Extending Jalview with Groovy - Feature Counter Example

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Chimera Help
diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index 254f92e..ead4436 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -108,9 +108,18 @@ print currentAlFrame.getTitle(); simplified the alignment analysis programming interface in Jalview 2.10 to make it easy for you to add your own dynamic annotation tracks with Groovy. Have a look at the featureCounter.groovy + href="../groovy/featuresCounter.html">featuresCounter.groovy example for more information.
+
+ Creating custom colourschemes
+ You can create your own alignment colourschemes with a groovy script. We've provided two examples:
+
+
colourConserved.groovy creates an 'Conserved' colourscheme - similar to the classic GeneDOC shading model.
+
colourUnconserved.groovy creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink.
+ +
+
diff --git a/help/html/features/overview.html b/help/html/features/overview.html index 9d36a1c..4f26592 100755 --- a/help/html/features/overview.html +++ b/help/html/features/overview.html @@ -31,6 +31,11 @@
The red box indicates the currently viewed region of the alignment, this may be moved by clicking and dragging with the mouse.
+
Right-click (or CMD-Click) to open the + overview's popup menu. This provides an option to include hidden + regions in the overview (shown as dark-grey rows and columns).

+ The option to include/exclude hidden regions in the + overview was introduced in Jalview 2.10.2.

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 6e8d3e4..acd7ba6 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -261,7 +261,11 @@ The Custom only button limits the entries in the table to just those you have configured yourself via the Edit Links buttons. Press Show all to clear any filters. -
+
+
The links table is prepoulated with persistent URLs for many common + bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from + the identifiers.org website, and the names and URLs are not + user editable. Read more about configuring URL links.
diff --git a/help/html/features/splitView.html b/help/html/features/splitView.html index 03b993c..3862c39 100644 --- a/help/html/features/splitView.html +++ b/help/html/features/splitView.html @@ -67,7 +67,11 @@ alignments, the "Format→Font" menu option has an option 'Scale protein residues to codons'. This option will make each protein residue the same width as a DNA - codon (so the alignments 'line up' vertically) + codon (so the alignments 'line up' vertically).

+ The 'Use same + font for cDNA and peptide' checkbox, when enabled, ensures that font or + font-size changes in either the cDNA or Protein alignment will also + be mirrored. (Added in 2.10.2)

"View→Protein" (in the cDNA panel) or "View→Nucleotide" (in the protein panel) diff --git a/help/html/groovy/featureCounter.html b/help/html/groovy/featureCounter.html deleted file mode 100644 index 2ebaf45..0000000 --- a/help/html/groovy/featureCounter.html +++ /dev/null @@ -1,269 +0,0 @@ - - - -Extending Jalview with Groovy - Feature Counter Example - - -
- Extending Jalview with Groovy - A customisable - feature counter

The groovy script below shows how to - add a new calculation track to a Jalview alignment window. -
-
As currently written, it will add two tracks to a protein - alignment view which count Pfam features in each column, and ones - where a charge residue also occur.
-
To try it for yourself:
-
-
Copy and paste it into the groovy script console
-
Load the example Feredoxin project (the one that opens by - default when you first launched Jalview)
-
Select Calculations→Execute Groovy - Script from the alignment window's menu bar to run the script on - the current view. -
-
- http://www.jalview.org/examples/groovy/featureCounter.groovy - - rendered with hilite.me - -
-
-/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.10) - * Copyright (C) 2016 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 - * 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 - * 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 <http://www.gnu.org/licenses/>. - * The Jalview Authors are detailed in the 'AUTHORS' file. - */ - -import jalview.workers.FeatureCounterI; -import jalview.workers.AlignmentAnnotationFactory; - -/* - * Example script that registers two alignment annotation calculators - * - one that counts residues in a column with Pfam annotation - * - one that counts only charged residues with Pfam annotation - * - * To try: - * 1. load uniref50.fa from the examples folder - * 2. load features onto it from from examples/exampleFeatures.txt - * 3. Open this script in the Groovy console. - * 4. Either execute this script from the console, or via Calculate->Run Groovy Script - - * To explore further, try changing this script to count other kinds of occurrences of - * residue and sequence features at columns in an alignment. - */ - -/* - * A closure that returns true for any Charged residue - */ -def isCharged = { residue -> - switch(residue) { - case ['D', 'd', 'E', 'e', 'H', 'h', 'K', 'k', 'R', 'r']: - return true - } - false -} - -/* - * A closure that returns 1 if sequence features include type 'Pfam', else 0 - * Argument should be a list of SequenceFeature - */ -def hasPfam = { features -> - for (sf in features) - { - /* - * Here we inspect the type of the sequence feature. - * You can also test sf.description, sf.score, sf.featureGroup, - * sf.strand, sf.phase, sf.begin, sf.end - * or sf.getValue(attributeName) for GFF 'column 9' properties - */ - if ("Pfam".equals(sf.type)) - { - return true - } - } - false -} - -/* - * Closure that computes an annotation based on - * presence of particular residues and features - * Parameters are - * - the name (label) for the alignment annotation - * - the description (tooltip) for the annotation - * - a closure (groovy function) that tests whether to include a residue - * - a closure that tests whether to increment count based on sequence features - */ -def getColumnCounter = { name, desc, acceptResidue, acceptFeatures -> - [ - getName: { name }, - getDescription: { desc }, - getMinColour: { [0, 255, 255] }, // cyan - getMaxColour: { [0, 0, 255] }, // blue - count: - { res, feats -> - def c = 0 - if (acceptResidue.call(res)) - { - if (acceptFeatures.call(feats)) - { - c++ - } - } - c - } - ] as FeatureCounterI -} - -/* - * Define an annotation row that counts any residue with Pfam domain annotation - */ -def pfamAnnotation = getColumnCounter("Pfam", "Count of residues with Pfam domain annotation", {true}, hasPfam) - -/* - * Define an annotation row that counts charged residues with Pfam domain annotation - */ -def chargedPfamAnnotation = getColumnCounter("Pfam charged", "Count of charged residues with Pfam domain annotation", isCharged, hasPfam) - -/* - * Register the annotations - */ -AlignmentAnnotationFactory.newCalculator(pfamAnnotation) -AlignmentAnnotationFactory.newCalculator(chargedPfamAnnotation) -
-
- - diff --git a/help/html/groovy/featuresCounter.html b/help/html/groovy/featuresCounter.html new file mode 100644 index 0000000..3b6705b --- /dev/null +++ b/help/html/groovy/featuresCounter.html @@ -0,0 +1,123 @@ + + + +Extending Jalview with Groovy - Feature Counter Example + + +
+ Extending Jalview with Groovy - A customisable + feature counter

