opens +the Text Colour dialog box. This contains a slider, and +two colour icons showing the text colour for dark backgrounds (left hand +end of slider), and light backgrounds (right hand end of slider). Drag +the slider to change the threshold for transitioning between dark and +light background colours, and select either of the colour boxes to open +a colour chooser to select a different text colour. +

+ + diff --git a/help/html/features/multipleViews.html b/help/html/features/multipleViews.html index e31a06b..c4929e5 100644 --- a/help/html/features/multipleViews.html +++ b/help/html/features/multipleViews.html @@ -4,41 +4,40 @@

Multiple Alignment Views

-
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. -
-
-A new view is created using the "View→New View" menu item, or by pressing -Control+T. 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. -
-
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. Right-clicking a view's tab opens -the View Name dialog box, allowing it to be renamed to something more -meaningful. -
+
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.
+
A new view is created using the "View→New +View" menu item, or by pressing Control+T. 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.
+
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. Right-clicking a view's +tab opens the View Name dialog box, allowing it to be renamed to +something more meaningful.

Viewing Multiple Views Simultaneously
-
Multiple views of an alignment are, by default, gathered together as tabs -within a single alignment window. They can be viewed simultanously by -pressing X (or via -"View→Expand") to expand each view -into its own linked alignment window. Expanded views are gathered -back into into a single tabbed alignment window by pressing +
Multiple views of an alignment are, by default, gathered together +as tabs within a single alignment window. They can be viewed +simultanously by pressing X (or via "View→Expand") +to expand each view into its own linked alignment window. Expanded views +are gathered back into into a single tabbed alignment window by pressing G, or by selecting "View→Gather").
-
Tree Viewers and Multiple Views
+
Tree Viewers, PCA Viewers, and Multiple Views

