edu.iastate.metnet.graphmodel
Class GraphValidity

java.lang.Object
  edu.iastate.metnet.graphmodel.GraphValidity

public class GraphValidity
extends java.lang.Object

store the information of the graph validity

Author:

Jie Li

Field Summary

static java.lang.String	ERROR_ADJACENT_ENTITY adjacent entities
static java.lang.String	ERROR_DUPLICATE_ENTITY duplicate entity error message
static java.lang.String	ERROR_ENZYME_TYPE enzyme type error message
static java.lang.String	ERROR_GENE_LOCATION gene location error message
static java.lang.String	ERROR_INTERACTION_STRUCTURE interaction structure error message
static java.lang.String	ERROR_NODE_USER_OBJECT user object error message
static java.lang.String	ERROR_NOTHING no errors
static java.lang.String	ERROR_ORPHAN_NODE orphan node
static java.lang.String	ERROR_TRANSPORT_LOCATION transport location error message
(package private) static org.apache.log4j.Logger	logger log4j facility
static java.lang.String	WARNING_ADJACENT_INTERACTION adjacent interaction.
static java.lang.String	WARNING_DUPLICATE_INTERACTION duplicate interaction warning message
static java.lang.String	WARNING_NOTHING no warnings
static java.lang.String	WARNING_UNKNOWN_LOCATION unknown location
static java.lang.String	WARNING_UNSUPPORTED_ORGANISM unsupported species

Constructor Summary

GraphValidity()
default constructor

Method Summary

void	clear() clear error message
void	error(java.lang.Integer modelId, java.lang.String message) add one error
java.lang.String	getErrorMessage(java.lang.Integer modelId) get the error message for model id
java.util.Map	getErrors() get the errors
java.lang.String	getWarningMessage(java.lang.Integer modelId) get the warning message for model id
java.util.Map	getWarnings() get the warnings
boolean	isPerfect() if there is no error and no warning, used for highlight
boolean	isValid() if the current informaiton is valid, used for saving
boolean	isValid(java.lang.Integer modelId) detect if the model id represents a correct data entry
void	warn(java.lang.Integer modelId, java.lang.String message) add one warning

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logger

static org.apache.log4j.Logger logger

log4j facility

ERROR_NODE_USER_OBJECT

public static final java.lang.String ERROR_NODE_USER_OBJECT

user object error message

See Also:

Constant Field Values

ERROR_GENE_LOCATION

public static final java.lang.String ERROR_GENE_LOCATION

gene location error message

See Also:

Constant Field Values

ERROR_ENZYME_TYPE

public static final java.lang.String ERROR_ENZYME_TYPE

enzyme type error message

See Also:

Constant Field Values

ERROR_TRANSPORT_LOCATION

public static final java.lang.String ERROR_TRANSPORT_LOCATION

transport location error message

See Also:

Constant Field Values

ERROR_DUPLICATE_ENTITY

public static final java.lang.String ERROR_DUPLICATE_ENTITY

duplicate entity error message

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Constant Field Values

WARNING_DUPLICATE_INTERACTION

public static final java.lang.String WARNING_DUPLICATE_INTERACTION

duplicate interaction warning message

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Constant Field Values

ERROR_INTERACTION_STRUCTURE

public static final java.lang.String ERROR_INTERACTION_STRUCTURE

interaction structure error message

See Also:

Constant Field Values

ERROR_ADJACENT_ENTITY

public static final java.lang.String ERROR_ADJACENT_ENTITY

adjacent entities

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Constant Field Values

WARNING_ADJACENT_INTERACTION

public static final java.lang.String WARNING_ADJACENT_INTERACTION

adjacent interaction. This is a warning because some enzymes catalysis the transport in Acetyl-CoA biotin network. We need the biologists to look at the data.

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Constant Field Values

ERROR_ORPHAN_NODE

public static final java.lang.String ERROR_ORPHAN_NODE

orphan node

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Constant Field Values

WARNING_UNKNOWN_LOCATION

public static final java.lang.String WARNING_UNKNOWN_LOCATION

unknown location

See Also:

Constant Field Values

WARNING_UNSUPPORTED_ORGANISM

public static final java.lang.String WARNING_UNSUPPORTED_ORGANISM

unsupported species

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Constant Field Values

ERROR_NOTHING

public static final java.lang.String ERROR_NOTHING

no errors

See Also:

Constant Field Values

WARNING_NOTHING

public static final java.lang.String WARNING_NOTHING

no warnings

See Also:

Constant Field Values

Constructor Detail

GraphValidity

public GraphValidity()

default constructor

Method Detail

getErrorMessage

public java.lang.String getErrorMessage(java.lang.Integer modelId)

get the error message for model id

Parameters:

modelId - the blockid of the graph cell

Returns:

the error message

getWarningMessage

public java.lang.String getWarningMessage(java.lang.Integer modelId)

get the warning message for model id

Parameters:

modelId - the blockid of the graph cell

Returns:

the warning message

clear

public void clear()

clear error message

getErrors

public java.util.Map getErrors()

get the errors

Returns:

the errors

getWarnings

public java.util.Map getWarnings()

get the warnings

Returns:

the warning

isValid

public boolean isValid()

if the current informaiton is valid, used for saving

Returns:

true if no errors and no warnings

isPerfect

public boolean isPerfect()

if there is no error and no warning, used for highlight

Returns:

true if perfect, false if not

isValid

public boolean isValid(java.lang.Integer modelId)

detect if the model id represents a correct data entry

Parameters:

modelId - the model id

Returns:

true if it is correct, false if not

error

public void error(java.lang.Integer modelId,
                  java.lang.String message)

add one error

Parameters:

message - the error message

warn

public void warn(java.lang.Integer modelId,
                 java.lang.String message)

add one warning

Parameters:

message - the warning message