diff --git a/browser/js/aligner.js b/browser/js/aligner.js
index 4e960faa18a4abe56f7caeab481c879a1f67895a..24627c424127645ff25c9c898c4d739ad763e49a 100644
--- a/browser/js/aligner.js
+++ b/browser/js/aligner.js
@@ -279,7 +279,7 @@ Aligner.prototype = {
connect_checkbox: function(elem, title, layers){
var self = this;
-
+
//connect event to checkbox and checkbox_label
$(function () {
$(elem).find('input').unbind("click");
@@ -289,6 +289,15 @@ Aligner.prototype = {
localStorage.setItem(`aligner_layers_${title}`, input.checked)
}
self.toggleLayers(layers, input.checked, true);
+
+ var exclusive = ["amino", "affect_values"]
+ exclusive.forEach( (layer, index) => {
+ var to_exclude = index === 0 ? exclusive[1]: exclusive[0]
+ if (input.checked && layers[0] == layer){
+ var checkbox = document.getElementById(`aligner_checkbox_${to_exclude}`)
+ if (checkbox.checked) {checkbox.click()} // disable affect; click on corresponding button
+ }
+ })
e.stopPropagation();
});
});
diff --git a/browser/js/aligner_layer.js b/browser/js/aligner_layer.js
index 84382e792c21c6b73446827fa5f333ee9f9e7030..79b28054842bbdff80efb349917c44169877071a 100644
--- a/browser/js/aligner_layer.js
+++ b/browser/js/aligner_layer.js
@@ -4,7 +4,7 @@ LAYERS = {
'nuc':
{
'className': "seq_layer_text",
- 'condition': function (s,c) { return !LAYERS.amino.enabled; },
+ 'condition': function (s,c) { return !LAYERS.amino.enabled && !LAYERS.affect_values.enabled; },
'text': function (s,c) { return s.nucleoString(); },
'enabled': true
},
@@ -12,10 +12,20 @@ LAYERS = {
'amino':
{
'className': "seq_layer_text",
+ 'condition': function (s,c) { return !LAYERS.affect_values.enabled; },
'text': function (s,c) { return s.aminoString(); },
'enabled': false
},
+
+ 'affect_values':
+ {
+ 'className': "seq_layer_text",
+ 'condition': function (s,c) { return !LAYERS.amino.enabled; },
+ 'text': function (s,c) { return s.affectValuesString(); },
+ 'enabled': false
+ },
+
'amino_separator':
{
'className': "seq_layer_text",
diff --git a/browser/js/aligner_menu.js b/browser/js/aligner_menu.js
index 8b2c28a9e211b1d28f1c814016ef43a3fc991e58..68d306ffca1a3152112efd027335a660db302149 100644
--- a/browser/js/aligner_menu.js
+++ b/browser/js/aligner_menu.js
@@ -75,6 +75,12 @@ ALIGNER_MENU = {
'layers': ["amino"],
'title': 'Show Amino Acid sequences (AA positions based on CDR3)',
'enabled': false
+ },{
+ 'id': 'affect_values',
+ 'text': 'Use affect sequence',
+ 'layers': ["affect_values"],
+ 'title': 'Show affectation values sequences (Kmers that match against germline sequences)',
+ 'enabled': false
}]
}
};
\ No newline at end of file
diff --git a/browser/js/aligner_sequence.js b/browser/js/aligner_sequence.js
index 4ee32eaced6a622bb225795155e899c80912c4e9..e4671dc1bcb1b11cd1183f0639393d56af5d64f0 100644
--- a/browser/js/aligner_sequence.js
+++ b/browser/js/aligner_sequence.js
@@ -184,6 +184,21 @@ Sequence.prototype = {
}
},
+ /**
+ * Return the assign string of clonotype
+ * */
+ affectValuesString: function () {
+ if (isNaN(this.id)) return ""
+
+ var clone = this.m.clone(this.id);
+ if (!clone.hasSequence()) return "";
+ if (clone.seg.affectValues != undefined && clone.seg.affectValues.seq != undefined){
+ return clone.seg.affectValues.seq
+ }
+ return ""
+
+ },
+
aminoSplitString: function () {
var start = -1;
var stop = -1;
@@ -381,6 +396,8 @@ Sequence.prototype = {
seq = this.align(this.seqAA.join(''), SYMBOL_VOID)
var r = this.segmenter.sequence[this.segmenter.sequence_order[0]];
ref = r.aminoString();
+ } else if (LAYERS.affect_values.enabled) {
+ return this.affectValuesString();
