What's new ?

From: jprocter Date: Tue, 4 Oct 2011 15:50:04 +0000 (+0100) Subject: Merge remote-tracking branch 'remotes/origin/2_5_1_rna_merge' into develop (JAL-826) X-Git-Tag: Jalview_2_9~576 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2026a420963f094072607c0495b6369ba96e60c0;p=jalview.git Merge remote-tracking branch 'remotes/origin/2_5_1_rna_merge' into develop (JAL-826) Conflicts: .classpath help/html/menus/alignmentMenu.html help/html/whatsNew.html src/jalview/gui/PopupMenu.java --- 2026a420963f094072607c0495b6369ba96e60c0 diff --cc .classpath index 1838768,86aa215..cafb124 --- a/.classpath +++ b/.classpath @@@ -36,11 -39,8 +37,13 @@@ + + + + + + + diff --cc help/helpTOC.xml index 926a710,5371ad4..6cc51dd --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@@ -20,12 -20,11 +20,9 @@@ - - - - - -- - - - - ++ ++ ++ diff --cc help/html/menus/alignmentMenu.html index ff74139,5b6535d..6a5ec9f --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@@ -21,547 -21,489 +21,555 @@@ -

Alignment Window Menus

File +

+ Alignment Window Menus +

Fetch Sequence
- Shows a dialog window in which you can select known ids from - Uniprot, EMBL, EMBLCDS, PDB, PFAM, or RFAM databases 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.

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 ++ dialog window in which you can retrieve known ids from Uniprot, ++ EMBL, EMBLCDS, PFAM, Rfam, 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. +
Make Groups
The currently + selected groups of the alignment will be subdivided according to + the contents of the currently selected region.
Use this to + subdivide an alignment based on the different combinations of + residues observed at specific positions. (new in jalview 2.5) +

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 / + Sequences and Columns)
All hidden Columns / + Sequences / Sequences and Columns will be revealed. +
Hide→(all Columns / Sequences / + Selected Region / All but Selected Region )
+ Hides the all the currently selected Columns / Sequences / Region + or everything but the selected Region. +
Automatic Scrolling
When + selected, the view will automatically scroll to display the + highlighted sequence position corresponding to the position under + the mouse pointer in a linked alignment or structure view.
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. +
Autocalculated Annotation
Settings + for the display of autocalculated annotation. +
- Apply to all groups
  When + ticked, any modification to the current settings will be applied + to all autocalculated annotation.
- Show Consensus Histogram
  + Enable or disable the display of the histogram above the + consensus sequence.
- Show Consensus Profile
  Enable + or disable the display of the sequence logo above the consensus + sequence.
- Group Conservation
  When + ticked, display a conservation row for all groups (only available + for protein alignments).
- Apply to all groups
  When + ticked, display a consensus row for all groups.
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. +