A tree calculated on a particular view, or loaded onto it, is by default associated with just that view. However, the Tree Viewer's -"View→Associate leaves" submenu -allows a tree's view association to be changed to to any or all other -views.
-
Multiple Views were introduced in Jalview 2.2
- \ No newline at end of file + href="../calculations/treeviewer.html">Tree Viewer's "View→Associate +leaves" submenu allows a tree's view association to be changed to +to any or all other views.
+
The results of a PCA calculation on a particular view +may also be associated with other views, using the "Associate +Nodes" submenu.
+
Multiple Views were introduced in Jalview 2.2
+ + diff --git a/help/html/features/newkeystrokes.html b/help/html/features/newkeystrokes.html new file mode 100644 index 0000000..110e21c --- /dev/null +++ b/help/html/features/newkeystrokes.html @@ -0,0 +1,23 @@ + +New Key Strokes and Menus + +New Key Strokes and Menus +
Many new keyboard shortcuts have been +added in Jalview 2.2 to make editing, selecting and navigating an +alignment even easier. Some of the commands in the Edit +and View menus present in earlier releases have also +been moved into their own Select and Format +menus. Some of the important new keystrokes are shown below : +
+
Page Up and Page Down + scrolls through the alignment view.
+
Control I inverts the currently selected + sequence set, and Control Alt I will invert the + currently selected set of columns. +
Control+V will paste the contents of the + clipboard to the current alignment window, and Control + Shift V pastes the data to a new window.
+
+
+ + diff --git a/help/html/menus/alwFormat.html b/help/html/menus/alwFormat.html new file mode 100644 index 0000000..fc1fd58 --- /dev/null +++ b/help/html/menus/alwFormat.html @@ -0,0 +1,56 @@ + + +Alignment Window Menus + + +
Alignment Window Format Menu
+
+
Font...
+ Opens the "Choose Font" dialog box, in order to + change the font of the display and enable or disable 'smooth fonts' + (anti-aliasing) for faster alignment rendering.
+
Wrap
+ When ticked, the alignment display is "wrapped" to the width of the + alignment window. This is useful if your alignment has only a few + sequences to view its full width at once.
+ Additional options for display of sequence numbering and scales are + also visible in wrapped layout mode:
+
+
Scale Above
Show the alignment column position scale.
+
Scale Left
Show the sequence position for the first aligned residue in each row in the left column of the alignment.
+
Scale Right
Show the sequence position for the last aligned residue in each row in the right-most column of the alignment.
+ +
Show Sequence Limits
+ If this box is selected the sequence name will have the start + and end position of the sequence appended to the name, in the format + NAME/START-END
+
Right Align Sequence ID
+ If this box is selected then the sequence names displayed in + the sequence label area will be aligned against the left-hand edge of + the alignment display, rather than the left-hand edge of the alignment + window.
+
Show Hidden Markers
+ When this box is selected, positions in the alignment where + rows and columns are hidden will be marked by blue arrows.
+
Boxes
+ If this is selected the background of a residue will be coloured using + the selected background colour. Useful if used in conjunction with + "Colour Text."
+
Text
+ If this is selected the residues will be displayed using the + standard 1 character amino acid alphabet.
+
Colour Text
+ If this is selected the residues will be coloured according to + the background colour associated with that residue. The colour is + slightly darker than background so the amino acid symbol remains + visible.
+
Show Gaps
+ When this is selected, gap characters will be displayed as + "." or "-". If unselected, then gap characters will + appear as blank spaces.
+ You may set the default gap character in preferences.
+
+ + diff --git a/help/html/menus/alwSelect.html b/help/html/menus/alwSelect.html new file mode 100644 index 0000000..2c66fc5 --- /dev/null +++ b/help/html/menus/alwSelect.html @@ -0,0 +1,31 @@ + + +Alignment Window Menus + + +
Alignment Window Select Menu
+
+
Find... + (Control F)
+ Opens the Find dialog box to perform regular expression searches on the + aligned sequences and their IDs and create new features. +
Select All (Control A)
+ Selects all the sequences and residues in the alignment.
+ Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
+
Deselect All (Escape)
+ Removes the current selection box (red dashed box) from the + alignment window. All selected sequences, residues and marked columns + will be deselected.
+ Use <ESCAPE> to deselect all.
+
Invert Sequence Selection (Control I)
+ Any sequence ids currently not selected will replace the + current selection.
+
Invert Column Selection (Control Alt I)
+ Any columns currently not selected will replace the current + column selection.
+
Undefine Groups (Control U)
+ The alignment will be reset with no defined groups.
+ WARNING: This cannot be undone.
+
+ + diff --git a/help/html/menus/alwcolour.html b/help/html/menus/alwcolour.html index 9a7d43b..2c90bf9 100755 --- a/help/html/menus/alwcolour.html +++ b/help/html/menus/alwcolour.html @@ -1,45 +1,43 @@ - -Alignment Window Menus - - -
Alignment Window Colour Menu
-
-
Colour
-
-
-
-
Apply Colour To All Groups
- If this is selected, any changes made to the background colour - will be applied to all currently defined groups.
-
-
Colour Scheme options: None, ClustalX, Blosum62 Score, Percentage - Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity, - Turn Propensity, Buried Index, Nucleotide, User Defined
- See colours for - a description of all colour schemes.
-
-
By Conservation
- See Colouring - by Conservation.
-
-
Modify Conservation Threshold
- 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!
-
-
Above Identity Threshold
- See Above Percentage - Identity.
-
-
Modify Identity Threshold
- Use this to set the threshold value for colouring above Identity. - Useful if the window has been closed.
-
-
By Annotation
- Colours the alignment on a per-column value from a specified annotation. - See Annotation Colouring.
-
-
-
- - + +Alignment Window Menus + + +
Alignment Window Colour Menu
+
+
Apply Colour To All Groups
+ If this is selected, any changes made to the background colour + will be applied to all currently defined groups.
+
+
Colour Text...
+ 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. +
+
Colour Scheme options: None, ClustalX, Blosum62 Score, Percentage + Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity, + Turn Propensity, Buried Index, Nucleotide, User Defined