} else {
seq = this.seq;
ref = this.segmenter.sequence[this.segmenter.sequence_order[0]].seq;
diff --git a/browser/test/QUnit/testFiles/data_test.js b/browser/test/QUnit/testFiles/data_test.js
index e11c346837576cf025c0654c228919f3dc0c5ee6..159483fe9ceacceb2b38fd38be7cb72b8eb28b50 100644
--- a/browser/test/QUnit/testFiles/data_test.js
+++ b/browser/test/QUnit/testFiles/data_test.js
@@ -300,6 +300,11 @@ json_data.clones = [
"5end": 178,
"5start": 0,
"N": 4,
+ "affectValues": {
+ "seq": "GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG_____gggggggggggggggggggggggggggggggggggggggggggggggggggggggggg",
+ "start": 1,
+ "stop": 324
+ },
"imgt": {
"Sequence ID": "TRGV3*01_-0/4/-5_TRGJP2*01",
"Functionality": "productive",
diff --git a/browser/test/QUnit/testFiles/segmenter_test.js b/browser/test/QUnit/testFiles/segmenter_test.js
index f3bda88302e91c49f8092abb32c073f51fb94c59..e178354aa37e901e6e4115045c9fd7f91fda3449 100644
--- a/browser/test/QUnit/testFiles/segmenter_test.js
+++ b/browser/test/QUnit/testFiles/segmenter_test.js
@@ -76,7 +76,7 @@ QUnit.test("segmenter", function(assert) {
}, delay+=step);
setTimeout( function() {
- assert.deepEqual(segment.findPotentialField(), ["","cdr3","fr1", "5", "f1", "V-REGION","J-REGION","D-REGION","CDR3-IMGT"], "potentialField : Ok")
+ assert.deepEqual(segment.findPotentialField(), ["","cdr3","fr1", "5", "affectValues", "f1", "V-REGION","J-REGION","D-REGION","CDR3-IMGT"], "potentialField : Ok")
m.select(0)
m.focusIn(0)
@@ -185,6 +185,12 @@ QUnit.test("sequence", function(assert) {
var amino4 = seq4.aminoString().replace(/(?=\s)[^\r\n\t]/g, '_');
assert.equal(amino4, "__I_##_H__D__A__T__I__L__?", amino4 + " amino sequence");
+ var affect3 = seq3.affectValuesString()
+ assert.equal(affect3, "GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG_____gggggggggggggggggggggggggggggggggggggggggggggggggggggggggg", "coorect affect sequence");
+
+ var affect4 = seq4.affectValuesString()
+ assert.equal(affect4, "", "affect sequence (not present in clone data)");
+
var aminoSplit4 = seq4.aminoSplitString().replace(/(?=\s)[^\r\n\t]/g, '_');
assert.equal(aminoSplit4, "___|_|__|__|__|__|__|__|_|", aminoSplit4 + " aminoSplit sequence ");
diff --git a/browser/test/cypress/e2e/external_aligner.cy.js b/browser/test/cypress/e2e/external_aligner.cy.js
index df933f2bba7aa64583421c11af84314202ddfb2b..b53e161772ec62cc4b8d2e9c528b7f4dd8cff7a7 100644
--- a/browser/test/cypress/e2e/external_aligner.cy.js
+++ b/browser/test/cypress/e2e/external_aligner.cy.js
@@ -21,7 +21,7 @@ describe('External Aligner', function () {
cy.get('#segmenter_axis_select').children().should('have.length', 10)
cy.get('#align-settings').click({force:true})
- cy.get('#align-settings_select').children().should('have.length', 4)
+ cy.get('#align-settings_select').children().should('have.length', 5)
cy.get('#align-segment-info').click({force:true})
cy.get('#align-segment-info_select').children().should('have.length', 7)
diff --git a/browser/test/cypress/e2e/test_aligner.cy.js b/browser/test/cypress/e2e/test_aligner.cy.js
index 859b7b6e7d6608f15272512c128c54ce73908ef2..2b2483027b862c07927ac6f4359839a4c3911fe6 100644
--- a/browser/test/cypress/e2e/test_aligner.cy.js
+++ b/browser/test/cypress/e2e/test_aligner.cy.js
@@ -20,7 +20,7 @@ describe('Aligner', function () {
cy.get('#segmenter_axis_select').children().should('have.length', 10)
cy.get('#align-settings').click({force:true})
- cy.get('#align-settings_select').children().should('have.length', 4)
+ cy.get('#align-settings_select').children().should('have.length', 5)
