public class Utils
extends java.lang.Object
Modifier and Type | Class and Description |
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static class |
Utils.Transparency |
Modifier and Type | Field and Description |
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static long |
lastUsedMemory |
Constructor and Description |
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Utils() |
Modifier and Type | Method and Description |
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static void |
addAttribute(GraphicEdge n,
java.lang.String label,
java.lang.String name,
java.lang.String value,
ObjectType.Enum typ)
Add an attribute to GraphicEdge
|
static void |
addAttribute(GraphicNode n,
java.lang.String label,
java.lang.String name,
java.lang.String value,
ObjectType.Enum typ)
Add an attribute to GraphicNode
|
static void |
addAttributeUniqueNameConcatenatedValues(GraphicNode n,
java.lang.String label,
java.lang.String name,
java.lang.String value,
ObjectType.Enum typ) |
static float |
calcMean(float[] f) |
static float |
calcStandardDeviation(float[] f) |
static int |
compareTwoSets(java.util.Vector v1,
java.util.Vector v2) |
static java.lang.String |
convertHGNC2HUGOthrowInternet(java.lang.String hgnc) |
static java.awt.Color |
convertPaintToColor(java.awt.Paint paint) |
static void |
CorrectCytoscapeEdgeIds(Graph graph) |
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 |
correctHtml(java.lang.String id) |
static java.lang.String |
correctName(java.lang.String name)
Substitutes strings ' ','*','-','[',']','__',':' to underscore symbol
|
static java.lang.String |
cutFinalAmpersand(java.lang.String label) |
static java.lang.String |
cutFirstLastNonVisibleSymbols(java.lang.String s) |
static java.lang.String |
cutFirstNonVisibleSymbols(java.lang.String s) |
static java.lang.String |
cutNameSpace(java.lang.String uri) |
static java.lang.String |
cutUri(java.lang.String uri)
Convert string from the form
|
static void |
downloadToFile(java.lang.String link,
java.lang.String fileName) |
static java.lang.String |
downloadURL(java.lang.String link) |
static java.lang.String |
eclipseError(java.lang.String s) |
static java.lang.String |
eclipseErrorln(java.lang.String s) |
static java.lang.String |
eclipseParentErrorln(java.lang.String s) |
static void |
eclipseParentPrintln(java.lang.String s) |
static void |
eclipsePrint(java.lang.String s) |
static void |
eclipsePrintln(java.lang.String s) |
static java.util.Vector<java.lang.String> |
extractAllStringBetween(java.lang.String text,
java.lang.String from,
java.lang.String to) |
static java.lang.String |
extractFolderName(java.lang.String fileName) |
static java.math.BigInteger |
factorial(int n)
Calculate the factorial of a given number
|
static AttDocument.Att |
getFirstAttribute(GraphicEdge n,
java.lang.String name)
Get first attribute in the list with name
|
static AttDocument.Att |
getFirstAttribute(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.lang.String |
getPropertyURI(Resource 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.awt.image.BufferedImage |
getScaledImage(java.awt.image.BufferedImage image,
int width,
int height) |
static java.awt.image.BufferedImage |
getScaledImageSlow(java.awt.image.BufferedImage image,
int width,
int height) |
static java.util.Vector<java.lang.String> |
getTagValues(java.lang.String notes,
java.lang.String tag) |
static java.lang.String |
getText(XmlObject xBean)
Read the text of XmlObject
|
static long |
getUsedMemory() |
static long |
getUsedMemoryMb() |
static long |
getUsedMemorySinceLastTime()
Returns a difference in used memory since last call of printUsedMemory,printUsedMemorySinceLastTime,
getUsedMemorySinceLastTime,printUsedMemorySinceLastTimeByte functions
|
static java.lang.String |
getValue(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.util.Vector<java.lang.String> |
guessProteinIdentifiers(java.lang.String name) |
static int |
indexOfS(java.lang.String[] ar,
java.lang.String s) |
static boolean |
isIntegerNumber(java.lang.String s) |
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 java.util.Vector<java.lang.String> |
loadStringListFromFile(java.lang.String fn) |
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 |
replaceByList(java.lang.String text,
java.util.HashMap<java.lang.String,java.lang.String> map) |
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 |
replaceStringChar(java.lang.String source,
java.lang.String shabl,
java.lang.String 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 |
saveStringToFile(java.lang.String s,
java.lang.String fn) |
static void |
setAttribute(GraphicEdge n,
java.lang.String label,
java.lang.String name,
java.lang.String value,
ObjectType.Enum typ)
Set attribute value for GraphicEdge
|
static void |
setAttribute(GraphicNode n,
java.lang.String label,
java.lang.String name,
java.lang.String value,
ObjectType.Enum typ)
Set attribute value for GraphicNode
|
static void |
setLitValue(XmlObject xBean,
java.lang.String value)
Same as SetValue
|
static void |
setNoteHtmlBodyValue(NotesDocument.Notes n,
java.lang.String value)
Sets NotesDocument.Notes content
|
static void |
setValue(XmlObject xBean,
java.lang.String value)
Set a string value for XmlObject
|
static int[] |
SortMass(float[] cais) |
static java.util.Set |
UnionOfSets(java.util.Set set1,
java.util.Set set2) |
public static void eclipsePrint(java.lang.String s)
public static void eclipsePrintln(java.lang.String s)
public static java.lang.String eclipseParentErrorln(java.lang.String s)
