java.lang.Object

org.forester.phylogeny.data.PhylogenyDataUtil

public final class PhylogenyDataUtil extends Object

Field Summary

Fields

Modifier and Type

Field

Description

static final double

BRANCH_LENGTH_DEFAULT

Value of -99.0 is used as default value.
Constructor Summary

Constructors

Constructor

Description

PhylogenyDataUtil()
Method Summary

Modifier and Type

Method

Description

static void

appendClose(Writer w, String element_name)

static void

appendElement(Writer w, String element_name, String value)

static void

appendElement(Writer w, String element_name, String value, String indentation)

static void

appendElement(Writer w, String element_name, String value, String attribute_name, String attribute_value)

static void

appendElement(Writer w, String element_name, String value, String attribute_name, String attribute_value, String indentation)

static void

appendElement(Writer w, String element_name, String value, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value)

static void

appendElement(Writer w, String element_name, String value, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value, String indentation)

static void

appendElement(Writer w, String element_name, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value, String attribute3_name, String attribute3_value, String attribute4_name, String attribute4_value, String indentation)

static void

appendElement(Writer w, String element_name, String value, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value, String attribute3_name, String attribute3_value, String attribute4_name, String attribute4_value, String attribute5_name, String attribute5_value, String indentation)

static void

appendOpen(Writer w, String element_name)

static void

appendOpen(Writer w, String element_name, String attribute_name, String attribute_value)

static void

appendOpen(Writer w, String element_name, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value)

static void

appendOpen(Writer w, String element_name, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value, String attribute3_name, String attribute3_value)

static void

appendOpen(Writer w, String element_name, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value, String attribute3_name, String attribute3_value, String attribute4_name, String attribute4_value)

static void

appendOpen(Writer w, String element_name, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value, String attribute3_name, String attribute3_value, String attribute4_name, String attribute4_value, String attribute5_name, String attribute5_value)

static ArrayList<PhylogenyData>

copy(ArrayList<PhylogenyData> list)

Creates a deep copy of ArrayList of PhylogenyData objects.

static void

drawLine(double x1, double y1, double x2, double y2, Graphics g)

static String

replaceIllegalXmlCharacters(String value)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- BRANCH_LENGTH_DEFAULT
  
  public static final double BRANCH_LENGTH_DEFAULT
  
  Value of -99.0 is used as default value.
  See Also:
  
  Constant Field Values
Constructor Details
- PhylogenyDataUtil
  
  public PhylogenyDataUtil()
Method Details
- appendClose
  
  public static void appendClose(Writer w, String element_name) throws IOException
  
  Throws:
  
  IOException
- appendElement
  
  public static void appendElement(Writer w, String element_name, String value) throws IOException
  
  Throws:
  
  IOException
- appendElement
  
  public static void appendElement(Writer w, String element_name, String value, String indentation) throws IOException
  
  Throws:
  
  IOException
- appendElement
  
  public static void appendElement(Writer w, String element_name, String value, String attribute_name, String attribute_value) throws IOException
  
  Throws:
  
  IOException
- appendElement
  
  public static void appendElement(Writer w, String element_name, String value, String attribute_name, String attribute_value, String indentation) throws IOException
  
  Throws:
  
  IOException
- appendElement
  
  public static void appendElement(Writer w, String element_name, String value, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value, String indentation) throws IOException
  
  Throws:
  
  IOException
- appendElement
  
  public static void appendElement(Writer w, String element_name, String value, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value) throws IOException
  
  Throws:
  
  IOException
- appendElement
  
  public static void appendElement(Writer w, String element_name, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value, String attribute3_name, String attribute3_value, String attribute4_name, String attribute4_value, String indentation) throws IOException
  
  Throws:
  
  IOException
- appendElement
  
  public static void appendElement(Writer w, String element_name, String value, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value, String attribute3_name, String attribute3_value, String attribute4_name, String attribute4_value, String attribute5_name, String attribute5_value, String indentation) throws IOException
  
  Throws:
  
  IOException
- appendOpen
  
  public static void appendOpen(Writer w, String element_name) throws IOException
  
  Throws:
  
  IOException
- appendOpen
  
  public static void appendOpen(Writer w, String element_name, String attribute_name, String attribute_value) throws IOException
  
  Throws:
  
  IOException
- appendOpen
  
  public static void appendOpen(Writer w, String element_name, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value) throws IOException
  
  Throws:
  
  IOException
- appendOpen
  
  public static void appendOpen(Writer w, String element_name, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value, String attribute3_name, String attribute3_value) throws IOException
  
  Throws:
  
  IOException
- appendOpen
  
  public static void appendOpen(Writer w, String element_name, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value, String attribute3_name, String attribute3_value, String attribute4_name, String attribute4_value) throws IOException
  
  Throws:
  
  IOException
- appendOpen
  
  public static void appendOpen(Writer w, String element_name, String attribute1_name, String attribute1_value, String attribute2_name, String attribute2_value, String attribute3_name, String attribute3_value, String attribute4_name, String attribute4_value, String attribute5_name, String attribute5_value) throws IOException
  
  Throws:
  
  IOException
- copy
  
  public static ArrayList<PhylogenyData> copy(ArrayList<PhylogenyData> list)
  
  Creates a deep copy of ArrayList of PhylogenyData objects.
  
  Parameters:
  
  list - an ArrayList of PhylogenyData objects
  
  Returns:
  
  a deep copy of ArrayList list
- drawLine
  
  public static void drawLine(double x1, double y1, double x2, double y2, Graphics g)
- replaceIllegalXmlCharacters
  
  public static String replaceIllegalXmlCharacters(String value)

Class PhylogenyDataUtil

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

BRANCH_LENGTH_DEFAULT

Constructor Details

PhylogenyDataUtil

Method Details

appendClose

appendElement

appendElement

appendElement

appendElement

appendElement

appendElement

appendElement

appendElement

appendOpen

appendOpen

appendOpen

appendOpen

appendOpen

appendOpen

copy

drawLine

replaceIllegalXmlCharacters