+ See colours for + a description of all colour schemes.
+
+
By Conservation
+ See Colouring + by Conservation.
+
+
Modify Conservation Threshold
+ 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!
+
+
Above Identity Threshold
+ See Above Percentage + Identity.
+
+
Modify Identity Threshold
+ Use this to set the threshold value for colouring above Identity. + Useful if the window has been closed.
+
+
By Annotation
+ Colours the alignment on a per-column value from a specified annotation. + See Annotation Colouring.
+
+
+ + diff --git a/help/html/menus/alwedit.html b/help/html/menus/alwedit.html index f6f8826..3fb874d 100755 --- a/help/html/menus/alwedit.html +++ b/help/html/menus/alwedit.html @@ -1,97 +1,84 @@ - -Alignment Window Menus - - -
Alignment Window Edit Menu
-
-
Undo
- 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. NOTE: - It DOES NOT undo colour changes, adjustments to group sizes, or changes to - the annotation panel.
-
Redo
- Any actions which you undo can be redone using redo.
-
Cut
- 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.
- Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.
-
Copy
- Copies the currently selected residues to the system clipboard - you can - also do this by pressing <CTRL> and C (<APPLE> and C on MacOSX). -
- If you try to paste the clipboard contents to a text editor, you will see - the format of the copied residues FASTA.
-
Paste -
-
To New Alignment
- A new alignment window will be created from sequences previously - copied or cut to the system clipboard.
- Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.
-
Add To This Alignment
- Copied sequences from another alignment window can be added - to the current Jalview alignment.
-
-
-
Delete
- This will delete the currently selected residues without copying - them to the clipboard. Like the other edit operations, this can be undone - with Undo.
-
Select All
- Selects all the sequences and residues in the alignment.
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
-
Deselect All
- Removes the current selection box (red dashed box) from the alignment - window. All selected sequences, residues and marked columns will be deselected. -
- Use <ESCAPE> to deselect all.
-
Invert Sequence Selection
- Any sequence ids currently not selected will replace the current - selection.
-
Invert Column Selection
- Any columns currently not selected will replace the current column - selection.
-
Undefine Groups
- The alignment will be reset with no defined groups.
- WARNING: This cannot be undone.
-
Remove Left
- 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.
-
Remove Right
- 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.
-
Remove Empty Columns
- All columns which only contain gap characters ("-", - ".") will be deleted.
- You may set the default gap character in preferences. -
-
Remove All Gaps
- 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.
- You may set the default gap character in preferences. -
-
Remove Redundancy
- 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.
-
Pad Gaps
- 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.
- 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.
- You may set the default for Pad Gaps in the preferences. -
-
- - + + +Alignment Window Menus + + + +
Alignment Window Edit Menu
+
+
Undo (Control Z)
+ 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. NOTE: It DOES NOT undo colour changes, + adjustments to group sizes, or changes to the annotation panel.
+
Redo (Control Y)
+ Any actions which you undo can be redone using redo.
+
Cut (Control X)
+ 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.
+ Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.
+
Copy (Control C)
+ Copies the currently selected residues to the system clipboard + - you can also do this by pressing <CTRL> and C (<APPLE> + and C on MacOSX).
+ If you try to paste the clipboard contents to a text editor, you will + see the format of the copied residues FASTA.
+
Paste +
+
To New Alignment (Control Shift V)
+ A new alignment window will be created from sequences + previously copied or cut to the system clipboard.
+ Use <CTRL> and <SHIFT> and V(<APPLE> and + <SHIFT;> and and V on MacOSX) to paste.
+
Add To This Alignment (Control V)
+ Copied sequences from another alignment window can be added + to the current Jalview alignment.
+
+
+
Delete (Backspace)
+ This will delete the currently selected residues without + copying them to the clipboard. Like the other edit operations, this can + be undone with Undo.
+
Remove Left (Control L)
+ 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.
+
Remove Right (Control R)
+ 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.
+
Remove Empty Columns (Control E)
+ All columns which only contain gap characters ("-", + ".") will be deleted.
+ You may set the default gap character in preferences.
+
Remove All Gaps (Control Shift E)
+ 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.
+ You may set the default gap character in preferences.
+
Remove Redundancy (Control D)
+ 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.
+
Pad Gaps
+ 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.
+ 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.
+ You may set the default for Pad Gaps in the preferences.
+
+ + diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html index f5ea091..eb45924 100755 --- a/help/html/menus/alwfile.html +++ b/help/html/menus/alwfile.html @@ -1,76 +1,88 @@ - -Alignment Window Menus - - -
Alignment Window File Menu
-
-
Add Sequences
- Add sequences to the visible alignment from file, URL, or cut & paste - window
-
Fetch Sequence
- 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 Sequence - Fetcher.
-
Save As
- Save the alignment to local file. A file selection window will - open, use the "Files of type:" selection box to determine which - alignment format to save as.
-
Export
- Creates an alignment graphic with the current annotation, alignment background - colours and group colours. If the alignment is wrapped, the output will also be wrapped - and will have the same visible residue width as the open alignment. -
-
HTML
- Create a web page from your - alignment.
-
EPS
- Create an Encapsulated Postscript - file from your alignment.
-
PNG
- Create a Portable Network Graphics - file from your alignment.
-
-
-
Output to Textbox
- 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.
- Select the format of the text by selecting one of the following menu items. -
-
FASTA
-
MSF
-
CLUSTAL
-
BLC
-
PIR
-
PFAM
-
-
-
Print
- 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.
