KeyNodes hub - Revision history

Lan@dote.ru at 09:28, 22 May 2015

2015-05-22T09:28:06Z

Lan@dote.ru at 09:16, 22 May 2015

2015-05-22T09:16:58Z

Lan@dote.ru: First draft

2015-05-22T09:00:23Z

First draft

New page

KeyNodes hub is a [[BioHub]] which can be used in [[Regulator search (analysis)|Regulator search]] and [[Effector search (analysis)|Effector search]] analyses as well as several helper analyses. Its main purpose is provide abilities to traverse through gene/molecules network represented as directed weighted graph.

== Implementation details ==
All the KeyNodes hubs must extends the {{Class|biouml.plugins.keynodes.biohub.KeyNodesHub}} class. If the hub is based on MySQL database, it's better to extend {{Class|biouml.plugins.keynodes.biohub.KeyNodesSqlHub}} class as it provides additional support for handling SQL connection. Both classes are parametrized by type which represents hub node.

=== Nodes representation ===
Hub node (molecule or gene) can be represented by any type. Sometimes it's ok to use {{Class|java.lang.Integer}}, {{Class|java.lang.String}}, sometimes it's better to create your own class. The {{Method|java.lang.Object.toString()}} of this class should produce stable accession number for the molecule or gene which belongs to the registered [[reference type]].

To support hub nodes you should override the following methods:
* {{Method|ru.biosoft.access.biohub.BioHubSupport.getSupportedInputTypes()}}: return an array of possible [[reference type]]s which can be converted to internal node type. Usually it's only one type.
* {{Method|biouml.plugins.keynodes.biohub.KeyNodesHub.getElementConverter()}}: return an {{Class|biouml.plugins.keynodes.graph.ElementConverter}} object which is capable to convert internal nodes from/to {{Class|ru.biosoft.access.biohub.Element}} objects:
** {{Method|biouml.plugins.keynodes.graph.ElementConverter.toNode(Element)}} method should create a hub node object using {{Class|ru.biosoft.access.biohub.Element}}. The toString() method of the resulting node should produce the same string as {{Method|ru.biosoft.access.biohub.Element.getAccession()}}.
** {{Method|biouml.plugins.keynodes.graph.ElementConverter.fromNode(N)}} method should create a new {{Class|ru.biosoft.access.biohub.Element}} object by existing node. It must have the full path set, preferably linked to the existing element in the [[repository]].

@@ Line 21: / Line 21: @@
 Additionally a toString() method must return an accession number for given relation.
-To spare memory it's recommended to make both node and edge objects as simple as possible. They should not be linked to each other or to the graph.
+To spare memory it's recommended to make both node and edge objects as simple as possible. They should not be linked to each other or to the graph. Also edges should not contain the weight: it might be changed by decorators.
 === Graph represenation ===
@@ Line 27: / Line 27: @@
 * {{Method|biouml.plugins.keynodes.graph.HubGraph.nodes()}} method must return the stream of all nodes in the graph
 * {{Method|biouml.plugins.keynodes.graph.HubGraph.hasNode(N)}} method must return true if given node appears in the graph
-* {{Method|biouml.plugins.keynodes.graph.HubGraph.visitEdges(N, boolean, HubEdgeVisitor<N>)}} method must call given visitor for all the nodes directly adjacent to supplied start node in either upstream or downstream direction.
+* {{Method|biouml.plugins.keynodes.graph.HubGraph.visitEdges()}} method must call given visitor for all the nodes directly adjacent to supplied start node in either upstream or downstream direction.

@@ Line 5: / Line 5: @@
 === Nodes representation ===
-Hub node (molecule or gene) can be represented by any type. Sometimes it's ok to use {{Class|java.lang.Integer}}, {{Class|java.lang.String}}, sometimes it's better to create your own class. The {{Method|java.lang.Object.toString()}} of this class should produce stable accession number for the molecule or gene which belongs to the registered [[reference type]].
+Hub node (molecule or gene) can be represented by any type. Sometimes it's ok to use {{Class|java.lang.Integer}}, {{Class|java.lang.String}}, sometimes it's better to create your own class. The {{Method|java.lang.Object.toString()}} of this class should produce stable accession number for the molecule or gene which belongs to the registered [[reference type]]. The {{Method|java.lang.Object.equals(Object)}} and {{Method|java.lang.Object.hashCode()}} methods must be redefined for node type. Nodes with the same string representation must be equal and have the same hashCode.
 To support hub nodes you should override the following methods:
@@ Line 11: / Line 11: @@
 * {{Method|biouml.plugins.keynodes.biohub.KeyNodesHub.getElementConverter()}}: return an {{Class|biouml.plugins.keynodes.graph.ElementConverter}} object which is capable to convert internal nodes from/to {{Class|ru.biosoft.access.biohub.Element}} objects:
 ** {{Method|biouml.plugins.keynodes.graph.ElementConverter.toNode(Element)}} method should create a hub node object using {{Class|ru.biosoft.access.biohub.Element}}. The toString() method of the resulting node should produce the same string as {{Method|ru.biosoft.access.biohub.Element.getAccession()}}.
-** {{Method|biouml.plugins.keynodes.graph.ElementConverter.fromNode(N)}} method should create a new {{Class|ru.biosoft.access.biohub.Element}} object by existing node. It must have the full path set, preferably linked to the existing element in the [[repository]].
+** {{Method|biouml.plugins.keynodes.graph.ElementConverter.fromNode(N)}} method must create a new {{Class|ru.biosoft.access.biohub.Element}} object by existing node. It must have the full path set, preferably linked to the existing element (substance/protein/gene/etc.) in the [[repository]].