Difference between revisions of "CytoscapeProperties"

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m (→‎Bypass Names)
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!colspan=3 align="left" id="Layout_Names"|Layout Names
 
!colspan=3 align="left" id="Layout_Names"|Layout Names
 
|-
 
|-
−
| [[#Attribute layout | Attribute layout]] || [[#Contig Layout | Contig Layout]] || [[#Fruchterman-Rheingold | Fruchterman-Rheingold]]
+
| [[#attribute-circle | attribute-circle]] || [[#attributes-layout | attributes-layout]] || [[#circular | circular]]
 
|-
 
|-
−
| [[#Handle Layout | Handle Layout]] || [[#Kamada-Kawai | Kamada-Kawai]] || [[#Kamada-Kawai-Noweight | Kamada-Kawai-Noweight]]
+
| [[#degree-circle | degree-circle]] || [[#force-directed | force-directed]] || [[#fruchterman-rheingold | fruchterman-rheingold]]
−
|-
+
−
| [[#Track Layout | Track Layout]] || [[#attribute-circle | attribute-circle]] || [[#attributes-layout | attributes-layout]]
+
−
|-
+
−
| [[#circular | circular]] || [[#degree-circle | degree-circle]] || [[#force-directed | force-directed]]
+
 
|-
 
|-
 
| [[#grid | grid]] || [[#hierarchical | hierarchical]] || [[#isom | isom]]
 
| [[#grid | grid]] || [[#hierarchical | hierarchical]] || [[#isom | isom]]
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| [[#jgraph-moen | jgraph-moen]] || [[#jgraph-radial-tree | jgraph-radial-tree]] || [[#jgraph-spring | jgraph-spring]]
 
| [[#jgraph-moen | jgraph-moen]] || [[#jgraph-radial-tree | jgraph-radial-tree]] || [[#jgraph-spring | jgraph-spring]]
 
|-
 
|-
−
| [[#jgraph-sugiyama | jgraph-sugiyama]] || [[#jgraph-tree | jgraph-tree]]
+
| [[#jgraph-sugiyama | jgraph-sugiyama]] || [[#jgraph-tree | jgraph-tree]] || [[#kamada-kawai | kamada-kawai]]
 +
|-
 +
| [[#kamada-kawai-noweight | kamada-kawai-noweight]]
 
|}
 
|}
−
===Attribute layout===
+
===attribute-circle===
 
{|class="wikitable"
 
{|class="wikitable"
−
!colspan=3 align="left" id="Attribute_layout"|Attribute layout
+
!colspan=3 align="left" id="attribute-circle"|attribute-circle
 
|-
 
|-
−
| xPosAttr || NODEATTRIBUTE || yPosAttr
+
| attribute || NODEATTRIBUTE || (none)
 
|-
 
|-
−
| yPosAttr || NODEATTRIBUTE ||  
+
| spacing || DOUBLE || 100.0
 
|-
 
|-
 
|}
 
|}
−
===Contig Layout===
+
===attributes-layout===
 
{|class="wikitable"
 
{|class="wikitable"
−
!colspan=3 align="left" id="Contig_Layout"|Contig Layout
+
!colspan=3 align="left" id="attributes-layout"|attributes-layout
 +
|-
 +
| attributeName || NODEATTRIBUTE ||
 +
|-
 +
| maxwidth || DOUBLE || 5000.0
 +
|-
 +
| minrad || DOUBLE || 100.0
 +
|-
 +
| radmult || DOUBLE || 50.0
 +
|-
 +
| spacingx || DOUBLE || 400.0
 +
|-
 +
| spacingy || DOUBLE || 400.0
 
|-
 
|-
 
|}
 
|}
−
===Fruchterman-Rheingold===
+
===force-directed===
 
{|class="wikitable"
 