The groovy script below shows how to + add a new calculation track to a Jalview alignment window. +
+
As currently written, it will add two tracks to a protein + alignment view which count Pfam features in each column, and ones + where a charge residue also occur.
+
To try it for yourself:
+
+
Copy and paste it into the groovy script console
+
Load the example Feredoxin project (the one that opens by + default when you first launched Jalview)
+
Select Calculations→Execute Groovy + Script from the alignment window's menu bar to run the script on + the current view. +
+
+ Please note: The 2.10.2 feature counting interface is not compatible with earlier versions.

+ http://www.jalview.org/examples/groovy/featuresCounter.groovy + - rendered with hilite.me +
/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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 + * 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 + * 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 <http://www.gnu.org/licenses/>. + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ + +import jalview.workers.AlignmentAnnotationFactory; +import jalview.workers.FeatureSetCounterI; + +/* + * Example script to compute two alignment annotations + * - count of Phosphorylation features + * - count of Turn features + * To try this, first load example file uniref50.fa and load on features file + * exampleFeatures.txt, before running this script + * + * The script only needs to be run once - it will be registered by Jalview + * and recalculated automatically when the alignment changes. + * + * Note: The feature api provided by 2.10.2 is not compatible with scripts + * that worked with earlier Jalview versions. Apologies for the inconvenience. + */ + +def annotator = + [ + getNames: { ['Phosphorylation', 'Turn'] as String[] }, + getDescriptions: { ['Count of Phosphorylation features', 'Count of Turn features'] as String[] }, + getMinColour: { [0, 255, 255] as int[] }, // cyan + getMaxColour: { [0, 0, 255] as int[] }, // blue + count: + { res, feats -> + int phos + int turn + for (sf in feats) + { + /* + * Here we inspect the type of the sequence feature. + * You can also test sf.description, sf.score, sf.featureGroup, + * sf.strand, sf.phase, sf.begin, sf.end + * or sf.getValue(attributeName) for GFF 'column 9' properties + */ + if (sf.type.contains('TURN')) + { + turn++ + } + if (sf.type.contains('PHOSPHORYLATION')) + { + phos++ + } + } + [phos, turn] as int[] + } + ] as FeatureSetCounterI + +/* + * Register the annotation calculator with Jalview + */ +AlignmentAnnotationFactory.newCalculator(annotator) +
+ + diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html index 20e784b..a93ce4b 100755 --- a/help/html/menus/desktopMenu.html +++ b/help/html/menus/desktopMenu.html @@ -86,6 +86,7 @@ the Groovy Console for interactive scripting.
+
Enable Experimental Features Enable or disable features still under development in Jalview's user interface. This setting is remembered in your preferences.

Vamsas For more details, read the diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index d42f854..7625606 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -189,8 +189,10 @@ href="../features/varna.html">VARNA.

