fr.curie.BiNoM.pathways.utils
Class Utils

java.lang.Object
  fr.curie.BiNoM.pathways.utils.Utils

public class Utils
extends java.lang.Object

Set of simple functions

Author:

Andrei Zinovyev

Field Summary

static long

lastUsedMemory

Constructor Summary

Utils()

Method Summary

static void	addAttribute(edu.rpi.cs.xgmml.GraphicEdge n, java.lang.String label, java.lang.String name, java.lang.String value, edu.rpi.cs.xgmml.ObjectType.Enum typ) Add an attribute to GraphicEdge
static void	addAttribute(edu.rpi.cs.xgmml.GraphicNode n, java.lang.String label, java.lang.String name, java.lang.String value, edu.rpi.cs.xgmml.ObjectType.Enum typ) Add an attribute to GraphicNode
static int	compareTwoSets(java.util.Vector v1, java.util.Vector v2)
static void	CorrectCytoscapeNodeIds(Graph graph) After reading XGMML files saved by Cytoscape, this function is used to recover the original Node Ids (Cytoscape will put negative numbers for it).
static java.lang.String	correctName(java.lang.String name) Substitutes strings ' ','*','-','[',']','__',':' to underscore symbol
static java.lang.String	cutUri(java.lang.String uri) Convert string from the form # to simply
static edu.rpi.cs.xgmml.AttDocument.Att	getFirstAttribute(edu.rpi.cs.xgmml.GraphicEdge n, java.lang.String name) Get first attribute in the list with name
static edu.rpi.cs.xgmml.AttDocument.Att	getFirstAttribute(edu.rpi.cs.xgmml.GraphicNode n, java.lang.String name) Get first attribute in the list with name
static java.lang.String	getPropertyURI(entity res, java.lang.String pname)
static java.util.Vector	getPropertyURIs(entity res, java.lang.String pname)
static java.util.Vector	getPropertyURIs(utilityClass res, java.lang.String pname)
static java.lang.String	getText(org.apache.xmlbeans.XmlObject xBean) Read the text of XmlObject
static long	getUsedMemorySinceLastTime() Returns a difference in used memory since last call of printUsedMemory,printUsedMemorySinceLastTime, getUsedMemorySinceLastTime,printUsedMemorySinceLastTimeByte functions
static java.lang.String	getValue(org.apache.xmlbeans.XmlObject xBean) read XmlObject value
static java.lang.String	getVocabularyTerm(java.util.Iterator it) Returns first in the alphabetic order string from iterator it
static java.lang.String	loadString(java.io.InputStream is) Converts InputStream into String
static java.lang.String	loadString(java.lang.String fn) Load a text file into memory and returns String
static void	printPropertyURIs(entity res) Simply prints all statement uris in the entity res
static void	printPropertyURIs(utilityClass res) Simply prints all statement uris in the utilityClass res
static void	printUsedMemory() Prints how much memory is used
static void	printUsedMemorySinceLastTime() Prints a difference in used memory since last call of printUsedMemory,printUsedMemorySinceLastTime, getUsedMemorySinceLastTime,printUsedMemorySinceLastTimeByte functions
static void	printUsedMemorySinceLastTimeByte() Same ad printUsedMemorySinceLastTime but in bytes
static java.lang.String	replaceString(java.lang.String source, java.lang.String shabl, java.lang.String val) In source string replaces shabl substring with val
static java.lang.String	replaceStringCount(java.lang.String source, java.lang.String shabl, java.lang.String val) In source string replaces shabl substring with val and providing some info about the number of changes made
static void	setAttribute(edu.rpi.cs.xgmml.GraphicEdge n, java.lang.String label, java.lang.String name, java.lang.String value, edu.rpi.cs.xgmml.ObjectType.Enum typ) Set attribute value for GraphicEdge
static void	setAttribute(edu.rpi.cs.xgmml.GraphicNode n, java.lang.String label, java.lang.String name, java.lang.String value, edu.rpi.cs.xgmml.ObjectType.Enum typ) Set attribute value for GraphicNode
static void	setLitValue(org.apache.xmlbeans.XmlObject xBean, java.lang.String value) Same as SetValue
static void	setNoteHtmlBodyValue(org.sbml.x2001.ns.celldesigner.NotesDocument.Notes n, java.lang.String value) Sets NotesDocument.Notes content
static void	setValue(org.apache.xmlbeans.XmlObject xBean, java.lang.String value) Set a string value for XmlObject
static java.util.Set	UnionOfSets(java.util.Set set1, java.util.Set set2)

Methods inherited from class java.lang.Object

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

Field Detail

lastUsedMemory

public static long lastUsedMemory

Constructor Detail

Utils

public Utils()

Method Detail

replaceString

public static java.lang.String replaceString(java.lang.String source,
                                             java.lang.String shabl,
                                             java.lang.String val)

In source string replaces shabl substring with val

Parameters:

source -

shabl -

val -

Returns:

replaceStringCount

public static java.lang.String replaceStringCount(java.lang.String source,
                                                  java.lang.String shabl,
                                                  java.lang.String val)

In source string replaces shabl substring with val and providing some info about the number of changes made

Parameters:

source -

shabl -

val -

Returns:

setValue

public static void setValue(org.apache.xmlbeans.XmlObject xBean,
                            java.lang.String value)

Set a string value for XmlObject

Parameters:

xBean -

value -

setLitValue

public static void setLitValue(org.apache.xmlbeans.XmlObject xBean,
                               java.lang.String value)

