Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a network file (eg. galFiltered.gml)
3. Click on Layout from the toolbar

L1

1. Click Rotate
2. Drag the pointer along the number line representing degree

The Tool Panel should appear at the bottom of the Control Panel with the Rotate tab selected. The graph should rotate through the number of degrees indicated (To hide the Tool Panel click Layout → Rotate again)

L2

1. Click Scale
2. Drag the pointer along the number line

The Tool Panel should appear at the bottom of the Control Panel with the Scale tab selected. The graph should change in size proportional to the number indicated. (To hide the Tool Panel click Layout → Scale again)

L3

1. Click Align and Distribute
2. Drag and select some nodes
3. Select some of the buttons from the Tool Panel

The Tool Panel should appear at the bottom of the Control Panel with the Align and Distribute tab selected. The buttons should arrange the nodes in various configurations. (To hide the Tool Panel click Layout → Align and Distribute again)

L4

To avoid repetition the Settings… sub menu contents will be tested under the JGraph and Cytoscape Layouts sub menus

L5

yFiles Layouts are tested under the core plugins test cases

L6.1

Select JGraph Layouts → Tree Layout

The nodes should be distributed in a branched arrangement

L6.2

Select JGraph Layouts → Radial Tree Layout

The graph should appear with concentric ovals of nodes with angular arms on the outside

L6.3

Select JGraph Layouts → Simulated Annealing Layout

Warning: Do not try this with a large network! Even galFiltered.sif is too large for this!

L6.4

Select JGraph Layouts → Circle Layout

All of the nodes are arranged at a locus equidistant from the centre of the circle

L6.5

Select JGraph Layouts → Spring Embedded Layout

Similar to an Organic yFiles layout in appearance nodes overlap slightly, edges are short and the angles created by edges are minimized

L6.6

Select JGraph Layouts → MOEN Layout

L6.7

Select JGraph Layouts → GEM Layout

The nodes with the most connected edges are further away from the nodes they are first neighbours with and most of the edges are directed in a 30° arc from each node

L6.8

Select JGraph Layouts → Sugiyama Layout

This layout should be hierarchical with edges creating obtuse angles between nodes

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a network file (eg. galFiltered.gml)
3. Click on Layout from the toolbar

L7.1

Select Cytoscape Layouts → Inverted Self-Organising Map Layout

Nodes are clustered but not overlapping extensively. Edges are fairly long and angular with <90° angles

L7.2

Select Cytoscape Layouts → Edge-weighted Force directed (BioLayout) → (unweighted)

Edges are very long and nodes overlap. Network arranged in arrow or comet shape

L7.3

Select Cytoscape Layouts → Degree Sorted Circle Layout

The nodes of the main network are arranged at a locus equidistant from the centre of the circle and sorted numerically according to Degree starting at the bottom of the circle going clockwise

L7.4

Select Cytoscape Layouts → Grid Layout

The nodes should be arranged in an almost square grid

L7.5

Select Cytoscape Layouts → Attribute Circle Layout → canonicalName

The nodes of the main network are arranged at a locus equidistant from the centre of the circle and sorted alphabetically according to canonicalName starting at the bottom of the circle going anti-clockwise

L7.6

Select Cytoscape Layouts → Circular Layout → All Nodes

Some of the nodes from the main network form a circle with branches off it

L7.7

Select Cytoscape Layouts → Group Attributes Layout → All Nodes → canonicalName

Nodes are arranged in a grid close to other nodes with similar canonicalName distributed alphanumerically

L7.8

Select Cytoscape Layouts → Force-Directed Layout → (unweighted)

Layout appears similar to Organic yFiles layout. Nodes and edges arranged to minimise force between them

L7.9

Select Cytoscape Layouts → Edge-weighted Spring Embedded → (unweighted)

Layout appears similar to Organic yFiles layout. Nodes and edges arranged to minimise force between them in an unweighted manner

L7.10

Select Cytoscape Layouts → Spring Embedded

Layout appears similar to Organic yFiles layout. Nodes and edges arranged to minimise force between them

L7.11

Select Cytoscape Layouts → Hierarchical → All Nodes

The graph should resemble a family tree, many of the edges have more than one angled bend