Alignment Window Menus

From f244cdf6267fd446edc039d49428fa8eabcca42c Mon Sep 17 00:00:00 2001 From: Charles Ofoegbu Date: Thu, 9 Oct 2014 16:16:58 +0100 Subject: [PATCH] Integration of Freemarker API to the Jalview help system to aid self-documentation where possible using predefined templates and boiler-plates codes from Jalview codebase --- .gitattributes | 7 + .gitignore | 14 +- help/freemarker_templates/alignmentMenu.ftl | 642 +++++++++++++++++++ .../html/freemarker_html_output/alignmentMenu.html | 649 ++++++++++++++++++++ src/jalview/datamodel/DBRefSource.java | 37 +- .../freemarker/AllignmentMenuTemplateData.java | 117 ++-- 6 files changed, 1385 insertions(+), 81 deletions(-) create mode 100644 .gitattributes create mode 100644 help/freemarker_templates/alignmentMenu.ftl create mode 100644 help/html/freemarker_html_output/alignmentMenu.html diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..50a7ed6 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,7 @@ +* text=auto + +# Windows users +core.autocrlf = true + +# Mac users +#core.autocrlf = input \ No newline at end of file diff --git a/.gitignore b/.gitignore index 9841761..c4c7880 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,8 @@ -.project -/dist -/classes -.externalToolBuilders/Jalview Release indices [Builder].launch -/.DS_Store -/.com.apple.timemachine.supported +.project +/dist +/classes +.externalToolBuilders/Jalview Release indices [Builder].launch +/.DS_Store +/.com.apple.timemachine.supported +/nbproject/private/ +.settings/ \ No newline at end of file diff --git a/help/freemarker_templates/alignmentMenu.ftl b/help/freemarker_templates/alignmentMenu.ftl new file mode 100644 index 0000000..c341a7a --- /dev/null +++ b/help/freemarker_templates/alignmentMenu.ftl @@ -0,0 +1,642 @@ + + + + Alignment Window Menus + + + +

Alignment Window Menus x

+ +

File +
- Fetch Sequence
  + Shows a 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. +
  - ${format_adapter}
  +
- 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.
- Create Group (Control G)
  + Create a group containing the currently selected +sequences.
- Remove Group (Shift Control G)
  + Ungroup the currently selected sequence group. +(Create/Remove group new in Jalview 2.8.1)
- Make Groups for selection
  + 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)
- 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 / 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 Logo
    + Enable or disable the display of the +Consensus Logo above the consensus sequence.
  - Normalise Consensus Logo
    + When enabled, scales all logo stacks to the +same height, making it easier to compare symbol diversity in highly +variable regions.
  - 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.
+

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
  +
+ Note: Since Version 2.8.1, a number of +additional similarity measures for tree calculation are provided in +this menu.

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 +similarity scores calculated with 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.
+

Show Flanking Regions
+ Opens a new alignment window showing any additional sequence +data either side of the current alignment. Useful in conjunction with +'Fetch Database References' when the 'Trim Retrieved Sequences' option +is disabled to retrieve full length sequences for a set of aligned +peptides.

+ + +

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 submenu contains options for accessing 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 sequence +start/end positions and retrieve all database cross references and PDB +ids associated with all or just the selected sequences in the +alignment. +
- 'Trim Retrieved Sequences' - when checked, +Jalview will discard any additional sequence data for accessions +associated with sequences in the alignment.
  + Note: Disabling this could cause out of memory errors +when working with genomic sequence records !
  + Added in Jalview 2.8.1
- 'Standard Databases' will check sequences +against the EBI databases plus any active DAS sequence sources<
+ Other sub-menus allow you to pick a specific +source to query - sources are listed alphabetically according to their +nickname.
+

+ +

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.
+

+ + + \ No newline at end of file diff --git a/help/html/freemarker_html_output/alignmentMenu.html b/help/html/freemarker_html_output/alignmentMenu.html new file mode 100644 index 0000000..d691be1 --- /dev/null +++ b/help/html/freemarker_html_output/alignmentMenu.html @@ -0,0 +1,649 @@ + + + + Alignment Window Menus + + + +

Alignment Window Menus x

+ +

File +
- Fetch Sequence
  + Shows a 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. +
  - AMSA
  - BLC
  - CLUSTAL
  - FASTA
  - MSF
  - PileUp
  - PIR
  - PHYLIP
  - PFAM
  - STH
  +
- 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.
- Create Group (Control G)
  + Create a group containing the currently selected +sequences.
- Remove Group (Shift Control G)
  + Ungroup the currently selected sequence group. +(Create/Remove group new in Jalview 2.8.1)
- Make Groups for selection
  + 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)
- 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 / 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 Logo
    + Enable or disable the display of the +Consensus Logo above the consensus sequence.
  - Normalise Consensus Logo
    + When enabled, scales all logo stacks to the +same height, making it easier to compare symbol diversity in highly +variable regions.
  - 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.
+

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
  +
+ Note: Since Version 2.8.1, a number of +additional similarity measures for tree calculation are provided in +this menu.

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 +similarity scores calculated with 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.
+

Show Flanking Regions
+ Opens a new alignment window showing any additional sequence +data either side of the current alignment. Useful in conjunction with +'Fetch Database References' when the 'Trim Retrieved Sequences' option +is disabled to retrieve full length sequences for a set of aligned +peptides.