+
Sequence ID Tooltip (application + only)
This submenu's options allow the inclusion or + exclusion of non-positional sequence features or database cross + references from the tooltip shown when the mouse hovers over the + sequence ID panel. +
+
Alignment Properties...
Displays + some simple statistics computed for the current alignment view and + any named properties defined on the whole alignment. +
+
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. +
+
Centre Annotation Labels
Select + this to center labels along an annotation row relative to their + associated column (default is off, i.e. left-justified). +
+
Show Unconserved
When + this is selected, all consensus sequence symbols will be + rendered as a '.', highlighting mutations in highly conserved + alignments. +
+ +
+
+
-
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.
-
Make Groups
- The currently selected groups of the alignment will be - subdivided according to the contents of the currently selected region. -
Use this to subdivide an alignment based on the - different combinations of residues observed at specific - positions. (new in jalview 2.5)
-
-
-
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 / Sequences and Columns)
- All hidden Columns / Sequences / Sequences and Columns will be revealed.
-
Hide→(all Columns / Sequences / Selected Region / All but Selected Region )
- Hides the all the currently selected Columns / Sequences / Region or everything but the selected Region.
-
Automatic Scrolling
- When selected, the view will automatically scroll to display the - highlighted sequence position corresponding to the position under the mouse - pointer in a linked alignment or structure view. -
-
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.
-
Autocalculated Annotation
Settings for the display of autocalculated annotation. -
- Apply to all groups
- When ticked, any modification to the current settings will be applied to all autocalculated annotation. -
-
- Show Consensus Histogram
- Enable or disable the display of the histogram above the consensus sequence. -
-
- Show Consensus Profile
- Enable or disable the display of the sequence logo above the consensus sequence. -
-
- Group Conservation
- When ticked, display a conservation row for all groups (only available for protein alignments). -
-
- Apply to all groups
- When ticked, display a consensus row for all groups. -
-
-
-
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.
-
Sequence ID Tooltip (application only) -
This submenu's options allow the inclusion or exclusion of - non-positional sequence features or database cross references - from the tooltip shown when the mouse hovers over the sequence ID panel.
-
Alignment Properties...
- Displays some simple statistics computed for the - current alignment view and any named properties defined on the - whole alignment.
-
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.
-
Centre Annotation Labels
- Select this to center labels along an annotation row - relative to their associated column (default is off, i.e. left-justified).
-
Show Unconserved
- When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments. -
- -
-
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, Purine/Pyrimidine, 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.
-
+ +
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 ++ Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, 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.
+
By RNA Helices
+ Colours the helices of an RNA alignment loaded from a Stockholm file. See + RNA Helices + 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 Length
This will + sort the sequences according to their length (excluding gap + characters). 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.
+
+
Extract Scores ... (optional)
This + option is only visible if Jalview detects one or more white-space + separated values in the description line of the alignment + sequences.
When selected, these numbers are parsed into + sequence associated annotation which can then be used to sort the + alignment via the Sort by→Score menu.
+
+
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.
+
+
Sort With New Tree
When + enabled, Jalview will automatically sort the alignment when a new + tree is calculated or loaded onto it.
+
+ +
Web Service Menu
This menu + is dynamic, and may contain user-defined web service entries in + addition to any of the following ones: +
+
Fetch DB References
This + will use any of the database services that Jalview is aware of + (e.g. DAS sequence servers and the WSDBFetch service provided by + the EBI) to verify the sequence and retrieve all database cross + references and PDB ids associated with all or just the selected + sequences in the alignment.
'Standard Databases' will check + sequences against the EBI databases plus any active DAS sequence + sources, or you can verify against a specific source from one of + the sub-menus.
+
Envision2 Services
Submits one or + more sequences, sequence IDs or database references to analysis + workflows provided by the EnVision2 web + application. This allows Jalview users to easily access the EnCore + network of databases and analysis services developed by members of + ENFIN.
+
+
Selecting items from the following submenus will start a + remote service on compute facilities at the University of Dundee, or + elsewhere. You need a continuous network connection in order to use + these services through Jalview. +
+
+
Alignment
Align the currently + selected sequences or all sequences in the alignment, or re-align + unaligned sequences to the aligned sequences. Entries in this menu + provide access to the various alignment programs supported by JABAWS. See the Multiple Sequence + Alignment webservice client entry for more information.
+
Secondary Structure Prediction +
+
JPred Secondary Structure Prediction
+ Secondary structure prediction by network consensus. See + the Jpred3 client entry for + more information. 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). +
+
+
+
Analysis
+
+
Multi-Harmony
Performs + functional residue analysis on a protein family alignment with + sub-families defined on it. See the Multi-Harmony service entry for more + information. +
+
+

-
-
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 Length
- This will sort the sequences according to their length (excluding gap characters). 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.
-
-
Extract Scores ... (optional)
- This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.
- When selected, these numbers are parsed into sequence associated annotation which can - then be used to sort the alignment via the Sort by→Score menu.
-
-
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
- -
Fetch DB References
- This will use any of the database services that Jalview is aware - of (e.g. DAS sequence servers and the WSDBFetch service provided by the EBI) - to verify the sequence and retrieve all database cross references and PDB ids - associated with all or just the selected sequences in the alignment.
-
-
- 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 --cc help/html/whatsNew.html index cf96d47,3f402dc..3ff173b --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@@ -20,84 -20,39 +20,39 @@@ What's new ? -
What's new ?
-
The Jalview 2.6.1 release fixes a number of minor bugs affecting -Jalview operation, including issues affecting the import and export of -PIR files and working with multiple multiple structure superpositions. -For full details see the Jalview -2.6.1 release history.
-
Highlights in Jalview Version 2.6
-
-
JABA Web Services for - multiple alignment using: +
+ What's new ? +
+
- The Jalview 2.7 release features new web services, and important - improvements to the way in which Jalview handles alignments and - associated PDB structures, as well as numerous minor improvements and - bug fixes. Version 2.7 of the JalviewLite applet also features a - significantly enhanced Javascript API enabling it to be more easily - integrated with javascript based web applications.
For full - details see the Jalview 2.7 ++ The Jalview 2.7.1 release features (tbc) ++
For full ++ details see the Jalview 2.7.1 + release history. +
+
- Highlights in Jalview Desktop Version 2.7 ++ Highlights in Jalview Desktop Version 2.7.1 +

