Function Namespace NaView
Defined in: naview.js.
| Constructor Attributes | Constructor Name and Description |
|---|---|
|
NaView(svg_id, container_id, svg_width, svg_height, style_obj_input, protein_input, protein_input, properties, color_rules, text_to_draw, relationships)
This is the main function
|
| Method Attributes | Method Name and Description |
|---|---|
| <inner> | |
| <inner> |
calcDomIDomWidths(svg_drawing_area, domain_names, helices_and_pores_by_domain)
|
| <inner> |
calcElementsDrawAreas(array_data, svg_drawing_area, domain_names, helices_and_pores_by_domain, internal_short_loops_by_domain, long_loops_by_prevdomain, longLoopWidthF, total_domain_width, inter_domain_width)
|
| <inner> |
calculateCustomPointData(short_loop_data, loop_length_calculation, loop_drawing_shape)
|
| <inner> |
calculateDotArrayMiddlePoint(dot1, dot2)
|
| <inner> |
calculateDotMiddlePoint(dot1, dot2)
|
| <inner> |
calculateDrawAreaHelicesPoresByDomain(domain_name, helices_and_pores_array, drawing_area, cumulative_x)
|
| <inner> |
calculateDrawAreaLongLoops(long_loop_obj, cumulative_x, last_y, longLoopWidthF, drawing_area)
|
| <inner> |
calculateDrawAreaMembrane(drawing_area)
|
| <inner> |
calculateDrawAreaShortLoopsByDomain(internal_short_loops_array, helixpore_objs, drawing_area, cumulative_x)
|
| <inner> |
calculateDrawAreaTermini(terminus_type, drawing_area, terminus_data, total_domain_width, inter_domain_width)
|
| <inner> |
calculateFixedCustomPointDataPore(pores_data, loop_length_calculation, loop_drawing_shape)
|
| <inner> |
calculateFixedPointData(short_loop_data, loop_length_calculation, loop_drawing_shape)
|
| <inner> |
calculateFixedPointTermini(termini_data, loop_length_calculation, loop_drawing_shape)
|
| <inner> |
calculateResidOrientation(helices_data, all_loop_data)
|
| <inner> |
calculateResLengthPointData(short_loop_data, loop_length_calculation, loop_drawing_shape)
|
| <inner> |
calculateResLengthPointDataPore(pores_data, loop_length_calculation, loop_drawing_shape)
|
| <inner> |
calculateScaledPointData(short_loop_data, loop_length_calculation, loop_drawing_shape)
|
| <inner> |
calculateScaledPointDataPore(pores_data, loop_length_calculation, loop_drawing_shape)
|
| <inner> |
checkFillResidue(data_obj)
|
| <inner> |
checkForNaN(points)
|
| <inner> |
checkWaveFold(loop_data, add_wave_fold_dict_array)
|
| <inner> |
colorToRGBA(color)
|
| <inner> |
convertToResInd(resobj)
|
| <inner> | |
| <inner> |
createFillRules(data_color)
|
| <inner> |
createFillScale(fillproperty, fillrange, filldomain)
|
| <inner> |
createResidData(data)
|
| <inner> | |
| <inner> |
createVector(p1, p2)
|
| <inner> |
deepCopy(obj)
|
| <inner> |
define_draw_areas(array_data)
|
| <inner> |
distributeLongLoopsWidth(total_width, long_loops_array)
|
| <inner> |
dotToCoords(dot1)
|
| <inner> |
draw_helices(helices_data)
|
| <inner> |
draw_helices_box(data, dataId)
|
| <inner> |
draw_helices_cartoon(data)
|
| <inner> |
draw_helices_cylinder(data, dataId)
|
| <inner> |
draw_helices_resids_box(enter_element)
|
| <inner> |
draw_helices_resids_cartoon(data, path_class)
|
| <inner> |
draw_helices_resids_cylinder(enter_element)
|
| <inner> |
draw_longLoops(longloop_data)
|
| <inner> |
draw_loop_paths(short_loop_data, class_naming)
|
| <inner> |
draw_loop_paths_resids(enter_element, class_naming)
|
| <inner> |
draw_membrane(data)
|
| <inner> |
draw_membrane_box(data, dataId)
|
| <inner> |
draw_membrane_lipid(data, dataId, tail_head_dist)