-
Export Features
- All features visible on the alignment can be saved to file or displayed in - a textbox in either Jalview or GFF format
-
Export Annotations
- All annotations visible on the alignment can be saved to file or displayed - in a textbox in Jalview annotations format.
-
Load Associated Tree
- Jalview can view trees 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.
-
Load Features / Annotations
- Load files describing precalculated sequence - features or alignment annotations.
-
Close
- Close the alignment window. Make sure you have saved your alignment before - you close - either as a Jalview project or by using the Save As - menu.
-
- - + + +Alignment Window Menus + + + +
Alignment Window File Menu
+
+
Fetch Sequence
+ 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 Sequence Fetcher.
+
Add Sequences
+ Add sequences to the visible alignment from file, URL, or cut & + paste window
+
Reload
+ Reloads the alignment from the original file, if available.
Warning: + This will delete any edits, analyses and colourings applied since the + alignment was last saved, and cannot be undone.
+
Save (Control S)
+ Saves the alignment to the file it was loaded from (if available), in + the same format, updating the original in place.
+
Save As (Control Shift S)
+ Save the alignment to local file. A file selection window will + open, use the "Files of type:" selection box to determine + which alignment format to save as.
+
Output to Textbox
+ 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.
+ Select the format of the text by selecting one of the following menu + items. +
+
FASTA
+
MSF
+
CLUSTAL
+
BLC
+
PIR
+
PFAM
+
+
+
Print (Control P)
+ 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.
+
Export Image
+ Creates an alignment graphic with the current view's annotation, alignment + background colours and group colours. If the alignment is wrapped, the output will also be + wrapped and will have the same visible residue width as the open + alignment. +
+
HTML
+ Create a web page from your + alignment.
+
EPS
+ Create an Encapsulated + Postscript file from your alignment.
+
PNG
+ Create a Portable Network + Graphics file from your alignment.
+
+
+
Export Features
+ All features visible on the alignment can be saved to file or displayed + in a textbox in either Jalview or GFF format
+
Export Annotations
+ All annotations visible on the alignment can be saved to file or + displayed in a textbox in Jalview annotations format.
+
Load Associated Tree
+ Jalview can view + trees 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.
+
Load Features / Annotations
+ Load files describing precalculated sequence features or alignment annotations.
+
Close (Control W)
+ Close the alignment window. Make sure you have saved your + alignment before you close - either as a Jalview project or by using + the Save As menu.
+
+ + diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index 28ad82e..ca8f81b 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -1,71 +1,42 @@ - -Alignment Window Menus - - -
Alignment Window View Menu
-
-
Font
- Change the font of the display from the "Choose Font" - dialog box, which is shown when this item is selected.
-
Smooth Fonts
- If selected, the alignment will be drawn with anti-aliasing on which looks - better, but performace is reduced.
-
Show (all Columns / Sequences)
- All hidden Columns / Sequences will be revealed.
-
Hide (all Columns / Sequences)
- Hides the all the currently selected Columns / Sequences
-
Wrap
- When ticked, the alignment display is "wrapped" - to the width of the alignment window. This is useful if your alignment has - only a few sequences to view its full width at once.
- Options are available to show the residue numbering at the start and/or end - of an alignment as well as showing the alignment position above each sequence - row.
- NOTE: When in wrapped alignment view, the alignment cannot - be edited or have regions selected on it.
-
Show Full Sequence ID
- If this box is selected the sequence name will have the start - and end position of the sequence appended to the name, in the format NAME/START-END
-
Boxes
- If this is selected the background of a residue will be coloured using the - selected background colour. Useful if used in conjunction with "Colour - Text."
-
Text
- If this is selected the residues will be displayed using the - standard 1 character amino acid alphabet.
-
Colour Text
- If this is selected the residues will be coloured according to - the background colour associated with that residue. The colour is slightly - darker than background so the amino acid symbol remains visible.
-
Show Gaps
- When this is selected, gap characters will be displayed as "." - or "-". If unselected, then gap characters will appear as blank - spaces.
- You may set the default gap character in preferences.
-
Show Annotations
- 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.
-
Fetch Sequence Features
- If the sequence names are Swissprot entries Jalview will use - the names to retrieve sequence features - from the EBI. Features which are 1 residue in length are coloured red, sequences - longer than 1 residue are coloured blue. Move the mouse over a coloured feature - to display the details of the feature.
- Note: The retrieved information will update the sequence start and end labels - if they are incorrect.
-
Show Sequence Features
- Show or hide sequence features on this alignment.
-
Seqence Feature Settings...
- Control the colour and display of sequence features on the alignment. - See Sequence Feature Settings.
-
Overview Window
- 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.
- -
-

- - + + +Alignment Window Menus + + + +
Alignment Window View Menu
+
+
New View (Control T)
+ Creates a new view from the current alignment view.
+
Expand Views (X)
+ Display each view associated with the alignment in its own alignment + window, allowing several views to be displayed simultaneously.
+
Gather Views (G)
+ Each view associated with the alignment will be displayed within its + own tab on the current alignment window.
+
Show→(all Columns / Sequences)
+ All hidden Columns / Sequences will be revealed.
+
Hide→(all Columns / Sequences)
+ Hides the all the currently selected Columns / Sequences
+
Show Annotations
+ 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.
+
Show Sequence Features
+ Show or hide sequence features on this alignment.
+
Seqence Feature Settings...
+ 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.
+
Overview + Window
+ 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.
+ +
+

+ + -- 1.7.10.2