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biouml.modules.genenet.access
Class DiagramTransformer

ru.biosoft.access.AbstractTransformer
  |
  +--biouml.modules.genenet.access.DiagramTransformer
public class DiagramTransformer
extends AbstractTransformer

The definition of compartment for the GeneNet database.

For formalized hierarchical description of the compartment structure the special format is used in the GeneNet database.

The fromEntry function is used for parsing of this format, and the toEntry function is used for generation of formalized description of the compartment structure.

The Backus-Naur form of the compartment description. 

compartment ::= compartment
{
<id>;
<alias>;
<size>;
<color>;
<shape>;
entities
{
<entity_list>
}
relations
{
<relation_list>
}
}

id     ::= <string>
alias  ::= alias=<string>
size   ::= size=(<number>;<number>)
color  ::= (<number>,<number>,<number>);
shape  ::= shape= rectangle|round_rectangle|oval

entity_list ::= <entity_description>|
<entity_list>;<entity_description>
entity_description ::= <coordinate><entity_type>
<entity_id>|<equalence_group>|<compartment>
coordinate  ::= (<number>,<number>)
entity_type ::= ?<?cell|gene|protein|process|substance?>?
entity_id   ::= <string>

equalence_group ::= (<entity_id_list>)
entity_id_list  ::= <entity_id>|<entyty_id_list>,<entity_id>

relation_list ::= <relation_id>|<relation_list>;<relation_id>
This a simple example of formalized herarchical decription of the compartent which consists from 2 objects and 1 other compartment inside of it. 
compartment
{
id=cell;
alias=cell;
size=(4,5);
color=128,128,128;
shape=rectangle;
entities
{
(0,1)<protein>Hs:Ifn-gamma;
(0,1)<protein>(Hs:Irf-1,Mm:Irf-1)
(1,1)compartment
{
id=nucleus;
alias=nucleus;
color=255,128,128;
shape=ellipse;
entities
{
(0,0)<gene>(Hs:Irf-1,Mm:Irf-1)
}
relations
{
}
}
}
relations
{
(R000001,R000002);
R000003;
}
}

todo transform "Diagram -> GeneNet entry".
Method Summary
 static StringgetArgument(String where, String var)
          Returns the argument for required variable.
 ClassgetInputType()
           
 ClassgetOutputType()
           
 static intgetSection(String str, int fromIndex)
          Returns the position where the section is ended, that is the position of reqired '}'.
 synchronized DataElementtransformInput(DataElement input)
          Parse the textual description of GeneNet diagram.
 DataElementtransformOutput(DataElement output)
           

Methods inherited from class ru.biosoft.access.AbstractTransformer
getPrimaryCollection, getTransformedCollection, init, isInputType, isOutputType

Method Detail

getArgument

public static String getArgument(String where, String var)
Returns the argument for required variable.
Parameters:
var - the varable (id, alias, size, color or shape).
where - string containing the variable

getInputType

public Class getInputType()

getOutputType

public Class getOutputType()

getSection

public static int getSection(String str, int fromIndex)
Returns the position where the section is ended, that is the position of reqired '}'.
Parameters:
str - the string cintaining required section
fromIndex - - the index to start the search from

transformInput

public synchronized DataElement transformInput(DataElement input)
                                         throws java.lang.Exception
Parse the textual description of GeneNet diagram.
pending shape creation for main compartment (not null case), initialize module variable NOT ising Module.getActiveInstance()

transformOutput

public DataElement transformOutput(DataElement output)
                             throws java.lang.Exception
pending todo

Association Links

to Class org.apache.log4j.Category

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