From b64d78cc81a4d3f87ac03b4f530757b840c4f943 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Fri, 11 Aug 2006 14:20:22 +0000 Subject: [PATCH] 2.1 updates --- help/html/menus/alignmentMenu.html | 343 +++++++++++++++++++----------------- 1 file changed, 177 insertions(+), 166 deletions(-) diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 70a2591..427ab2d 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -4,39 +4,42 @@

Alignment Window Menus

File +
File
- 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 + 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.

-
Edit +
Edit

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 + 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 + 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 + 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 + If you try to paste the clipboard contents to a text editor, you will see the format of the copied residues FASTA.
-
Paste +
Paste

To New Alignment
- A new alignment window will be created from sequences + 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 + 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 + 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. + 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 + 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 Selection
- Any sequence ids currently not selected will replace the +
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, + 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, + 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 ("-", + All columns which only contain gap characters ("-", ".") will be deleted.
- You may set the default gap character in preferences. + 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 + 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. + 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 + 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. -
+
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.

-
Search +
Search

Find
- Select this to search - for residues, sequence name or residue position within the - alignment and create new sequence features from the queries. -
+ Select this to search + for residues, sequence name or residue position within the alignment and + create new sequence features from the queries.

-
View +
View

Font
- Change the font of the display from the "Choose 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. -
+ 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 + 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 + 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 + 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 + 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 + 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 + 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 + 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 + 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 + 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. + 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 + 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.
-
+
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 + 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.

-
Colour +
Colour

Apply Colour To All Groups
- If this is selected, any changes made to the background colour + 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, +
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 + See colours for a description of all colour schemes.

By Conservation
- See Colouring + 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 + 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 + 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.
-
+ 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 +
Calculate
-
Sort +
Sort

by ID
- This will sort the sequences according to sequence name. If the sort + 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 + 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 + 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 +
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 + Functions for calculating trees on the alignment or the currently selected region. See calculating trees. + href="../calculations/tree.html">calculating trees.

Average Distance Using % Identity

Neighbour Joining Using % Identity
@@ -296,54 +307,54 @@

Pairwise Alignments
- Applies Smith and Waterman algorithm to selected sequences. See pairwise + 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 + Shows a spatial clustering of the sequences based on the BLOSUM62 + scores in the alignment. See Principal Component Analysis.

Translate cDNA
- If you are viewing a cDNA alignment a very simple translation service - is available. The translation ignores all gaps in the cDNA sequences. + If you are viewing a cDNA alignment a very simple translation service + is available. The translation ignores all gaps in the cDNA sequences.

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. + 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 +
Alignment

ClustalW Multiple Sequence Alignment
- Submits all, or just the currently selected sequences for 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 + 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.

Muscle Multiple Protein Sequence Alignment
- Submits all, or jut the currently selected sequences for alignment - using Muscle. Do not use this if you are working with nucleic acid + Submits all, or jut the currently selected sequences for alignment + using Muscle. Do not use this if you are working with nucleic acid sequences.

-
Secondary Structure Prediction +
Secondary Structure Prediction

JPred Secondary Structure Prediction
- Secondary structure prediction by network consensus. The behaviour + 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 +
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 +
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 selected in the set (that is, the one that was first clicked +
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 selected in the set (that is, the one that was first clicked on).

-- 1.7.10.2