{|class="wikitable"
−
!colspan=3 align="left" id="Fruchterman-Rheingold"|Fruchterman-Rheingold
+
!colspan=3 align="left" id="force-directed"|force-directed
 +
|-
 +
| defaultNodeMass || DOUBLE || 3.0
 +
|-
 +
| defaultSpringCoefficient || DOUBLE || 9.99999974738e-05
 +
|-
 +
| defaultSpringLength || DOUBLE || 50.0
 +
|-
 +
| discrete || BOOLEAN || False
 +
|-
 +
| edge_attribute || EDGEATTRIBUTE || weight
 +
|-
 +
| edge_weight_group || GROUP || 4
 +
|-
 +
| force_alg_settings || GROUP || 6
 +
|-
 +
| max_weight || DOUBLE || 1.79769313486e+308
 +
|-
 +
| min_weight || DOUBLE || 0.0
 +
|-
 +
| numIterations || INTEGER || 100
 +
|-
 +
| partition || BOOLEAN || True
 +
|-
 +
| selected_only || BOOLEAN || False
 +
|-
 +
| standard || GROUP || 2
 +
|-
 +
| weight_type || LIST || 0
 +
|-
 +
|}
 +
===fruchterman-rheingold===
 +
{|class="wikitable"
 +
!colspan=3 align="left" id="fruchterman-rheingold"|fruchterman-rheingold
 
|-
 
|-
 
| algorithm_settings || GROUP || 9
 
| algorithm_settings || GROUP || 9
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|-
 
|-
 
|}
 
|}
−
===Handle Layout===
+
===isom===
 
{|class="wikitable"
 
{|class="wikitable"
−
!colspan=3 align="left" id="Handle_Layout"|Handle Layout
+
!colspan=3 align="left" id="isom"|isom
 
|-
 
|-
−
| handleXoffset || INTEGER || 20
+
| coolingFactor || DOUBLE || 2.0
 
|-
 
|-
−
| handleYoffset || INTEGER || 20
+
| initialAdaptation || DOUBLE || 0.9
 
|-
 
|-
−
| sourceIndicator || EDGEATTRIBUTE || targetIndicator
+
| maxEpoch || INTEGER || 5000
 
|-
 
|-
−
| targetIndicator || EDGEATTRIBUTE ||  
+
| minAdaptation || DOUBLE || 0.0
 +
|-
 +
| minRadius || INTEGER || 1
 +
|-
 +
| radius || INTEGER || 5
 +
|-
 +
| radiusConstantTime || INTEGER || 20
 +
|-
 +
| sizeFactor || INTEGER || 10
 
|-
 
|-
 
|}
 
|}
−
===Kamada-Kawai===
+
===kamada-kawai===
 
{|class="wikitable"
 
{|class="wikitable"
−
!colspan=3 align="left" id="Kamada-Kawai"|Kamada-Kawai
+
!colspan=3 align="left" id="kamada-kawai"|kamada-kawai
 
|-
 
|-
 
| algorithm_settings || GROUP || 7
 
| algorithm_settings || GROUP || 7
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|-
 
|-
 
|}
 
|}
−
===Kamada-Kawai-Noweight===
+
===kamada-kawai-noweight===
 
{|class="wikitable"
 
{|class="wikitable"
−
!colspan=3 align="left" id="Kamada-Kawai-Noweight"|Kamada-Kawai-Noweight
+
!colspan=3 align="left" id="kamada-kawai-noweight"|kamada-kawai-noweight
 
|-
 
|-
 
| algorithm_settings || GROUP || 7
 
| algorithm_settings || GROUP || 7
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|-
 
|-
 
| weight_type || LIST || 0
 
| weight_type || LIST || 0
−
|-
 
−
|}
 
−
===attribute-circle===
 
−
{|class="wikitable"
 
−
!colspan=3 align="left" id="attribute-circle"|attribute-circle
 
−
|-
 
−
| attribute || NODEATTRIBUTE || ()
 
−
|-
 
−
| spacing || DOUBLE || 100.0
 
−
|-
 
−
|}
 
−
===attributes-layout===
 
−
{|class="wikitable"
 