cy.get('#align-segment-info').click({force:true})
cy.get('#align-segment-info_select').children().should('have.length', 7)
@@ -219,6 +219,57 @@ describe('Aligner', function () {
return
})
+
+
+
+ it('Aligner layers, see affect and amino (and exclusive)', function() {
+ cy.openAnalysis("browser/test/data/demo_lil_l3_one_full_clone.vidjil")
+ cy.selectClone(0)
+ cy.get('#seq0 > .sequence-holder > .seq-fixed > .axisBox > .Size > .sizeBox')
+ .should("exist")
+ .should("be.visible")
+
+ // Initial view
+ cy.get('.seq_layer_nuc')
+ .should("contain", "GGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCACCCGGAGGTATGGACGTCTGGGGCCAAGGGACCCTGGTCACCGTCTCCTCAGGT")
+
+ // First check affect
+ cy.get("#aligner_checkbox_affect_values")
+ .check({force: true})
+ cy.get('.seq_layer_affect_values')
+ .should("contain", "HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH?HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH?HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH?HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH?HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH_________________hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh_____________")
+
+ cy.get("#aligner_checkbox_amino")
+ .should('not.be.checked');
+
+ // Check amino
+ cy.get("#aligner_checkbox_amino")
+ .check({force: true})
+
+ cy.get('.seq_layer_amino')
+ .contains("G") // exclusive letter neither in nucleotide or affect
+ cy.get("#aligner_checkbox_affect_values")
+ .should('not.be.checked');
+
+ // Check again affect
+ cy.get("#aligner_checkbox_affect_values")
+ .check({force: true})
+ cy.get('.seq_layer_affect_values')
+ .should("contain", "HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH?HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH?HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH?HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH?HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH_________________hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh_____________")
+ cy.get("#aligner_checkbox_amino")
+ .should('not.be.checked');
+
+
+ // Uncheck affect, should return to raw sequence
+ cy.get("#aligner_checkbox_affect_values")
+ .check({force: true})
+
+ cy.get('.seq_layer_nuc')
+ .should("contain", "GGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCACCCGGAGGTATGGACGTCTGGGGCCAAGGGACCCTGGTCACCGTCTCCTCAGGT")
+
+ })
+
+
//menu in aligner top right corner (focus/hide/tag) are already tested in test_filter.js
diff --git a/browser/test/data/demo_lil_l3_one_full_clone.vidjil b/browser/test/data/demo_lil_l3_one_full_clone.vidjil
new file mode 100644
index 0000000000000000000000000000000000000000..8b97f8b601503d84ad29b2d17194dd00f04d7688
--- /dev/null
+++ b/browser/test/data/demo_lil_l3_one_full_clone.vidjil
@@ -0,0 +1,191 @@
+{
+ "clones": [
+ {
+ "_average_read_length": [
+ "317.35"
+ ],
+ "_coverage": [
+ 1.0209637880325317
+ ],
+ "_coverage_info": [
+ "324 bp (102% of 317.3 bp)"
+ ],
+ "germline": "IGH",
+ "id": "CACGGCCTTGTATTACTGTGCACCCGGAGGTATGGACGTCTGGGGCCAAG",
+ "name": "IGHV3-9*01 7/CCCGGA/17 IGHJ6*02",
+ "reads": [
+ 189991
+ ],
+ "seg": {
+ "3": {
+ "delLeft": 17,
+ "delRight": 60,
+ "name": "IGHJ6*02",
+ "start": 277,
+ "stop": 321
+ },
+ "5": {
+ "delRight": 7,
+ "name": "IGHV3-9*01",
+ "stop": 270
+ },
+ "N": 6,
+ "affectSigns": {
+ "seq": "+++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++ ",
+ "start": 1,
+ "stop": 324
+ },
+ "affectValues": {
