PhylogenyDataUtil

java.lang.Object
- org.forester.phylogeny.data.PhylogenyDataUtil

public final class PhylogenyDataUtil
extends java.lang.Object

Field Summary

Fields
Modifier and Type Field and Description

static double BRANCH_LENGTH_DEFAULT
Value of -99.0 is used as default value.

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()

Constructors
Constructor and Description
`PhylogenyDataUtil()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`appendClose(java.io.Writer w, java.lang.String element_name)`
`static void`	`appendElement(java.io.Writer w, java.lang.String element_name, java.lang.String value)`
`static void`	`appendElement(java.io.Writer w, java.lang.String element_name, java.lang.String value, java.lang.String indentation)`
`static void`	`appendElement(java.io.Writer w, java.lang.String element_name, java.lang.String value, java.lang.String attribute_name, java.lang.String attribute_value)`
`static void`	`appendElement(java.io.Writer w, java.lang.String element_name, java.lang.String value, java.lang.String attribute_name, java.lang.String attribute_value, java.lang.String indentation)`
`static void`	`appendElement(java.io.Writer w, java.lang.String element_name, java.lang.String value, java.lang.String attribute1_name, java.lang.String attribute1_value, java.lang.String attribute2_name, java.lang.String attribute2_value)`
`static void`	`appendElement(java.io.Writer w, java.lang.String element_name, java.lang.String value, java.lang.String attribute1_name, java.lang.String attribute1_value, java.lang.String attribute2_name, java.lang.String attribute2_value, java.lang.String indentation)`
`static void`	`appendElement(java.io.Writer w, java.lang.String element_name, java.lang.String attribute1_name, java.lang.String attribute1_value, java.lang.String attribute2_name, java.lang.String attribute2_value, java.lang.String attribute3_name, java.lang.String attribute3_value, java.lang.String attribute4_name, java.lang.String attribute4_value, java.lang.String indentation)`
`static void`	`appendElement(java.io.Writer w, java.lang.String element_name, java.lang.String value, java.lang.String attribute1_name, java.lang.String attribute1_value, java.lang.String attribute2_name, java.lang.String attribute2_value, java.lang.String attribute3_name, java.lang.String attribute3_value, java.lang.String attribute4_name, java.lang.String attribute4_value, java.lang.String attribute5_name, java.lang.String attribute5_value, java.lang.String indentation)`
`static void`	`appendOpen(java.io.Writer w, java.lang.String element_name)`
`static void`	`appendOpen(java.io.Writer w, java.lang.String element_name, java.lang.String attribute_name, java.lang.String attribute_value)`
`static void`	`appendOpen(java.io.Writer w, java.lang.String element_name, java.lang.String attribute1_name, java.lang.String attribute1_value, java.lang.String attribute2_name, java.lang.String attribute2_value)`
`static void`	`appendOpen(java.io.Writer w, java.lang.String element_name, java.lang.String attribute1_name, java.lang.String attribute1_value, java.lang.String attribute2_name, java.lang.String attribute2_value, java.lang.String attribute3_name, java.lang.String attribute3_value)`
`static void`	`appendOpen(java.io.Writer w, java.lang.String element_name, java.lang.String attribute1_name, java.lang.String attribute1_value, java.lang.String attribute2_name, java.lang.String attribute2_value, java.lang.String attribute3_name, java.lang.String attribute3_value, java.lang.String attribute4_name, java.lang.String attribute4_value)`
`static void`	`appendOpen(java.io.Writer w, java.lang.String element_name, java.lang.String attribute1_name, java.lang.String attribute1_value, java.lang.String attribute2_name, java.lang.String attribute2_value, java.lang.String attribute3_name, java.lang.String attribute3_value, java.lang.String attribute4_name, java.lang.String attribute4_value, java.lang.String attribute5_name, java.lang.String attribute5_value)`
`static java.util.ArrayList<PhylogenyData>`	`copy(java.util.ArrayList<PhylogenyData> list)` Creates a deep copy of ArrayList of PhylogenyData objects.
`static void`	`drawLine(double x1, double y1, double x2, double y2, java.awt.Graphics g)`
`static java.lang.String`	`replaceIllegalXmlCharacters(java.lang.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(java.io.Writer w,
                               java.lang.String element_name)
                        throws java.io.IOException

Throws:: java.io.IOException

appendElement

public static void appendElement(java.io.Writer w,
                                 java.lang.String element_name,
                                 java.lang.String value)
                          throws java.io.IOException

Throws:: java.io.IOException

appendElement

public static void appendElement(java.io.Writer w,
                                 java.lang.String element_name,
                                 java.lang.String value,
                                 java.lang.String indentation)
                          throws java.io.IOException

Throws:: java.io.IOException

appendElement

public static void appendElement(java.io.Writer w,
                                 java.lang.String element_name,
                                 java.lang.String value,
                                 java.lang.String attribute_name,
                                 java.lang.String attribute_value)
                          throws java.io.IOException