Hide Insertions
- Hides columns containing gaps in the current sequence or - selected region, and reveals columns not including gaps. + Hides columns containing gaps in both the current + sequence and selected region, and reveals columns not including + gaps. (before 2.10.2, this option hid or revealed columns + according to gaps in just the current sequence)

Hide Sequences
Hides the currently selected sequences in this alignment view.

diff --git a/help/html/releases.html b/help/html/releases.html index 6f44b3d..97d6789 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -21,6 +21,29 @@ --> Release History +
@@ -47,6 +70,140 @@
+ 2.10.2
+ 20/6/2017 +
+ +
+ General +
+
More robust colours and shader model for alignments and groups
+
Custom shading schemes created via groovy scripts
+
linked scrolling of CDS/Protein views via Overview or sequence motif search operations
+
Efficiency improvements for interacting with alignment and overview windows
+
Hidden columns and sequences can be omitted in Overview
+
+ Posterior probability annotation from + Stockholm files imported as sequence associated annotation +
+
+ Sequence names don't include file + extension when importing structure files without embedded + names or PDB accessions +
+
Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent
+
+ Application +
+
+ + Experimental Features Checkbox in Desktop's Tools + menu to hide or show untested features in the application. +
+
Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera
+
Faster Chimera/Jalview communication by file-based command exchange
+
URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB
+
Updated JABAWS client to v2.2
+
+ Experimental features +
+
+ New entries in the Chimera menu + to transfer Chimera's structure attributes as Jalview + features, and vice-versa. +
+
+ Applet +
+
+
+ Test Suite +
Added PrivilegedAccessor to test suite
+
Prevent or clear modal dialogs raised during tests
+
+ +
+ General +
+
+ Fixed incorrect value in BLOSUM 62 score + matrix - C->R should be '3'
Old matrix restored with + this one-line groovy script:
jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3 +
+
+ Fixed Jalview's treatment of gaps in PCA + and substitution matrix based Tree calculations.
In + earlier versions of Jalview, gaps matching gaps were + penalised, and gaps matching non-gaps penalised even more. + In the PCA calculation, gaps were actually treated as + non-gaps - so different costs were applied, which mean't + Jalview's PCAs were different to those produced by + SeqSpace.
Jalview now treats gaps in the same way as + SeqSpace (ie it scores them as 0). To restore pre-2.10.2 + behaviour
+ jalview.viewmodel.PCAModel.scoreGapAsAny=true // for + 2.10.1 mode
+ jalview.viewmodel.PCAModel.scoreGapAsAny=false // to + restore 2.10.2 mode +
+
Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view
+
Hidden regions in alignment views are not coloured in linked structure views
+
Current selection lost if popup menu opened on a region of alignment without groups
+
Popup menu not always shown for regions of an alignment with overlapping groups
+
Finder double counts if both a sequence's name and description match
+
Hiding column selection containing two hidden regions results in incorrect hidden regions
+
PCA calculation could hang when generating output report when working with highly redundant alignments
+
Cannot configure feature colours with lightGray or darkGray via features file
+
Overview window visible region moves erratically when hidden rows or columns are present
+
Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring
+
Protein specific colours only offered in colour and group colour menu for protein alignments
+
'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups
+
Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds
+
Percentage identity and conservation menu items do not show a tick or allow shading to be disabled
+
Conservation shading or PID threshold lost when base colourscheme changed if slider not visible
+
Sequence features shown in tooltip for gaps before start of features
+
Very large alignments take a long time to load
+
Cannot load Newick trees from eggnog ortholog database
+
+ Application +
+
Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)
+
Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds
+
Feature settings panel does not update as new features are added to alignment
+
Structure viewer's View -> Colour By view selection menu changes colours of alignment views
+
Proxy server address and port always appear enabled in Preferences->Connections
+
Spurious exceptions in console raised from alignment calculation workers after alignment has been closed
+
Typo in selection popup menu - Create groups now 'Create Group'
+
CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work
+
Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'
+
DAS registry not found exceptions removed from console output
+
Above PID colour threshold not recovered when alignment view imported from project
+
No mappings generated between structure and sequences extracted from structure files imported via URL
+
+ Structures loaded via URL are saved in + Jalview Projects rather than fetched via URL again when + the project is loaded and the structure viewed +
+
Trackpad horizontal scroll gesture adjusts start position in wrap mode
+
Status bar doesn't show positions for ambiguous amino acids
+
Hide insertions in PopUp menu excludes gaps in selection, current sequence and only within selected columns
+
+ Applet +
+
Features not rendered as transparent on overview or linked structure view
+
Colour group by conservation doesn't work (since 2.8)
+
Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme
+
+ New Known Issues +
+
Protein/CDS view scrolling not always in phase after a sequence motif find operation
+
Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols
+
+ +
+ + +
2.10.1
29/11/2016
@@ -188,6 +345,9 @@ Attempting to view structure for Hen lysozyme results in a PDB Client error dialog box +
+ Structure View's mapping report switched ranges for PDB and sequence for SIFTS
+ SIFTS 'Not_Observed' residues mapped to non-existant coordindate data