Alignment Window Menus

From d587f1aa61946dc14f6f089cf1dc2a3116cfb773 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 28 Nov 2006 18:03:54 +0000 Subject: [PATCH] Format changes --- help/html/menus/alignmentMenu.html | 847 ++++++++++++++++++------------------ help/html/menus/alwformat.html | 112 ++--- help/html/menus/alwselect.html | 61 ++- help/html/menus/alwview.html | 82 ++-- help/html/menus/desktopMenu.html | 149 +++---- 5 files changed, 623 insertions(+), 628 deletions(-) diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 0795189..22a0bd7 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,425 +1,422 @@ - - -Alignment Window Menus - - - -

Alignment Window Menus

File -
- 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. The - output window also has a "New Window" - button to import the (possibly edited) text as a new alignment.
  - 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.
-
Edit -
- 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.
-
Select -
- Find... - (Control F)
  - Opens the Find dialog box to search for residues, sequence name or - residue position within the alignment and create new sequence features - from the queries.
- 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.
-
View -
- 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.
-

-
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.
-
-
-
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 - 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.
-
-
-
-
Calculate -
-
Sort -
-
by ID
- This will sort the sequences according to sequence name. If the sort - is repeated, the order of the sorted sequences will be inverted.
-
by Group
- This will sort the sequences according to sequence name. If - the sort is repeated, the order of the sorted sequences will be - inverted.
-
by Pairwise Identity
- This will sort the selected sequences by their percentage - identity to the consensus sequence. The most similar sequence is put - at the top.
-
The Sort - menu will have some additional options if you have just done a - multiple alignment calculation, or opened a tree viewer window.
-
-
-
-
Calculate Tree
- Functions for calculating trees on the alignment or the - currently selected region. See calculating - trees. -
-
Average Distance Using % Identity
-
Neighbour Joining Using % Identity
-
Average Distance Using Blosum62
-
Neighbour Joining Using Blosum62
-
-
-
-
Pairwise Alignments
- Applies Smith and Waterman algorithm to selected sequences. - See pairwise alignments.
-
-
Principal Component Analysis
- Shows a spatial clustering of the sequences based on the - BLOSUM62 scores in the alignment. See Principal Component Analysis.
-
-
Autocalculate Consensus
- For large alignments it can be useful to deselect - "Autocalculate Consensus" when editing. This prevents the - sometimes lengthy calculations performed after each sequence edit.
-
-
-
-
Web Service
- Selecting one of the following menu items starts a remote - service on compute facilities at the University of Dundee. You need a - continuous network connection in order to use these services through - Jalview. -
-
Alignment -
-
ClustalW Multiple Sequence Alignment
- Submits all, or just the currently selected sequences for - alignment with clustal W.
-
ClustalW Multiple Sequence Alignment - Realign
- Submits the alignment or currently selected region for - re-alignment with clustal W. Use this if you have added some new - sequences to an existing alignment.
-
MAFFT Multiple Sequence Alignment
- Submits all, or just the currently selected region for - alignment with MAFFT.
-
Muscle Multiple Protein Sequence Alignment
- Submits all, or just the currently selected sequences for - alignment using Muscle. Do not use this if you are working with - nucleic acid sequences.
-
-
-
Secondary Structure Prediction -
-
JPred Secondary Structure Prediction
- Secondary structure prediction by network consensus. The - behaviour of this calculation depends on the current selection:
-
If nothing is selected, and the displayed sequences - appear to be aligned, then a JNet prediction will be run for the - first sequence in the alignment, using the current alignment. - Otherwise the first sequence will be submitted for prediction.
-
If just one sequence (or a region on one sequence) - has been selected, it will be submitted to the automatic JNet - prediction server for homolog detection and prediction.
-
If a set of sequences are selected, and they appear - to be aligned, then the alignment will be used for a Jnet prediction - on the first sequence in the set (that is, the one - that appears first in the alignment window).
-
-
-
-
-
- - + + +Alignment Window Menus + + + +
Alignment Window Menus
+
File +
+
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. The + output window also has a "New Window" + button to import the (possibly edited) text as a new alignment.
+ 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.
+
+
+
Edit +
+
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.
+
+
+
Select +
+
Find... + (Control F)
+ Opens the Find dialog box to search for residues, sequence name or + residue position within the alignment and create new sequence features + from the queries.
+
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.
+
+
+
View +
+
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.
+
+
+
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.
+
+
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 + 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.
+
+
+
+
Calculate +
+
Sort +
+
by ID
+ This will sort the sequences according to sequence name. If the sort + is repeated, the order of the sorted sequences will be inverted.
+
by Group
+ This will sort the sequences according to sequence name. If + the sort is repeated, the order of the sorted sequences will be + inverted.
+
by Pairwise Identity
+ This will sort the selected sequences by their percentage + identity to the consensus sequence. The most similar sequence is put + at the top.
+
The Sort + menu will have some additional options if you have just done a + multiple alignment calculation, or opened a tree viewer window.
+
+
+
+
Calculate Tree
+ Functions for calculating trees on the alignment or the + currently selected region. See calculating + trees. +
+
Average Distance Using % Identity
+
Neighbour Joining Using % Identity
+
Average Distance Using Blosum62
+
Neighbour Joining Using Blosum62
+
+
+
+
Pairwise Alignments
+ Applies Smith and Waterman algorithm to selected sequences. + See pairwise alignments.
+
+
Principal Component Analysis
+ Shows a spatial clustering of the sequences based on the + BLOSUM62 scores in the alignment. See Principal Component Analysis.
+
+
Autocalculate Consensus
+ For large alignments it can be useful to deselect + "Autocalculate Consensus" when editing. This prevents the + sometimes lengthy calculations performed after each sequence edit.
+
+
+
+
Web Service
+ Selecting one of the following menu items starts a remote + service on compute facilities at the University of Dundee. You need a + continuous network connection in order to use these services through + Jalview. +
+
Alignment +
+
ClustalW Multiple Sequence Alignment
+ Submits all, or just the currently selected sequences for + alignment with clustal W.
+
ClustalW Multiple Sequence Alignment + Realign
+ Submits the alignment or currently selected region for + re-alignment with clustal W. Use this if you have added some new + sequences to an existing alignment.
+
MAFFT Multiple Sequence Alignment
+ Submits all, or just the currently selected region for + alignment with MAFFT.
+
Muscle Multiple Protein Sequence Alignment
+ Submits all, or just the currently selected sequences for + alignment using Muscle. Do not use this if you are working with + nucleic acid sequences.
+
+
+
Secondary Structure Prediction +
+
JPred Secondary Structure Prediction
+ Secondary structure prediction by network consensus. The + behaviour of this calculation depends on the current selection:
+
If nothing is selected, and the displayed sequences + appear to be aligned, then a JNet prediction will be run for the + first sequence in the alignment, using the current alignment. + Otherwise the first sequence will be submitted for prediction.
+
If just one sequence (or a region on one sequence) + has been selected, it will be submitted to the automatic JNet + prediction server for homolog detection and prediction.
+
If a set of sequences are selected, and they appear + to be aligned, then the alignment will be used for a Jnet prediction + on the first sequence in the set (that is, the one + that appears first in the alignment window).
+
+
+
+
+
+ + diff --git a/help/html/menus/alwformat.html b/help/html/menus/alwformat.html index 0c45d46..d7224b3 100644 --- a/help/html/menus/alwformat.html +++ b/help/html/menus/alwformat.html @@ -1,56 +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.
-
- - + + +
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 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.
+
+ +
Scale Above
+ Show the alignment column position scale.
+
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 index 7c5085a..34438cd 100644 --- a/help/html/menus/alwselect.html +++ b/help/html/menus/alwselect.html @@ -1,32 +1,29 @@ - - -Alignment Window Menus - - -
Alignment Window Select Menu
-
-
Find... - (Control F)
- Opens the Find dialog box to search for residues, sequence name or - residue position within the alignment and create new sequence features - from the queries. -
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.
-
- - + + +
Alignment Window Select Menu
+
+ +
Find... (Control F)
+ Opens the Find dialog box to search for residues, sequence name or residue + position within the alignment and create new sequence features from the queries. + +
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/alwview.html b/help/html/menus/alwview.html index 2d341fa..e58d4c2 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -1,41 +1,41 @@ - - -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.
-
-