−
!colspan=3 align="left" id="attributes-layout"|attributes-layout
 
−
|-
 
−
| attributeName || NODEATTRIBUTE ||
 
−
|-
 
−
| maxwidth || DOUBLE || 5000.0
 
−
|-
 
−
| minrad || DOUBLE || 100.0
 
−
|-
 
−
| radmult || DOUBLE || 50.0
 
−
|-
 
−
| spacingx || DOUBLE || 400.0
 
−
|-
 
−
| spacingy || DOUBLE || 400.0
 
−
|-
 
−
|}
 
−
===force-directed===
 
−
{|class="wikitable"
 
−
!colspan=3 align="left" id="force-directed"|force-directed
 
−
|-
 
−
| defaultNodeMass || DOUBLE || 3.0
 
−
|-
 
−
| defaultSpringCoefficient || DOUBLE || 9.99999974738e-05
 
−
|-
 
−
| defaultSpringLength || DOUBLE || 50.0
 
−
|-
 
−
| edge_attribute || EDGEATTRIBUTE || weight
 
−
|-
 
−
| edge_weight_group || GROUP || 4
 
−
|-
 
−
| force_alg_settings || GROUP || 5
 
−
|-
 
−
| max_weight || DOUBLE || 1.79769313486e+308
 
−
|-
 
−
| min_weight || DOUBLE || 0.0
 
−
|-
 
−
| numIterations || INTEGER || 100
 
−
|-
 
−
| partition || BOOLEAN || True
 
−
|-
 
−
| selected_only || BOOLEAN || False
 
−
|-
 
−
| standard || GROUP || 2
 
−
|-
 
−
| weight_type || LIST || 0
 
−
|-
 
−
|}
 
−
===isom===
 
−
{|class="wikitable"
 
−
!colspan=3 align="left" id="isom"|isom
 
−
|-
 
−
| coolingFactor || DOUBLE || 2.0
 
−
|-
 
−
| initialAdaptation || DOUBLE || 0.9
 
−
|-
 
−
| maxEpoch || INTEGER || 5000
 
−
|-
 
−
| minAdaptation || DOUBLE || 0.0
 
−
|-
 
−
| minRadius || INTEGER || 1
 
−
|-
 
−
| radius || INTEGER || 5
 
−
|-
 
−
| radiusConstantTime || INTEGER || 20
 
−
|-
 
−
| sizeFactor || INTEGER || 10
 
 
|-
 
|-
 
|}
 
|}
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| trapezoid_2 || triangle || vee
 
| trapezoid_2 || triangle || vee
 
|}
 
|}
−
 
+
None
 
=Edge Properties=
 
=Edge Properties=
 
==Arrow Shape Names==
 
==Arrow Shape Names==
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| No Arrow || T
 
| No Arrow || T
 
|}
 
|}
−
 
+
None
 +
==Line Type Names==
 +
{|class="wikitable"
 +
!colspan=3 align="left" id="Line_Style_Names"|Line Style Names
 +
|-
 +
| BACKWARD_SLASH || CONTIGUOUS_ARROW || DASH_DOT
 +
|-
 +
| DOT || EQUAL_DASH || FORWARD_SLASH
 +
|-
 +
| LONG_DASH || PARALLEL_LINES || SEPARATE_ARROW
 +
|-
 +
| SINEWAVE || SOLID || VERTICAL_SLASH
 +
|-
 +
| ZIGZAG
 +
|}
 +
None
 
=Visual Properties=
 
=Visual Properties=
 
==Visual Style Names==
 
==Visual Style Names==
Line 280: Line 268:
 
|-
 
|-
 
| Solid || Universe || default
 
| Solid || Universe || default
−
|-
 
−
| default-backup
 
 
|}
 
|}
−
 
+
None
 
==Visual Style Modifiables==
 
==Visual Style Modifiables==
 
{|class="wikitable"
 
