org.forester.phylogeny.data

Class PhylogenyDataUtil

java.lang.Object

org.forester.phylogeny.data.PhylogenyDataUtil

public final class PhylogenyDataUtil
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static double	BRANCH_LENGTH_DEFAULT Value of -99.0 is used as default value.

Constructor Summary

Constructors

Constructor and Description
PhylogenyDataUtil()

Method Summary

Modifier and Type	Method and 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 Detail

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 Detail

PhylogenyDataUtil

public PhylogenyDataUtil()

Method Detail

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)