|
| <inner> |
draw_poreLoops(pores_data)
|
| <inner> |
draw_relation_paths(residue_relation_data)
|
| <inner> |
draw_residue_relations(residue_relation_data, centroid_data, full_protein_data)
|
| <inner> |
draw_shortLoops(short_loop_data)
|
| <inner> |
draw_symbols(symbols_data, centroid_data, property_data, full_protein_data)
|
| <inner> |
draw_termini(termini_data)
|
| <inner> |
draw_text_symbols(symbols_data)
|
| <inner> |
drawDataParsing(array_data)
|
| <inner> |
drawEverything(parsed_protein_data)
|
| <inner> |
drawHalfHelixResidPolygons(data, path_class, data_index, dom_created_path, dom_created_path_length, bottom_curve_points, top_curve_points, height_sline, curve_length, division_curve_lengths)
|
| <inner> |
drawSingleHalfHelixResidue(data, path_class, data_index, dom_created_path)
|
| <inner> |
ellipsis_equation_y(gx, cx, cy, rx, ry)
|
| <inner> |
euclideanDistance(p1, p2)
|
| <inner> |
find_angle(A, B, C)
|
| <inner> |
foldAddition(resulting_points, add_fold_obj)
|
| <inner> |
gen_centroids_loop_paths_resids(given_class)
|
| <inner> | |
| <inner> |
gen_lipid_head_data(number_of_lipids, shead_x, head_y1, head_y2, head_fill, head_opacity, head_stroke, head_stroke_s, lip_rad, lip_rad_y)
|
| <inner> |
gen_lipid_tail_data(head_data, lipid_tail_number, lipid_break_num, tail_max_length, tail_head_dist, tail_fill, tail_opacity, tail_stroke, tail_stroke_s)
|
| <inner> |
gen_longloop_anchordata(longloop_data, helices_data)
|
| <inner> |
gen_poreloop_anchordata(pores_data, short_loop_data)
|
| <inner> |
gen_shortloop_anchordata(short_loop_data, helices_pores_data)
|
| <inner> |
gen_termini_anchordata(termini_data, neighboring_helix, termini_type)
|
| <inner> |
generateBulbLoopPoints(p1, p2, step_x, step_y, perc_step_y, y_direction, x_skew_perc, add_wavefold_obj)
|
| <inner> | |
| <inner> |
generateMushRoomLoopPoints(p1, p2, step_x, step_y, perc_center_x, perc_step_y1, perc_step_y2, y_direction, x_skew_perc, add_wavefold_obj)
|
| <inner> |
generateNWaveCurves(p1, p2, n_of_centers, step_height, perc_centers_height, clockwise, rotate_loop)
|
| <inner> |
generatePathWithLength(p1, p2, loop_length, y_direction, loop_drawing_shape, loop_drawing_shape_type, extra_variables, loop_data)
|
| <inner> |
generateSimpleLoopPoints(p1, p2, step_y, y_direction, x_skew_perc, add_wavefold_obj)
|
| <inner> |
generateSkewedSimpleLoopPoints(p1, p2, perc_center_x, step_y, y_direction)
|
| <inner> |
generateSwirlLoopPoints(p1, p2, swirl_x, step_y, perc_step_y, y_direction, add_wavefold_obj)
|
| <inner> |
generateXMidPts(dot1, dot2, xmids)
|
| <inner> |
get_helices_endpoints(helix_mode, helices_data)
|
| <inner> |
getBBoxGhostText(data, path_id_keep)
|
| <inner> |
getGhostPathLength(pts, path_id_keep)
|
| <inner> |
getHalfHelixBoundaries(dom_created_path, dom_created_path_length, height_sline, division)
|
| <inner> |
getPointAtAngleDistance(x, y, angle, distance)
|
| <inner> |
getRandomFloatInclusive(min, max)
|
| <inner> |
getRandomIntInclusive(min, max)
|
| <inner> |
indexDrawAreas(protein_dict, array_to_dict)
|
| <inner> |
initData()
|
| <inner> |
initLib()
|
| <inner> |
initMainSvg(svg_id, container_id, svg_width, svg_height)
|
| <inner> |
initViz()
|
| <inner> |
makeLoopScaling(scale_var, loop_length_calculation)
|
| <inner> |
mergeDrawData(mergeType, data)
|
| <inner> |
normalizeVector(v1)
|
| <inner> |
onlyUnique(value, index, self)
|
| <inner> |