{|class="wikitable"
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| Node Tooltip || Node Width
 
| Node Tooltip || Node Width
 
|}
 
|}
−
 
+
None
 
==Bypass Names==
 
==Bypass Names==
 
{|class="wikitable"
 
{|class="wikitable"
Line 373: Line 359:
 
| node.toolTip || node.width
 
| node.toolTip || node.width
 
|}
 
|}
 +
None

Revision as of 15:23, 2 March 2011

Layouts

Layout Properties

Layout Names
attribute-circle attributes-layout circular
degree-circle force-directed fruchterman-rheingold
grid hierarchical isom
jgraph-annealing jgraph-circle jgraph-gem
jgraph-moen jgraph-radial-tree jgraph-spring
jgraph-sugiyama jgraph-tree kamada-kawai
kamada-kawai-noweight

attribute-circle

attribute-circle
attribute NODEATTRIBUTE (none)
spacing DOUBLE 100.0

attributes-layout

attributes-layout
attributeName NODEATTRIBUTE
maxwidth DOUBLE 5000.0
minrad DOUBLE 100.0
radmult DOUBLE 50.0
spacingx DOUBLE 400.0
spacingy DOUBLE 400.0

force-directed

force-directed
defaultNodeMass DOUBLE 3.0
defaultSpringCoefficient DOUBLE 9.99999974738e-05
defaultSpringLength DOUBLE 50.0
discrete BOOLEAN False
edge_attribute EDGEATTRIBUTE weight
edge_weight_group GROUP 4
force_alg_settings GROUP 6
max_weight DOUBLE 1.79769313486e+308
min_weight DOUBLE 0.0
numIterations INTEGER 100
partition BOOLEAN True
selected_only BOOLEAN False
standard GROUP 2
weight_type LIST 0

fruchterman-rheingold

fruchterman-rheingold
algorithm_settings GROUP 9
attraction_multiplier DOUBLE 0.001
conflict_avoidance DOUBLE 20.0
edge_attribute EDGEATTRIBUTE weight
edge_weight_group GROUP 4
gravity_multiplier DOUBLE 0.0
iterations INTEGER 500
labels_settings GROUP 4
layout_type LIST 0
max_distance_factor DOUBLE 20.0
max_weight DOUBLE 1.79769313486e+308
min_weight DOUBLE 0.0
partition BOOLEAN True
randomize BOOLEAN True
repulsion_multiplier DOUBLE 1.0
resetAllLabelsButton BUTTON Reset Label Positions
resetSelectedLabelsButton BUTTON Reset Label Positions
selected_only BOOLEAN False
spread_factor DOUBLE 2.0
standard GROUP 3
temperature DOUBLE 80.0
update_iterations INTEGER 0
weightCoefficient DOUBLE 10.0
weight_type LIST 0

isom

isom
coolingFactor DOUBLE 2.0
initialAdaptation DOUBLE 0.9
maxEpoch INTEGER 5000
minAdaptation DOUBLE 0.0
minRadius INTEGER 1
radius INTEGER 5
radiusConstantTime INTEGER 20
sizeFactor INTEGER 10

kamada-kawai

kamada-kawai
algorithm_settings GROUP 7
anticollisionStrength DOUBLE 100.0
disconnected_rest_length DOUBLE 2000.0
disconnected_strength DOUBLE 0.05
distance_strength DOUBLE 15.0
iterations_pernode INTEGER 20
layout_passes INTEGER 2
partition BOOLEAN True
randomize BOOLEAN True
rest_length DOUBLE 45.0
selected_only BOOLEAN False
standard GROUP 3

kamada-kawai-noweight

kamada-kawai-noweight
algorithm_settings GROUP 7
anticollisionStrength DOUBLE 100.0
disconnected_rest_length DOUBLE 2000.0
disconnected_strength DOUBLE 0.05
distance_strength DOUBLE 15.0
edge_attribute EDGEATTRIBUTE weight
edge_weight_group GROUP 4
iterations_pernode INTEGER 40
layout_passes INTEGER 2
max_weight DOUBLE 1.79769313486e+308
min_weight DOUBLE 0.0
partition BOOLEAN True
randomize BOOLEAN True
rest_length DOUBLE 45.0
selected_only BOOLEAN False
standard GROUP 3
weight_type LIST 0

