From: Jim Procter Date: Wed, 17 May 2017 13:31:54 +0000 (+0100) Subject: Merge branch 'features/JAL-2447experimentalFlag' into develop X-Git-Tag: Release_2_10_2~3^2~82 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=36e7c887ef91f49f6065dea063180f7de146b3e1;hp=124aa4823768a2c745a5e41f2ebfe13ab77bbea4;p=jalview.git Merge branch 'features/JAL-2447experimentalFlag' into develop --- diff --git a/examples/groovy/colourConserved.groovy b/examples/groovy/colourConserved.groovy new file mode 100644 index 0000000..4a15922 --- /dev/null +++ b/examples/groovy/colourConserved.groovy @@ -0,0 +1,88 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +import java.awt.Color +import jalview.schemes.ColourSchemeI +import jalview.schemes.ColourSchemes +import jalview.datamodel.AnnotatedCollectionI +import jalview.datamodel.SequenceI +import jalview.datamodel.SequenceCollectionI +import jalview.util.Comparison + +/* + * Closure that defines a colour scheme where fully conserved residues are red, + * partly conserved (match consensus but < 100% consensus) are yellow, + * unconserved and gaps are white + */ +def conserved +conserved = { -> + [ + /* + * name shown in the colour menu + */ + getSchemeName: { -> 'Conserved' }, + + /* + * to make a new instance for each alignment view + */ + getInstance: { AnnotatedCollectionI coll, Map map -> conserved() }, + + /* + * method only needed if colour scheme has to recalculate + * values when an alignment is modified + */ + alignmentChanged: { AnnotatedCollectionI coll, Map map -> }, + + /* + * determine colour for a residue at an aligned position of a + * sequence, given consensus residue(s) for the column and the + * consensus percentage identity score for the column + */ + findColour: { char res, int col, SequenceI seq, String consensus, float pid -> + if ('a' <= res && res <= 'z') + { + res -= ('a' - 'A'); + } + if (Comparison.isGap(res) || !consensus.contains(String.valueOf(res))) + { + Color.white + } else if (pid < 100) + { + Color.yellow + } else + { + Color.red + } + }, + + /* + * true means applicable to nucleotide or peptide data + */ + isApplicableTo: {AnnotatedCollectionI coll -> true}, + + /* + * simple colour schemes are those that depend on the residue + * only (these are also available to colour structure viewers) + */ + isSimple: { false } + ] as ColourSchemeI +} + +ColourSchemes.instance.registerColourScheme(conserved()) diff --git a/examples/groovy/colourUnconserved.groovy b/examples/groovy/colourUnconserved.groovy new file mode 100644 index 0000000..68730f3 --- /dev/null +++ b/examples/groovy/colourUnconserved.groovy @@ -0,0 +1,84 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +import java.awt.Color +import jalview.schemes.ColourSchemeI +import jalview.schemes.ColourSchemes +import jalview.datamodel.AnnotatedCollectionI +import jalview.datamodel.SequenceI +import jalview.datamodel.SequenceCollectionI +import jalview.util.Comparison + +/* + * Closure that defines a colour scheme where non-consensus residues are pink, + * other residues (and gaps) are white + */ +def unconserved +unconserved = { -> + [ + /* + * name shown in the colour menu + */ + getSchemeName: { -> 'Unconserved' }, + + /* + * to make a new instance for each alignment view + */ + getInstance: { AnnotatedCollectionI coll, Map map -> unconserved() }, + + /* + * method only needed if colour scheme has to recalculate + * values when an alignment is modified + */ + alignmentChanged: { AnnotatedCollectionI coll, Map map -> }, + + /* + * determine colour for a residue at an aligned position of a + * sequence, given consensus residue(s) for the column and the + * consensus percentage identity score for the column + */ + findColour: { char res, int col, SequenceI seq, String consensus, float pid -> + if ('a' <= res && res <= 'z') + { + res -= ('a' - 'A'); + } + if (Comparison.isGap(res) || consensus.contains(String.valueOf(res))) + { + Color.white + } else + { + Color.pink + } + }, + + /* + * true means applicable to nucleotide or peptide data + */ + isApplicableTo: {AnnotatedCollectionI coll -> true}, + + /* + * simple colour schemes are those that depend on the residue + * only (these are also available to colour structure viewers) + */ + isSimple: { false } + ] as ColourSchemeI +} + +ColourSchemes.instance.registerColourScheme(unconserved()) diff --git a/examples/groovy/featureCounter.groovy b/examples/groovy/featureCounter.groovy deleted file mode 100644 index 9059dd0..0000000 --- a/examples/groovy/featureCounter.groovy +++ /dev/null @@ -1,116 +0,0 @@ -/* - * 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 . - * 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/examples/groovy/featuresCounter.groovy b/examples/groovy/featuresCounter.groovy new file mode 100644 index 0000000..dc4c97c --- /dev/null +++ b/examples/groovy/featuresCounter.groovy @@ -0,0 +1,73 @@ +/* + * 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 . + * 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/examples/groovy/multipleFeatureAnnotations.groovy