public static java.lang.String eclipseErrorln(java.lang.String s)
public static java.lang.String eclipseError(java.lang.String s)
public static void eclipseParentPrintln(java.lang.String s)
public static java.lang.String replaceString(java.lang.String source, java.lang.String shabl, java.lang.String val)
source
- shabl
- val
- public static java.lang.String replaceStringCount(java.lang.String source, java.lang.String shabl, java.lang.String val)
source
- shabl
- val
- public static java.lang.String replaceStringChar(java.lang.String source, java.lang.String shabl, java.lang.String val)
public static void setValue(XmlObject xBean, java.lang.String value)
xBean
- value
- public static void setLitValue(XmlObject xBean, java.lang.String value)
xBean
- value
- public static java.lang.String getText(XmlObject xBean)
xBean
- public static java.lang.String getValue(XmlObject xBean)
public static java.lang.String loadString(java.lang.String fn)
fn
- public static java.util.Vector<java.lang.String> loadStringListFromFile(java.lang.String fn)
public static java.lang.String loadString(java.io.InputStream is)
is
- public static void addAttribute(GraphicNode n, java.lang.String label, java.lang.String name, java.lang.String value, ObjectType.Enum typ)
n
- label
- name
- value
- typ
- public static void addAttributeUniqueNameConcatenatedValues(GraphicNode n, java.lang.String label, java.lang.String name, java.lang.String value, ObjectType.Enum typ)
public static void addAttribute(GraphicEdge n, java.lang.String label, java.lang.String name, java.lang.String value, ObjectType.Enum typ)
n
- label
- name
- value
- typ
- public static AttDocument.Att getFirstAttribute(GraphicNode n, java.lang.String name)
n
- name
- public static AttDocument.Att getFirstAttribute(GraphicEdge n, java.lang.String name)
n
- name
- public static void setAttribute(GraphicEdge n, java.lang.String label, java.lang.String name, java.lang.String value, ObjectType.Enum typ)
n
- name
- public static void setAttribute(GraphicNode n, java.lang.String label, java.lang.String name, java.lang.String value, ObjectType.Enum typ)
n
- name
- public static java.lang.String cutUri(java.lang.String uri)
n
- name
- public static java.lang.String cutNameSpace(java.lang.String uri)
public static java.lang.String correctName(java.lang.String name)
name
- public static java.lang.String getVocabularyTerm(java.util.Iterator it)
it
- public static void printPropertyURIs(Entity res)
res
- public static void printPropertyURIs(UtilityClass res)
res
- public static void printUsedMemory()
public static void printUsedMemorySinceLastTime()
public static long getUsedMemorySinceLastTime()
public static long getUsedMemory()
public static long getUsedMemoryMb()
public static void printUsedMemorySinceLastTimeByte()
public static int compareTwoSets(java.util.Vector v1, java.util.Vector v2)
v1
- v2
- public static java.util.Set UnionOfSets(java.util.Set set1, java.util.Set set2)
set1
- set2
- public static void CorrectCytoscapeNodeIds(Graph graph)
graph
- public static void CorrectCytoscapeEdgeIds(Graph graph)
public static void setNoteHtmlBodyValue(NotesDocument.Notes n, java.lang.String value)
n
- value
- public static java.lang.String getPropertyURI(Entity res, java.lang.String pname)
res
- pname
- public static java.lang.String getPropertyURI(Resource res, java.lang.String pname)
public static java.util.Vector getPropertyURIs(Entity res, java.lang.String pname)
res
- pname
- public static java.util.Vector getPropertyURIs(UtilityClass res, java.lang.String pname)
res
- pname
- public static int indexOfS(java.lang.String[] ar, java.lang.String s)
public static java.lang.String cutFinalAmpersand(java.lang.String label)
public static java.lang.String correctHtml(java.lang.String id)
public static float calcMean(float[] f)
public static float calcStandardDeviation(float[] f)
public static int[] SortMass(float[] cais)
public static java.awt.Color convertPaintToColor(java.awt.Paint paint) throws java.lang.Exception
java.lang.Exception
public static java.util.Vector<java.lang.String> extractAllStringBetween(java.lang.String text, java.lang.String from, java.lang.String to)
public static void saveStringToFile(java.lang.String s, java.lang.String fn)
public static java.lang.String extractFolderName(java.lang.String fileName)
public static java.math.BigInteger factorial(int n)
n
- integerpublic static void downloadToFile(java.lang.String link, java.lang.String fileName)
public static java.lang.String downloadURL(java.lang.String link)
public static java.awt.image.BufferedImage getScaledImageSlow(java.awt.image.BufferedImage image, int width, int height) throws java.io.IOException
java.io.IOException
public static java.awt.image.BufferedImage getScaledImage(java.awt.image.BufferedImage image, int width, int height) throws java.io.IOException
java.io.IOException
public static java.lang.String cutFirstLastNonVisibleSymbols(java.lang.String s)
public static java.lang.String cutFirstNonVisibleSymbols(java.lang.String s)
public static java.util.Vector<java.lang.String> guessProteinIdentifiers(java.lang.String name) throws java.lang.Exception
java.lang.Exception
public static java.lang.String convertHGNC2HUGOthrowInternet(java.lang.String hgnc) throws java.lang.Exception
java.lang.Exception
public static boolean isIntegerNumber(java.lang.String s)
public static java.util.Vector<java.lang.String> getTagValues(java.lang.String notes, java.lang.String tag)
public static java.lang.String replaceByList(java.lang.String text, java.util.HashMap<java.lang.String,java.lang.String> map)