- - + + +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.
+
+

+ + diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html index 7dd7b40..c7d2656 100755 --- a/help/html/menus/desktopMenu.html +++ b/help/html/menus/desktopMenu.html @@ -1,74 +1,75 @@ - - -Desktop Menus - - - -
Desktop Menus
-
-
File -
-
Input Alignment from (See more on file formats) -
-
File (Control O)
- open file(s) on your local file system
-
URL
- open a file from a website. The URL MUST start with http://
-
Textbox
- copy and paste an alignment into a text 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.
-
Save Project
- Saves all currently open alignment windows with their current - view settings and any associated trees, as a Jalview Archive (which has a - .jar extension).
-
Load Project
- Loads Jalview archives only.
-
Quit
- Close Jalview.
Note - any annotation you have made on - alignments will be lost unless you Save your work before quitting.

-
-
-
-
Tools -
-
Preferences
- Change the default visual settings for opening new alignment - windows.
-
-
-
-
Help -
-
About
- Displays the version and creation date of the application, as - well as acknowledgements and a citation reference.
-
Documentation
- Displays help files as a browseable, searchable set of pages - with a table of contents.
-
-
-
-
Window
- Each time a new window is added to the Jalview Desktop a - corresponding menu item will be added to the "Window" menu - that will bring the window to the top of the pile when it is selected. -
-
Close All
- Close all alignment and analysis windows.
Note: This will erase all alignments from memory, and cannot be undone!
-
Raise Associated Windows
- Bring all windows associated with the current alignment to the top of the pile. -
-
Minimise Associated Windows
- Hide all windows related to the current alignment behind icons on the Jalview Desktop. -
-
-
- - + + +Desktop Menus + + + +
Desktop Menus
+
+
File +
+
Input Alignment from (See more on file formats) +
+
File (Control O)
+ open file(s) on your local file system
+
URL
+ open a file from a website. The URL MUST start with http://
+
Textbox
+ copy and paste an alignment into a text 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.
+
Save Project
+ Saves all currently open alignment windows with their current + view settings and any associated trees, as a Jalview Archive (which has a + .jar extension).
+
Load Project
+ Loads Jalview archives only.
+
Quit
+ Close Jalview.
+ Note - any annotation you have made on alignments will be lost + unless you Save your work before quitting.
+
+
+
+
Tools +
+
Preferences
+ Change the default visual settings for opening new alignment + windows.
+
+
+
+
Help +
+
About
+ Displays the version and creation date of the application, as + well as acknowledgements and a citation reference.
+
Documentation
+ Displays help files as a browseable, searchable set of pages + with a table of contents.
+
+
+
+
Window
+ Each time a new window is added to the Jalview Desktop a + corresponding menu item will be added to the "Window" menu + that will bring the window to the top of the pile when it is selected. +
+
Close All
+ Close all alignment and analysis windows.
Note: This will erase all alignments from memory, and cannot be undone!
+
Raise Associated Windows
+ Bring all windows associated with the current alignment to the top of the pile. +
+
Minimise Associated Windows
+ Hide all windows related to the current alignment behind icons on the Jalview Desktop. +
+
+
+ + -- 1.7.10.2