pathSegmentToXYPoints(dompath, segmentstart, segmentend, sampling_step, sampling_stepend)
|
| <inner> |
pathStringToStringPoints(d3path, searchchar)
|
| <inner> |
processRawUniProt(test_raw_protein)
|
| <inner> |
pSBC(p, c0, c1, l)
|
| <inner> |
rangeArray(size, startAt)
|
| <inner> |
rotate90(v1, direction, centerp)
|
| <inner> |
rotateByAng(v1, centerp, angle)
|
| <inner> |
roundDecimals(num, after_comma)
|
| <inner> |
scaleVector(v1, val)
|
| <inner> |
stringToChunks(str, n)
|
| <inner> |
stringToChunksSkip(str, n, s)
|
| <inner> |
whereIsResIdElName(resid_or_elname, full_protein_data)
|
Function Namespace Detail
NaView(svg_id, container_id, svg_width, svg_height, style_obj_input, protein_input, protein_input, properties, color_rules, text_to_draw, relationships)
This is the main function
- Parameters:
- {string} svg_id
- id of selected/created svg
- {string} container_id
- id of selected/created svg container
- {number} svg_width
- width of selected/created svg (default:1200px)
- {number} svg_height
- height of selected/created svg (default:500px)
- {Object} style_obj_input
- styling object for all drawing options. See style_obj in Docs
- {string} protein_input
- UniProt raw text to be processed See parsed_protein_data and also processRawUniProt in Docs
- {Object} protein_input
- processed data input See parsed_protein_data and also processRawUniProt in Docs
- {Object} properties
- residue properties for color mapping and Text drawing by residue selection. See current_resid_properties in Docs
- {Array} color_rules
- Array of strings containing color rules in the color selection syntax. See fillRules and also createFillRules in Docs
- {Array} text_to_draw
- Array of strings containing text drawing rules in the text selection syntax. See draw_symbols in Docs
- {Array} relationships
- Array of Objects describing residue relationships to be drawn in plot See draw_residue_relations in Docs
Method Detail
<inner>
buildPathStringFromData(d)
- Parameters:
- d
<inner>
calcDomIDomWidths(svg_drawing_area, domain_names, helices_and_pores_by_domain)
- Parameters:
- svg_drawing_area
- domain_names
- helices_and_pores_by_domain
<inner>
calcElementsDrawAreas(array_data, svg_drawing_area, domain_names, helices_and_pores_by_domain, internal_short_loops_by_domain, long_loops_by_prevdomain, longLoopWidthF, total_domain_width, inter_domain_width)
- Parameters:
- array_data
- svg_drawing_area
- domain_names
- helices_and_pores_by_domain
- internal_short_loops_by_domain
- long_loops_by_prevdomain
- longLoopWidthF
- total_domain_width
- inter_domain_width
<inner>
calculateCustomPointData(short_loop_data, loop_length_calculation, loop_drawing_shape)
- Parameters:
- short_loop_data
- loop_length_calculation
- loop_drawing_shape
<inner>
calculateDotArrayMiddlePoint(dot1, dot2)
- Parameters:
- dot1
- dot2
<inner>
calculateDotMiddlePoint(dot1, dot2)
- Parameters:
- dot1
- dot2
<inner>
calculateDrawAreaHelicesPoresByDomain(domain_name, helices_and_pores_array, drawing_area, cumulative_x)
- Parameters:
- domain_name
- helices_and_pores_array
- drawing_area
- cumulative_x
<inner>
calculateDrawAreaLongLoops(long_loop_obj, cumulative_x, last_y, longLoopWidthF, drawing_area)
- Parameters:
- long_loop_obj
- cumulative_x
- last_y
- longLoopWidthF
- drawing_area
<inner>
calculateDrawAreaMembrane(drawing_area)
- Parameters:
- drawing_area
<inner>
calculateDrawAreaShortLoopsByDomain(internal_short_loops_array, helixpore_objs, drawing_area, cumulative_x)