Node Properties

Node Shape Names

Node Shapes Names
diamond ellipse hexagon
octagon parallelogram rect
rect_3d round_rect trapezoid
trapezoid_2 triangle vee

None

Edge Properties

Arrow Shape Names

Arraw Shape Names
Arrow Circle Delta
Diamond Half Arrow Bottom Half Arrow Top
No Arrow T

None

Line Type Names

Line Style Names
BACKWARD_SLASH CONTIGUOUS_ARROW DASH_DOT
DOT EQUAL_DASH FORWARD_SLASH
LONG_DASH PARALLEL_LINES SEPARATE_ARROW
SINEWAVE SOLID VERTICAL_SLASH
ZIGZAG

None

Visual Properties

Visual Style Names

Visual Style Names
Minimal Nested Network Style Sample1
Solid Universe default

None

Visual Style Modifiables

Visual Style Modifiables
Edge Color Edge Font Face Edge Font Size
Edge Label Edge Label Color Edge Label Opacity
Edge Label Position Edge Label Width Edge Line Style
Edge Line Type Edge Line Width Edge Opacity
Edge Source Arrow Edge Source Arrow Color Edge Source Arrow Opacity
Edge Source Arrow Shape Edge Target Arrow Edge Target Arrow Color
Edge Target Arrow Opacity Edge Target Arrow Shape Edge Tooltip
Node Border Color Node Border Opacity Node Color
Node Custom Graphics 1 Node Custom Graphics 2 Node Custom Graphics 3
Node Custom Graphics 4 Node Custom Graphics 5 Node Custom Graphics 6
Node Custom Graphics 7 Node Custom Graphics 8 Node Custom Graphics 9
Node Custom Graphics Position 1 Node Custom Graphics Position 2 Node Custom Graphics Position 3
Node Custom Graphics Position 4 Node Custom Graphics Position 5 Node Custom Graphics Position 6
Node Custom Graphics Position 7 Node Custom Graphics Position 8 Node Custom Graphics Position 9
Node Font Face Node Font Size Node Height
Node Label Node Label Color Node Label Opacity
Node Label Position Node Label Width Node Line Style
Node Line Type Node Line Width Node Opacity
Node Shape Node Show Nested Network Node Size
Node Tooltip Node Width

None

Bypass Names

Visual Bypass Names
edge.color edge.font edge.fontSize
edge.label edge.labelColor edge.labelOpacity
edge.labelPosition edge.labelWidth edge.lineStyle
edge.lineType edge.lineWidth edge.opacity
edge.sourceArrow edge.sourceArrowColor edge.sourceArrowOpacity
edge.sourceArrowShape edge.targetArrow edge.targetArrowColor
edge.targetArrowOpacity edge.targetArrowShape edge.toolTip
node.LabelOpacity node.borderColor node.borderOpacity
node.customGraphics1 node.customGraphics2 node.customGraphics3
node.customGraphics4 node.customGraphics5 node.customGraphics6
node.customGraphics7 node.customGraphics8 node.customGraphics9
node.customGraphicsPosition1 node.customGraphicsPosition2 node.customGraphicsPosition3
node.customGraphicsPosition4 node.customGraphicsPosition5 node.customGraphicsPosition6
node.customGraphicsPosition7 node.customGraphicsPosition8 node.customGraphicsPosition9
node.fillColor node.font node.fontSize
node.height node.label node.labelColor
node.labelPosition node.labelWidth node.lineStyle
node.lineType node.lineWidth node.opacity
node.shape node.showNestedNetwork node.size
node.toolTip node.width

None

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