Column names

This is the documentation for all data table columns used or added by CytoGEDEVO.

Treat all of the following columns as read-only and do not modify them by hand!

CCS

(Node table, edge table)

Added or updated with the Common tasks -> CCS button.

Index of the Common Connected Subgraph (CCS) that this node/edge belongs to. CCSs start at 0 and are sorted by size, so CCS #0 is the largest one. -1 denotes that a node/edge is not part of a CCS.

CCS_size

(Node table, edge table)

Added or updated with the Common tasks -> CCS button.

Denotes the total number of nodes in the the CCS this node/edge belongs to. 0 if not part of a CCS.

gedevo*Score*

(Node table)

Added or updated after an alignment run is finished

All scores used or added by CytoGEDEVO follow this naming scheme. Column names that match this pattern are autmatically imported from an alignment file. When using custom scores, they are added as gedevoCustomScore0, gedevoCustomScore1, ... in the order they were supplied.

CytoGEDEVO's built-in scores are all distances in [0 .. 1], but external / imported scores may also be similarities or E-values.

gedevoAgreement

(Node table)

Added or updated after an alignment run is finished

Stores the fraction of how many of the high-ranking individuals in the evolutionary algorithm share the opinion with the top result that a node and its partner should be mapped together.

A high value indicates a rather converged position, a lower value indicates an unstable position.

gedevoEditType

(Node table, edge table)

Added or updated with the Common tasks -> Graph edits button.

This stores the different cases for graph edits necessary to transform the first graph into the second graph. It also handles directed edges.

The values are as follows:

SUBSTITUTED       = 0
ADDED             = 1
DELETED,          = 2
DIRECTION_CHANGED = 3
FLIPPED,          = 4

Note that with the above cases, it is not possible to distinguish the case of (1) a directed edge turning into an undirected one, with (b) a directed edge becoming undirected, as both are appear as DIRECTION_CHANGED.

gedevoFixedMapping

(edge table)

Added after an alignment run is finished, updated when mapping edges are marked as fixed (via Common tasks -> Fixate [...] )

Edges that have this set to true are handled specially and are never broken in subsequent alignment runs.

gedevoIsMappingEdge

(edge table)

Added after an alignment run is finished

Set to true for every edge that is to be considered a visual indicator showing that two nodes have been aligned. All edges created with the Common tasks -> Generate mapping edges button have this property set.

They are not considered part of the network topology by CytoGEDEVO, and are automatically broken by a re-alignment if necessary, unless fixated. See Resuming an alignment for more info.

gedevoPartnerUID

(node table)

Added or updated after an alignment run is finished

Stores UID of aligned node (in the other network).

gedevoPartnerName

(node table)

Added or updated after an alignment run is finished

Stores name of aligned node (in the other network).

gedevoSourceNetworks

(network table)

Added to the resulting network when two source networks are merged

2-element list holding the names of the source networks that were merged together.

gedevoUID

(node table)

Added to the resulting network when two source networks are merged

Custom identifier used to keep track of nodes across multiple alignment runs and various other things. Atuomatically assigned & distributed as necessary.

sourceNetworkID

(Node table, edge table)

Added to the resulting network when two source networks are merged

Used to keep track of which source network each node originates from. 0 = first network, 1 = second network.