b/examples/groovy/multipleFeatureAnnotations.groovy deleted file mode 100644 index 592c7f5..0000000 --- a/examples/groovy/multipleFeatureAnnotations.groovy +++ /dev/null @@ -1,110 +0,0 @@ -import jalview.workers.AlignmentAnnotationFactory; -import jalview.workers.AnnotationProviderI; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.Annotation; -import jalview.util.ColorUtils; -import jalview.util.Comparison; -import java.awt.Color; - -/* - * 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. - */ - -/* - * A closure that returns true if value includes "PHOSPHORYLATION" - */ -def phosCounter = { type -> type.contains("PHOSPHORYLATION") } - -/* - * A closure that returns true if value includes "TURN" - */ -def turnCounter = { type -> type.contains("TURN") } - -/* - * A closure that computes and returns an array of Annotation values, - * one for each column of the alignment - */ -def getAnnotations(al, fr, counter) -{ - def width = al.width - def counts = new int[width] - def max = 0 - - /* - * count features in each column, record the maximum value - */ - for (col = 0 ; col < width ; col++) - { - def count = 0 - for (row = 0 ; row < al.height ; row++) - { - seq = al.getSequenceAt(row) - if (seq != null && col < seq.getLength()) - { - def res = seq.getCharAt(col) - if (!Comparison.isGap(res)) - { - pos = seq.findPosition(col) - features = fr.findFeaturesAtRes(seq, pos) - for (feature in features) - { - if (counter.call(feature.type)) - { - count++ - } - } - } - } - } - counts[col] = count - if (count > max) - { - max = count - } - } - - /* - * make the Annotation objects, with a graduated colour scale - * (from min value to max value) for the histogram bars - */ - def zero = '0' as char - def anns = new Annotation[width] - for (col = 0 ; col < width ; col++) - { - def c = counts[col] - if (c > 0) - { - Color color = ColorUtils.getGraduatedColour(c, 0, Color.cyan, - max, Color.blue) - anns[col] = AlignmentAnnotationFactory.newAnnotation(String.valueOf(c), - String.valueOf(c), zero, c, color) - } - } - anns -} - -/* - * Define the method that performs the calculations, and builds two - * AlignmentAnnotation objects - */ -def annotator = - [ calculateAnnotation: { al, fr -> - def phosAnns = getAnnotations(al, fr, phosCounter) - def ann1 = AlignmentAnnotationFactory.newAlignmentAnnotation("Phosphorylation", "Count of Phosphorylation features", phosAnns) - def turnAnns = getAnnotations(al, fr, turnCounter) - def ann2 = AlignmentAnnotationFactory.newAlignmentAnnotation("Turn", "Count of Turn features", turnAnns) - return [ann1, ann2] - } - ] as AnnotationProviderI - -/* - * Register the annotation calculator with Jalview - */ -AlignmentAnnotationFactory.newCalculator(annotator) diff --git a/examples/groovy/visibleFeaturesCounter.groovy b/examples/groovy/visibleFeaturesCounter.groovy new file mode 100644 index 0000000..b3180f8 --- /dev/null +++ b/examples/groovy/visibleFeaturesCounter.groovy @@ -0,0 +1,89 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +import jalview.bin.Jalview +import jalview.workers.FeatureSetCounterI +import jalview.workers.AlignmentAnnotationFactory + +/* + * Demonstration of FeatureSetCounterI + * compute annotation tracks counting number of displayed + * features of each type in each column + */ + +/* + * discover features on the current view + */ + +def featuresDisp=Jalview.currentAlignFrame.currentView.featuresDisplayed +if (featuresDisp == null) { + print 'Need at least one feature visible on alignment' +} +def visibleFeatures=featuresDisp.visibleFeatures.toList() +assert 'java.util.ArrayList' == visibleFeatures.class.name + +/* + * A closure that returns an array of features present + * for each feature type in visibleFeatures + * Argument 'features' will be a list of SequenceFeature + */ +def getCounts = + { features -> + int[] obs = new int[visibleFeatures.size] + 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 + */ + int pos = 0 + for (type in visibleFeatures) + { + if (type.equals(sf.type)) + { + obs[pos]++ + } + pos++ + } + } + obs +} + +/* + * Define something that counts each visible feature type + */ +def columnSetCounter = + [ + getNames: { visibleFeatures as String[] }, + getDescriptions: { visibleFeatures as String[] }, + getMinColour: { [0, 255, 255] as int[] }, // cyan + getMaxColour: { [0, 0, 255] as int[] }, // blue + count: + { res, feats -> + getCounts.call(feats) + } + ] as FeatureSetCounterI + +/* + * and register the counter + */ +AlignmentAnnotationFactory.newCalculator(columnSetCounter) diff --git a/help/help.jhm b/help/help.jhm index 984c2d1..54cce2a 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -22,7 +22,7 @@ - + @@ -75,6 +75,7 @@ + @@ -130,7 +131,8 @@ - + + @@ -158,4 +160,6 @@ + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 482ccdf..a8aadf5 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -24,6 +24,11 @@ + + + + + @@ -132,7 +137,7 @@ - + @@ -157,7 +162,7 @@ - + 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:
+