Same as SetValue

Parameters:

xBean -

value -

getText

public static java.lang.String getText(org.apache.xmlbeans.XmlObject xBean)

Read the text of XmlObject

Parameters:

xBean -

Returns:

getValue

public static java.lang.String getValue(org.apache.xmlbeans.XmlObject xBean)

read XmlObject value

loadString

public static java.lang.String loadString(java.lang.String fn)

Load a text file into memory and returns String

Parameters:

fn -

Returns:

loadString

public static java.lang.String loadString(java.io.InputStream is)

Converts InputStream into String

Parameters:

is -

Returns:

addAttribute

public static void addAttribute(edu.rpi.cs.xgmml.GraphicNode n,
                                java.lang.String label,
                                java.lang.String name,
                                java.lang.String value,
                                edu.rpi.cs.xgmml.ObjectType.Enum typ)

Add an attribute to GraphicNode

Parameters:

n -

label -

name -

value -

typ -

addAttribute

public static void addAttribute(edu.rpi.cs.xgmml.GraphicEdge n,
                                java.lang.String label,
                                java.lang.String name,
                                java.lang.String value,
                                edu.rpi.cs.xgmml.ObjectType.Enum typ)

Add an attribute to GraphicEdge

Parameters:

n -

label -

name -

value -

typ -

getFirstAttribute

public static edu.rpi.cs.xgmml.AttDocument.Att getFirstAttribute(edu.rpi.cs.xgmml.GraphicNode n,
                                                                 java.lang.String name)

Get first attribute in the list with name

Parameters:

n -

name -

Returns:

getFirstAttribute

public static edu.rpi.cs.xgmml.AttDocument.Att getFirstAttribute(edu.rpi.cs.xgmml.GraphicEdge n,
                                                                 java.lang.String name)

Get first attribute in the list with name

Parameters:

n -

name -

Returns:

setAttribute

public static void setAttribute(edu.rpi.cs.xgmml.GraphicEdge n,
                                java.lang.String label,
                                java.lang.String name,
                                java.lang.String value,
                                edu.rpi.cs.xgmml.ObjectType.Enum typ)

Set attribute value for GraphicEdge

Parameters:

n -

name -

setAttribute

public static void setAttribute(edu.rpi.cs.xgmml.GraphicNode n,
                                java.lang.String label,
                                java.lang.String name,
                                java.lang.String value,
                                edu.rpi.cs.xgmml.ObjectType.Enum typ)

Set attribute value for GraphicNode

Parameters:

n -

name -

cutUri

public static java.lang.String cutUri(java.lang.String uri)

Convert string from the form # to simply

Parameters:

n -

name -

Returns:

correctName

public static java.lang.String correctName(java.lang.String name)

Substitutes strings ' ','*','-','[',']','__',':' to underscore symbol

Parameters:

name -

Returns:

getVocabularyTerm

public static java.lang.String getVocabularyTerm(java.util.Iterator it)

Returns first in the alphabetic order string from iterator it

Parameters:

it -

Returns:

printPropertyURIs

public static void printPropertyURIs(entity res)

Simply prints all statement uris in the entity res

Parameters:

res -

printPropertyURIs

public static void printPropertyURIs(utilityClass res)

Simply prints all statement uris in the utilityClass res

Parameters:

res -

printUsedMemory

public static void printUsedMemory()

Prints how much memory is used

printUsedMemorySinceLastTime

public static void printUsedMemorySinceLastTime()

Prints a difference in used memory since last call of printUsedMemory,printUsedMemorySinceLastTime, getUsedMemorySinceLastTime,printUsedMemorySinceLastTimeByte functions

getUsedMemorySinceLastTime

public static long getUsedMemorySinceLastTime()

Returns a difference in used memory since last call of printUsedMemory,printUsedMemorySinceLastTime, getUsedMemorySinceLastTime,printUsedMemorySinceLastTimeByte functions

Returns:

printUsedMemorySinceLastTimeByte

public static void printUsedMemorySinceLastTimeByte()

Same ad printUsedMemorySinceLastTime but in bytes

compareTwoSets

public static int compareTwoSets(java.util.Vector v1,
                                 java.util.Vector v2)

Parameters:

v1 -

v2 -

Returns:

The number of common entries

UnionOfSets

public static java.util.Set UnionOfSets(java.util.Set set1,
                                        java.util.Set set2)

Parameters:

set1 -

set2 -

Returns:

Union of two sets

CorrectCytoscapeNodeIds

public static void CorrectCytoscapeNodeIds(Graph graph)

After reading XGMML files saved by Cytoscape, this function is used to recover the original Node Ids (Cytoscape will put negative numbers for it). Ids are read from NodeLabels.

Parameters:

graph -

setNoteHtmlBodyValue

public static void setNoteHtmlBodyValue(org.sbml.x2001.ns.celldesigner.NotesDocument.Notes n,
                                        java.lang.String value)

Sets NotesDocument.Notes content

Parameters:

n -

value -

getPropertyURI

public static java.lang.String getPropertyURI(entity res,
                                              java.lang.String pname)

Parameters:

res -

pname -

Returns:

URI of the resource refered in res by property pname

getPropertyURIs

public static java.util.Vector getPropertyURIs(entity res,
                                               java.lang.String pname)

Parameters:

res -

pname -

Returns:

All URIs of the resources refered in res by property pname

getPropertyURIs

public static java.util.Vector getPropertyURIs(utilityClass res,
                                               java.lang.String pname)

Parameters:

res -

pname -

Returns:

All URIs of the resources refered in res by property pname