- Parameters:
- internal_short_loops_array
- helixpore_objs
- drawing_area
- cumulative_x
<inner>
calculateDrawAreaTermini(terminus_type, drawing_area, terminus_data, total_domain_width, inter_domain_width)
- Parameters:
- terminus_type
- drawing_area
- terminus_data
- total_domain_width
- inter_domain_width
<inner>
calculateFixedCustomPointDataPore(pores_data, loop_length_calculation, loop_drawing_shape)
- Parameters:
- pores_data
- loop_length_calculation
- loop_drawing_shape
<inner>
calculateFixedPointData(short_loop_data, loop_length_calculation, loop_drawing_shape)
- Parameters:
- short_loop_data
- loop_length_calculation
- loop_drawing_shape
<inner>
calculateFixedPointTermini(termini_data, loop_length_calculation, loop_drawing_shape)
- Parameters:
- termini_data
- loop_length_calculation
- loop_drawing_shape
<inner>
calculateResidOrientation(helices_data, all_loop_data)
- Parameters:
- helices_data
- all_loop_data
<inner>
calculateResLengthPointData(short_loop_data, loop_length_calculation, loop_drawing_shape)
- Parameters:
- short_loop_data
- loop_length_calculation
- loop_drawing_shape
<inner>
calculateResLengthPointDataPore(pores_data, loop_length_calculation, loop_drawing_shape)
- Parameters:
- pores_data
- loop_length_calculation
- loop_drawing_shape
<inner>
calculateScaledPointData(short_loop_data, loop_length_calculation, loop_drawing_shape)
- Parameters:
- short_loop_data
- loop_length_calculation
- loop_drawing_shape
<inner>
calculateScaledPointDataPore(pores_data, loop_length_calculation, loop_drawing_shape)
- Parameters:
- pores_data
- loop_length_calculation
- loop_drawing_shape
<inner>
checkFillResidue(data_obj)
- Parameters:
- data_obj
<inner>
checkForNaN(points)
- Parameters:
- points
<inner>
checkWaveFold(loop_data, add_wave_fold_dict_array)
- Parameters:
- loop_data
- add_wave_fold_dict_array
<inner>
colorToRGBA(color)
- Parameters:
- color
<inner>
convertToResInd(resobj)
- Parameters:
- resobj
<inner>
createDrawingArea()
<inner>
createFillRules(data_color)
- Parameters:
- data_color
<inner>
createFillScale(fillproperty, fillrange, filldomain)
- Parameters:
- fillproperty
- fillrange
- filldomain
<inner>
createResidData(data)
- Parameters:
- data
<inner>
createResidElementToCentroidData()
<inner>
createVector(p1, p2)
- Parameters:
- p1
- p2
<inner>
deepCopy(obj)
- Parameters:
- obj
<inner>
define_draw_areas(array_data)
- Parameters:
- array_data
<inner>
distributeLongLoopsWidth(total_width, long_loops_array)
- Parameters:
- total_width
- long_loops_array
<inner>
dotToCoords(dot1)
- Parameters:
- dot1
<inner>
draw_helices(helices_data)
- Parameters:
- helices_data
<inner>
draw_helices_box(data, dataId)
- Parameters:
- data
- dataId
<inner>
draw_helices_cartoon(data)
- Parameters:
- data
<inner>
draw_helices_cylinder(data, dataId)
- Parameters:
- data
- dataId
<inner>
draw_helices_resids_box(enter_element)
- Parameters:
- enter_element
<inner>
draw_helices_resids_cartoon(data, path_class)
- Parameters:
- data
- path_class
<inner>
draw_helices_resids_cylinder(enter_element)
- Parameters:
- enter_element
<inner>
draw_longLoops(longloop_data)
- Parameters:
- longloop_data
<inner>
draw_loop_paths(short_loop_data, class_naming)
- Parameters:
- short_loop_data
- class_naming
<inner>
draw_loop_paths_resids(enter_element, class_naming)
- Parameters:
- enter_element
- class_naming
<inner>
draw_membrane(data)
- Parameters:
- data
<inner>
draw_membrane_box(data, dataId)