+ + +

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 submenu contains options for accessing 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 sequence +start/end positions and retrieve all database cross references and PDB +ids associated with all or just the selected sequences in the +alignment. +
- 'Trim Retrieved Sequences' - when checked, +Jalview will discard any additional sequence data for accessions +associated with sequences in the alignment.
  + Note: Disabling this could cause out of memory errors +when working with genomic sequence records !
  + Added in Jalview 2.8.1
- 'Standard Databases' will check sequences +against the EBI databases plus any active DAS sequence sources<
+ Other sub-menus allow you to pick a specific +source to query - sources are listed alphabetically according to their +nickname.
+

+ +

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.
+

+ + + \ No newline at end of file diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java index 1af18b6..2022a7f 100755 --- a/src/jalview/datamodel/DBRefSource.java +++ b/src/jalview/datamodel/DBRefSource.java @@ -1,19 +1,19 @@ /* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) * Copyright (C) 2014 The Jalview Authors - * + * * This file is part of Jalview. - * + * * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License + * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. @@ -24,9 +24,9 @@ package jalview.datamodel; * Defines internal constants for unambiguous annotation of DbRefEntry source * strings and describing the data retrieved from external database sources (see * jalview.ws.DbSourcProxy) - * + * * @author JimP - * + * */ public class DBRefSource { @@ -36,6 +36,11 @@ public class DBRefSource public static String UNIPROT = "UNIPROT"; /** + * INTERMINE ID + */ + public static String INTERMINE = "INTERMINE"; + + /** * UNIPROT Entry Name */ public static String UP_NAME = "UNIPROT_NAME"; @@ -79,22 +84,22 @@ public class DBRefSource * List of databases whose sequences might have coding regions annotated */ public static final String[] DNACODINGDBS = - { EMBL, EMBLCDS, GENEDB }; + { EMBL, EMBLCDS, GENEDB }; public static final String[] CODINGDBS = - { EMBLCDS, GENEDB }; + { EMBLCDS, GENEDB }; public static final String[] PROTEINDBS = - { UNIPROT, PDB, UNIPROTKB }; + { UNIPROT, PDB, UNIPROTKB }; public static final String[] PROTEINSEQ = - { UNIPROT, UNIPROTKB }; + { UNIPROT, UNIPROTKB }; public static final String[] PROTEINSTR = - { PDB }; + { PDB }; public static final String[] DOMAINDBS = - { PFAM, RFAM }; + { PFAM, RFAM }; /** * set of unique DBRefSource property constants. These could be used to diff --git a/src/jalview/help/freemarker/AllignmentMenuTemplateData.java b/src/jalview/help/freemarker/AllignmentMenuTemplateData.java index a1b808b..61c94d9 100644 --- a/src/jalview/help/freemarker/AllignmentMenuTemplateData.java +++ b/src/jalview/help/freemarker/AllignmentMenuTemplateData.java @@ -1,59 +1,58 @@ -package jalview.help.freemarker; - -import jalview.io.AppletFormatAdapter; - -import java.io.File; -import java.io.FileWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.Writer; -import java.util.HashMap; -import java.util.Map; - -import freemarker.template.Configuration; -import freemarker.template.Template; -import freemarker.template.TemplateException; - -public class AllignmentMenuTemplateData -{ - - public static void main(String[] args) - { - // System.out.println("Absolute Path " + new File().getAbsoluteFile()); - generateAllignmentMenuTemplateData(); - } - public static void generateAllignmentMenuTemplateData() - { - Configuration cfg = new Configuration(); - try - { - // Load template from source folder - Template template = cfg - .getTemplate("/help/freemarker_templates/alignmentMenu.ftl"); - - // Build the data-model - Map data = new HashMap(); - data.put("format_adapters", AppletFormatAdapter.WRITEABLE_FORMATS); - - // Console output - Writer out = new OutputStreamWriter(System.out); - template.process(data, out); - out.flush(); - - // File output - Writer file = new FileWriter( - new File( - "help/html/freemarker_html_output/alignmentMenu.html")); - template.process(data, file); - file.flush(); - file.close(); - - } catch (IOException e) - { - e.printStackTrace(); - } catch (TemplateException e) - { - e.printStackTrace(); - } - } -} +package jalview.help.freemarker; + +import jalview.io.AppletFormatAdapter; + +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import java.io.OutputStreamWriter; +import java.io.Writer; +import java.util.HashMap; +import java.util.Map; + +import freemarker.template.Configuration; +import freemarker.template.Template; +import freemarker.template.TemplateException; + +public class AllignmentMenuTemplateData +{ + + public static void main(String[] args) + { + generateAllignmentMenuTemplateData(); + } + public static void generateAllignmentMenuTemplateData() + { + Configuration cfg = new Configuration(); + try + { + // Load template from source folder + Template template = cfg + .getTemplate("/help/freemarker_templates/alignmentMenu.ftl"); + + // Build the data-model + Map data = new HashMap(); + data.put("format_adapters", AppletFormatAdapter.WRITEABLE_FORMATS); + + // Console output + Writer out = new OutputStreamWriter(System.out); + template.process(data, out); + out.flush(); + + // File output + Writer file = new FileWriter( + new File( + "help/html/freemarker_html_output/alignmentMenu.html")); + template.process(data, file); + file.flush(); + file.close(); + + } catch (IOException e) + { + e.printStackTrace(); + } catch (TemplateException e) + { + e.printStackTrace(); + } + } +} -- 1.7.10.2