Throws:: java.io.IOException

appendElement

public static void appendElement(java.io.Writer w,
                                 java.lang.String element_name,
                                 java.lang.String value,
                                 java.lang.String attribute_name,
                                 java.lang.String attribute_value,
                                 java.lang.String indentation)
                          throws java.io.IOException

Throws:: java.io.IOException

appendElement

public static void appendElement(java.io.Writer w,
                                 java.lang.String element_name,
                                 java.lang.String value,
                                 java.lang.String attribute1_name,
                                 java.lang.String attribute1_value,
                                 java.lang.String attribute2_name,
                                 java.lang.String attribute2_value,
                                 java.lang.String indentation)
                          throws java.io.IOException

Throws:: java.io.IOException

appendElement

public static void appendElement(java.io.Writer w,
                                 java.lang.String element_name,
                                 java.lang.String value,
                                 java.lang.String attribute1_name,
                                 java.lang.String attribute1_value,
                                 java.lang.String attribute2_name,
                                 java.lang.String attribute2_value)
                          throws java.io.IOException

Throws:: java.io.IOException

appendElement

public static void appendElement(java.io.Writer w,
                                 java.lang.String element_name,
                                 java.lang.String attribute1_name,
                                 java.lang.String attribute1_value,
                                 java.lang.String attribute2_name,
                                 java.lang.String attribute2_value,
                                 java.lang.String attribute3_name,
                                 java.lang.String attribute3_value,
                                 java.lang.String attribute4_name,
                                 java.lang.String attribute4_value,
                                 java.lang.String indentation)
                          throws java.io.IOException

Throws:: java.io.IOException

appendElement

public static void appendElement(java.io.Writer w,
                                 java.lang.String element_name,
                                 java.lang.String value,
                                 java.lang.String attribute1_name,
                                 java.lang.String attribute1_value,
                                 java.lang.String attribute2_name,
                                 java.lang.String attribute2_value,
                                 java.lang.String attribute3_name,
                                 java.lang.String attribute3_value,
                                 java.lang.String attribute4_name,
                                 java.lang.String attribute4_value,
                                 java.lang.String attribute5_name,
                                 java.lang.String attribute5_value,
                                 java.lang.String indentation)
                          throws java.io.IOException

Throws:: java.io.IOException

appendOpen

public static void appendOpen(java.io.Writer w,
                              java.lang.String element_name)
                       throws java.io.IOException

Throws:: java.io.IOException

appendOpen

public static void appendOpen(java.io.Writer w,
                              java.lang.String element_name,
                              java.lang.String attribute_name,
                              java.lang.String attribute_value)
                       throws java.io.IOException

Throws:: java.io.IOException

appendOpen

public static void appendOpen(java.io.Writer w,
                              java.lang.String element_name,
                              java.lang.String attribute1_name,
                              java.lang.String attribute1_value,
                              java.lang.String attribute2_name,
                              java.lang.String attribute2_value)
                       throws java.io.IOException

Throws:: java.io.IOException

appendOpen

public static void appendOpen(java.io.Writer w,
                              java.lang.String element_name,
                              java.lang.String attribute1_name,
                              java.lang.String attribute1_value,
                              java.lang.String attribute2_name,
                              java.lang.String attribute2_value,
                              java.lang.String attribute3_name,
                              java.lang.String attribute3_value)
                       throws java.io.IOException

Throws:: java.io.IOException

appendOpen

public static void appendOpen(java.io.Writer w,
                              java.lang.String element_name,
                              java.lang.String attribute1_name,
                              java.lang.String attribute1_value,
                              java.lang.String attribute2_name,
                              java.lang.String attribute2_value,
                              java.lang.String attribute3_name,
                              java.lang.String attribute3_value,
                              java.lang.String attribute4_name,
                              java.lang.String attribute4_value)
                       throws java.io.IOException

Throws:: java.io.IOException

appendOpen

public static void appendOpen(java.io.Writer w,
                              java.lang.String element_name,
                              java.lang.String attribute1_name,
                              java.lang.String attribute1_value,
                              java.lang.String attribute2_name,
                              java.lang.String attribute2_value,
                              java.lang.String attribute3_name,
                              java.lang.String attribute3_value,
                              java.lang.String attribute4_name,
                              java.lang.String attribute4_value,
                              java.lang.String attribute5_name,
                              java.lang.String attribute5_value)
                       throws java.io.IOException

Throws:: java.io.IOException

copy
```
public static java.util.ArrayList<PhylogenyData> copy(java.util.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,
                            java.awt.Graphics g)

replaceIllegalXmlCharacters

public static java.lang.String replaceIllegalXmlCharacters(java.lang.String value)

Class PhylogenyDataUtil

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

BRANCH_LENGTH_DEFAULT

Constructor Detail

PhylogenyDataUtil

Method Detail

appendClose

appendElement

appendElement

appendElement

appendElement

appendElement

appendElement

appendElement

appendElement

appendOpen

appendOpen

appendOpen

appendOpen

appendOpen

appendOpen

copy

drawLine

replaceIllegalXmlCharacters