+ "seq": "HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH?HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH?HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH?HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH?HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH_________________hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh_____________",
+ "start": 1,
+ "stop": 324
+ },
+ "cdr3": {
+ "aa": "APGGMDV",
+ "seq": "GCACCCGGAGGTATGGACGTC",
+ "start": 268,
+ "stop": 288
+ },
+ "evalue": {
+ "val": "3.07e-136"
+ },
+ "evalue_left": {
+ "val": "0.00e+00"
+ },
+ "evalue_right": {
+ "val": "3.07e-136"
+ },
+ "junction": {
+ "aa": "CAPGGMDVW",
+ "productive": true,
+ "start": 265,
+ "stop": 291
+ },
+ "quality": {
+ "seq": "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!=>>?8?8>7=??@8>>=>==>=>?2<6;?9>=>=9?>:;;==>>.<4:4:!!!!!!!!!!!!!!!!!!!!!!!!!!",
+ "start": 1,
+ "stop": 324
+ }
+ },
+ "sequence": "GGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCACCCGGAGGTATGGACGTCTGGGGCCAAGGGACCCTGGTCACCGTCTCCTCAGGT",
+ "top": 1
+ }
+ ],
+ "config": {
+ "all": false,
+ "alternative-genes": "0",
+ "analysis-e-value-D": "0.05",
+ "analysis-filter": "1",
+ "clean-memory": false,
+ "cluster-N": "10",
+ "cluster-epsilon": "0",
+ "cluster-load-matrix": false,
+ "cluster-save-matrix": false,
+ "consensus-on-longest-sequences": false,
+ "dir": "lil-l3-0-clone0",
+ "e-value": "1",
+ "e-value-kmer": "-1",
+ "filter-reads": false,
+ "germline": "germline/homo-sapiens.g",
+ "gz": false,
+ "help-advanced": false,
+ "label-filter": false,
+ "max-consensus": "100",
+ "min-ratio": "0",
+ "min-reads": "5",
+ "no-airr": false,
+ "no-vidjil": false,
+ "not-analyzed-as-clones": false,
+ "out-affects": false,
+ "out-clone-files": false,
+ "out-details": false,
+ "out-detected": false,
+ "out-reads": false,
+ "out-undetected": false,
+ "out-vdjfa": false,
+ "plain-index": false,
+ "several-D": false,
+ "show-junction": false,
+ "verbose": false
+ },
+ "diversity": {
+ "index_Ds_diversity": 0.0,
+ "index_E_equitability": 0.0,
+ "index_H_entropy": 0.0
+ },
+ "germlines": {
+ "ref": "https://www.vidjil.org/germlines/germline-2021-01-21.tar.gz",
+ "species": "Homo sapiens",
+ "species_taxon_id": 9606
+ },
+ "reads": {
+ "germline": {
+ "IGH": [
+ 189991
+ ],
+ "IGH+": [
+ 0
+ ],
+ "IGK": [
+ 0
+ ],
+ "IGK+": [
+ 0
+ ],
+ "IGL": [
+ 0
+ ],
+ "TRA": [
+ 0
+ ],
+ "TRA+D": [
+ 0
+ ],
+ "TRB": [
+ 0
+ ],
+ "TRB+": [
+ 0
+ ],
+ "TRD": [
+ 0
+ ],
+ "TRD+": [
+ 0
+ ],
+ "TRG": [
+ 0
+ ]
+ },
+ "segmented": [
+ 189991
+ ],
+ "total": [
+ 189995
+ ]
+ },
+ "samples": {
+ "commandline": [
+ "vidjil-algo -g germline/homo-sapiens.g -o lil-l3-0-clone0 full_reads_forward_reverse.fastq "
+ ],
+ "log": [
+ " ==> junction detected in 189991 reads (100%)\n ==> found 1 windows in 189991 reads (100% of 189995 reads)\n reads av. len clones clo/rds\n IGH -> 189991 317.3 1 0.000\n IGH+ -> 0 - 0 -\n IGK -> 0 - 0 -\n IGK+ -> 0 - 0 -\n IGL -> 0 - 0 -\n TRA -> 0 - 0 -\n TRA+D -> 0 - 0 -\n TRB -> 0 - 0 -\n TRB+ -> 0 - 0 -\n TRD -> 0 - 0 -\n TRD+ -> 0 - 0 -\n TRG -> 0 - 0 -\n\n SEG -> 189991 317.3\n SEG_+ -> 55411 340.2\n SEG_- -> 134580 308.0\n SEG changed w -> 0 -\n\n UNSEG too short -> 0 -\n UNSEG strand -> 4 208.8\n UNSEG too few V/J -> 0 -\n UNSEG only V/5' -> 0 -\n UNSEG only J/3' -> 0 -\n UNSEG < delta_min -> 0 -\n UNSEG ambiguous -> 0 -\n UNSEG too short w -> 0 -\n"
+ ],
+ "number": 1,
+ "original_names": [
+ "full_reads_forward_reverse.fastq"
+ ],
+ "producer": [
+ "vidjil-algo dev b59846a2a (2022-01-11)"
+ ],
+ "run_timestamp": [
+ "2024-09-06 14:32:25"
+ ]
+ },
+ "similarity": [
+ [
+ 0.0
+ ]
+ ],
+ "vidjil_json_version": "2016b"
+}
\ No newline at end of file