- Parameters:
- data
- dataId
<inner>
draw_membrane_lipid(data, dataId, tail_head_dist)
- Parameters:
- data
- dataId
- tail_head_dist
<inner>
draw_poreLoops(pores_data)
- Parameters:
- pores_data
<inner>
draw_relation_paths(residue_relation_data)
- Parameters:
- residue_relation_data
<inner>
draw_residue_relations(residue_relation_data, centroid_data, full_protein_data)
- Parameters:
- residue_relation_data
- centroid_data
- full_protein_data
<inner>
draw_shortLoops(short_loop_data)
- Parameters:
- short_loop_data
<inner>
draw_symbols(symbols_data, centroid_data, property_data, full_protein_data)
- Parameters:
- symbols_data
- centroid_data
- property_data
- full_protein_data
<inner>
draw_termini(termini_data)
- Parameters:
- termini_data
<inner>
draw_text_symbols(symbols_data)
- Parameters:
- symbols_data
<inner>
drawDataParsing(array_data)
- Parameters:
- array_data
<inner>
drawEverything(parsed_protein_data)
- Parameters:
- parsed_protein_data
<inner>
drawHalfHelixResidPolygons(data, path_class, data_index, dom_created_path, dom_created_path_length, bottom_curve_points, top_curve_points, height_sline, curve_length, division_curve_lengths)
- Parameters:
- data
- path_class
- data_index
- dom_created_path
- dom_created_path_length
- bottom_curve_points
- top_curve_points
- height_sline
- curve_length
- division_curve_lengths
<inner>
drawSingleHalfHelixResidue(data, path_class, data_index, dom_created_path)
- Parameters:
- data
- path_class
- data_index
- dom_created_path
<inner>
ellipsis_equation_y(gx, cx, cy, rx, ry)
- Parameters:
- gx
- cx
- cy
- rx
- ry
<inner>
euclideanDistance(p1, p2)
- Parameters:
- p1
- p2
<inner>
find_angle(A, B, C)
- Parameters:
- A
- B
- C
<inner>
foldAddition(resulting_points, add_fold_obj)
- Parameters:
- resulting_points
- add_fold_obj
<inner>
gen_centroids_loop_paths_resids(given_class)
- Parameters:
- given_class
<inner>
gen_helix_cartoon_halfturn_data(data)
- Parameters:
- data
<inner>
gen_lipid_head_data(number_of_lipids, shead_x, head_y1, head_y2, head_fill, head_opacity, head_stroke, head_stroke_s, lip_rad, lip_rad_y)
- Parameters:
- number_of_lipids
- shead_x
- head_y1
- head_y2
- head_fill
- head_opacity
- head_stroke
- head_stroke_s
- lip_rad
- lip_rad_y
<inner>
gen_lipid_tail_data(head_data, lipid_tail_number, lipid_break_num, tail_max_length, tail_head_dist, tail_fill, tail_opacity, tail_stroke, tail_stroke_s)
- Parameters:
- head_data
- lipid_tail_number
- lipid_break_num
- tail_max_length
- tail_head_dist
- tail_fill
- tail_opacity
- tail_stroke
- tail_stroke_s
<inner>
gen_longloop_anchordata(longloop_data, helices_data)
- Parameters:
- longloop_data
- helices_data
<inner>
gen_poreloop_anchordata(pores_data, short_loop_data)
- Parameters:
- pores_data
- short_loop_data
<inner>
gen_shortloop_anchordata(short_loop_data, helices_pores_data)
- Parameters:
- short_loop_data
- helices_pores_data
<inner>
gen_termini_anchordata(termini_data, neighboring_helix, termini_type)
- Parameters:
- termini_data
- neighboring_helix
- termini_type
<inner>
generateBulbLoopPoints(p1, p2, step_x, step_y, perc_step_y, y_direction, x_skew_perc, add_wavefold_obj)
- Parameters:
- p1
- p2
- step_x
- step_y
- perc_step_y
- y_direction
- x_skew_perc
- add_wavefold_obj
<inner>
generateDefaultStyleObject()
<inner>
generateMushRoomLoopPoints(p1, p2, step_x, step_y, perc_center_x, perc_step_y1, perc_step_y2, y_direction, x_skew_perc, add_wavefold_obj)
- Parameters:
- p1
- p2
- step_x
- step_y
- perc_center_x
- perc_step_y1
- perc_step_y2
- y_direction
- x_skew_perc
- add_wavefold_obj
<inner>
generateNWaveCurves(p1, p2, n_of_centers, step_height, perc_centers_height, clockwise, rotate_loop)
- Parameters:
- p1
- p2
- n_of_centers
- step_height
- perc_centers_height
- clockwise
- rotate_loop
<inner>
generatePathWithLength(p1, p2, loop_length, y_direction, loop_drawing_shape, loop_drawing_shape_type, extra_variables, loop_data)
- Parameters:
- p1
- p2
- loop_length
- y_direction
- loop_drawing_shape
- loop_drawing_shape_type
- extra_variables
- loop_data
<inner>
generateSimpleLoopPoints(p1, p2, step_y, y_direction, x_skew_perc, add_wavefold_obj)
- Parameters:
- p1
- p2
- step_y
- y_direction
- x_skew_perc
- add_wavefold_obj
<inner>
generateSkewedSimpleLoopPoints(p1, p2, perc_center_x, step_y, y_direction)
- Parameters:
- p1
- p2
- perc_center_x
- step_y
- y_direction
<inner>
generateSwirlLoopPoints(p1, p2, swirl_x, step_y, perc_step_y, y_direction, add_wavefold_obj)
- Parameters:
- p1
- p2
- swirl_x
- step_y
- perc_step_y
- y_direction
- add_wavefold_obj
<inner>
generateXMidPts(dot1, dot2, xmids)
- Parameters:
- dot1
- dot2
- xmids
<inner>
get_helices_endpoints(helix_mode, helices_data)
- Parameters:
- helix_mode
- helices_data
<inner>
getBBoxGhostText(data, path_id_keep)
- Parameters:
- data
- path_id_keep
<inner>
getGhostPathLength(pts, path_id_keep)
- Parameters:
- pts
- path_id_keep
<inner>
getHalfHelixBoundaries(dom_created_path, dom_created_path_length, height_sline, division)
- Parameters:
- dom_created_path
- dom_created_path_length
- height_sline
- division
<inner>
getPointAtAngleDistance(x, y, angle, distance)
- Parameters:
- x
- y
- angle
- distance
<inner>
getRandomFloatInclusive(min, max)
- Parameters:
- min
- max
<inner>
getRandomIntInclusive(min, max)
- Parameters:
- min
- max
<inner>
indexDrawAreas(protein_dict, array_to_dict)
- Parameters:
- protein_dict
- array_to_dict
<inner>
initData()
<inner>
initLib()
<inner>
initMainSvg(svg_id, container_id, svg_width, svg_height)
- Parameters:
- svg_id
- container_id
- svg_width
- svg_height
<inner>
initViz()
<inner>
makeLoopScaling(scale_var, loop_length_calculation)
- Parameters:
- scale_var
- loop_length_calculation
<inner>
mergeDrawData(mergeType, data)
- Parameters:
- mergeType
- data
<inner>
normalizeVector(v1)
- Parameters:
- v1
<inner>
onlyUnique(value, index, self)
- Parameters:
- value
- index
- self
<inner>
pathSegmentToXYPoints(dompath, segmentstart, segmentend, sampling_step, sampling_stepend)
- Parameters:
- dompath
- segmentstart
- segmentend
- sampling_step
- sampling_stepend
<inner>
pathStringToStringPoints(d3path, searchchar)
- Parameters:
- d3path
- searchchar
<inner>
processRawUniProt(test_raw_protein)
- Parameters:
- test_raw_protein
<inner>
pSBC(p, c0, c1, l)
- Parameters:
- p
- c0
- c1
- l
<inner>
rangeArray(size, startAt)
- Parameters:
- size
- startAt
<inner>
rotate90(v1, direction, centerp)
- Parameters:
- v1
- direction
- centerp
<inner>
rotateByAng(v1, centerp, angle)
- Parameters:
- v1
- centerp
- angle
<inner>
roundDecimals(num, after_comma)
- Parameters:
- num
- after_comma
<inner>
scaleVector(v1, val)
- Parameters:
- v1
- val
<inner>
stringToChunks(str, n)
- Parameters:
- str
- n
<inner>
stringToChunksSkip(str, n, s)
- Parameters:
- str
- n
- s
<inner>
whereIsResIdElName(resid_or_elname, full_protein_data)
- Parameters:
- resid_or_elname
- full_protein_data