+

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:

    -
      -
    1. Copy and paste it into the groovy script console
      2. -
    2. Load the example Feredoxin project (the one that opens by - default when you first launched Jalview)
      3. -
    3. Select Calculations→Execute Groovy - Script from the alignment window's menu bar to run the script on - the current view. -
      4. -
    -     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:

    +
      +
    1. Copy and paste it into the groovy script console
      2. +
    2. Load the example Feredoxin project (the one that opens by + default when you first launched Jalview)
      3. +
    3. Select Calculations→Execute Groovy + Script from the alignment window's menu bar to run the script on + the current view. +
      4. +
    + 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/releases.html b/help/html/releases.html index 6f44b3d..2f983fa 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -21,6 +21,29 @@ --> Release History +

    @@ -47,6 +70,97 @@

    + 2.10.2
    + 30/5/2017     +
    + +
    + General +
      +
    • More robust colours and shader model for alignments and groups
      • +
    • Custom shading schemes created via groovy scripts
      • +
    • Test suite expanded and debugged (over 940 functional unit tests, only 3 failing due to ongoing work!) +
    + Application +
      +
      • +
    • 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
      • + +
    + Applet +
      +
      • +
    +
    + General +
      +
    • + Fixed incorrect value in BLOSUM 62 score + matrix - C->R should be '3'
      Old matrix restored with + this one-line groovy script:
      jalview.schemes.ResidueProperties.BLOSUM62[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
      • +
    + 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
      • + +
    + Applet +
      +
    • Features not rendered as transparent on overview or linked structure view
      • +
    • Colour group by conservation doesn't work (since 2.8)
      • +
    + New Known Issues +
      +
    • +
    + +
    + + +
    2.10.1
    29/11/2016
    @@ -188,6 +302,9 @@ 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