-
New structure viewer - options: -
-
Colour and superimpose 3D structures of complexes and - multi-domain chains using several different alignments
-
Drag and drop to associate PDB files with sequences that - have the same name
-
Open and superimpose all associated structures for the - current selection
-
-
New web services for alignment - analysis
-
Improved graphical user interface for JABAWSservices. -
-
Sort associated alignment views option in tree viewer
-
Default colours for shading alignment - by quantitative annotation. -
-
Jalview Desktop RSS - reader - following important updates at http://www.jalview.org/feeds/desktop/rss -
ClustalW
-
MAFFT
-
Muscle
-
ProbCons
-
T-COFFEE
-
-
-
User modifiable alignment service parameters
-
Visualization of superposed structures associated with protein - or nucleotide sequence alignments.
-
Export coordinates and projection as CSV from PCA viewer
++ +
New Purine/Pyrimidine colour scheme
+
Colouring of RNA secondary structure by helices. See Nucleic Acid Support
- -
- -
Issues Resolved (a select list - see release -history for details)
-
++
Embedded VARNA RNA secondary structure viewer. +
- -
See the Release History page for -details of all new features and resolved issues.
+
+ Issues Resolved (a select list - see the release history for full details) ++ href="releases.html#Jalview2.7.1">release history for full details) + +
+
+ Issues in the Jalview Desktop +
-
Problems viewing associated structures for sequences - retrieved from UNIPROT
-
Problems viewing Jalview projects from older versions in - version 2.6
-
Preservation of hidden annotation rows and tree bootstrap - values in projects
-
Newly added JABAWS servers not always visible in web services - menu
+
+ Issues specific to the JalviewLite Applet +
-
Layout problems when lots of annotation rows are displayed
-
<= shown as = in annotation row tooltip
-
export features raises exception when no features exist
-
relative URLs not handled properly when used in parameters - and annotation files
+
+ Issues affecting both applet and application +
-
sequence numbering not preserved in MSF alignment output
-
sequence associated secondary structure not correctly parsed - in interleaved stockholm
-
sequences containing lowercase letters are not properly - associated with their pdb files
-
Jalview PDB file reader does not extract sequence from deoxy - nucleotide chains correctly
-
Sequence length given in alignment properties window is off - by 1
+
diff --cc src/jalview/commands/EditCommand.java index d18cb62,03b94d3..717d3d2 --- a/src/jalview/commands/EditCommand.java +++ b/src/jalview/commands/EditCommand.java @@@ -192,6 -194,10 +194,10 @@@ public class EditCommand implements Com case REPLACE: replace(edits[e]); break; + //TODO:add deleteNuc for UNDO - case INSERT_NUC: - insertNuc(edits[e]); - break; ++// case INSERT_NUC: ++// insertNuc(edits[e]); ++// break; } } } @@@ -234,10 -240,23 +240,23 @@@ { command.seqs[s].insertCharAt(command.position, command.number, command.gapChar); - System.out.println("pos: "+command.position+" number: "+command.number); - } - - adjustAnnotations(command, true, false, null); - } - - final void insertNuc(Edit command) - { - - for (int s = 0; s < command.seqs.length; s++) - { - System.out.println("pos: "+command.position+" number: "+command.number); - command.seqs[s].insertCharAt(command.position, command.number,'A'); ++// System.out.println("pos: "+command.position+" number: "+command.number); } adjustAnnotations(command, true, false, null); } ++// ++// final void insertNuc(Edit command) ++// { ++// ++// for (int s = 0; s < command.seqs.length; s++) ++// { ++// System.out.println("pos: "+command.position+" number: "+command.number); ++// command.seqs[s].insertCharAt(command.position, command.number,'A'); ++// } ++// ++// adjustAnnotations(command, true, false, null); ++// } final void deleteGap(Edit command) { diff --cc src/jalview/gui/AlignFrame.java index 2ecd947,5beebfd..b61d44b --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@@ -401,7 -401,22 +402,22 @@@ public class AlignFrame extends GAlignF || evt.isShiftDown() || evt.isAltDown()); } break; - + - case KeyEvent.VK_A: - if (viewport.cursorMode) - { - alignPanel.seqPanel.insertNucAtCursor(false,"A"); - //System.out.println("A"); - } - break; ++ //case KeyEvent.VK_A: ++ // if (viewport.cursorMode) ++ // { ++ // alignPanel.seqPanel.insertNucAtCursor(false,"A"); ++ // //System.out.println("A"); ++ // } ++ // break; + /* + case KeyEvent.VK_CLOSE_BRACKET: + if (viewport.cursorMode) + { + System.out.println("closing bracket"); + } + break; + */ case KeyEvent.VK_DELETE: case KeyEvent.VK_BACK_SPACE: if (!viewport.cursorMode)