RenderableDomainArchitecture

java.lang.Object
- org.forester.phylogeny.data.DomainArchitecture
- - org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

All Implemented Interfaces:: RenderablePhylogenyData, PhylogenyData

public final class RenderableDomainArchitecture
extends DomainArchitecture
implements RenderablePhylogenyData

Field Summary
- Fields inherited from class org.forester.phylogeny.data.DomainArchitecture
  NHX_SEPARATOR

Constructor Summary

Constructors
Constructor and Description
`RenderableDomainArchitecture(DomainArchitecture domain_structure)`
`RenderableDomainArchitecture(DomainArchitecture domain_structure, java.lang.String node_name)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`java.lang.StringBuffer`	`asSimpleText()`
`java.lang.StringBuffer`	`asText()`
`PhylogenyData`	`copy()` Creates a new PhylogenyData object with identical values as this PhylogenyData.
`ProteinDomain`	`getDomain(int i)`
`java.util.SortedMap<java.math.BigDecimal,ProteinDomain>`	`getDomains()`
`int`	`getNumberOfDomains()`
`java.awt.Dimension`	`getOriginalSize()`
`java.lang.Object`	`getParameter()`
`float`	`getRenderingFactorWidth()`
`java.awt.Dimension`	`getRenderingSize()`
`int`	`getTotalLength()`
`boolean`	`isEqual(PhylogenyData data)` Returns true if the names and the order of the domains match (domain and linker lengths are ignored).
`void`	`render(float x1, float y1, java.awt.Graphics2D g, TreePanel tree_panel, boolean to_pdf)` This can be used to render phylogeny data as graphics (for example, display of the domain structure).
`static void`	`setColorMap(java.util.Map<java.lang.String,java.awt.Color> domain_colors)`
`void`	`setParameter(double e_value_threshold_exp)`
`void`	`setRenderingFactorWidth(float rendering_factor_width)`
`void`	`setRenderingHeight(float rendering_height)`
`java.lang.StringBuffer`	`toNHX()`
`void`	`toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation)` Writes a phyloXML representation of this phylogeny data.

Methods inherited from class org.forester.phylogeny.data.DomainArchitecture
addDomain, setTotalLength, toString

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

- Constructor Detail
  - RenderableDomainArchitecture
```
public RenderableDomainArchitecture(DomainArchitecture domain_structure)
```
  - RenderableDomainArchitecture
```
public RenderableDomainArchitecture(DomainArchitecture domain_structure,
                                    java.lang.String node_name)
```
- Method Detail
  - setColorMap
```
public static void setColorMap(java.util.Map<java.lang.String,java.awt.Color> domain_colors)
```
  - asSimpleText
```
public java.lang.StringBuffer asSimpleText()
```
    Specified by:
    
    asSimpleText in interface PhylogenyData
    
    Overrides:
    
    asSimpleText in class DomainArchitecture
  - asText
```
public java.lang.StringBuffer asText()
```
    Specified by:
    
    asText in interface PhylogenyData
    
    Overrides:
    
    asText in class DomainArchitecture
  - copy
```
public PhylogenyData copy()
```
    Description copied from interface: PhylogenyData
    
    Creates a new PhylogenyData object with identical values as this PhylogenyData. This ~should~ return a deep copy, but not there yet.
    
    Specified by:
    
    copy in interface PhylogenyData
    
    Overrides:
    
    copy in class DomainArchitecture
    
    Returns:
    
    a ~deep~ copy of this PhylogenyData
  - getDomain
```
public ProteinDomain getDomain(int i)
```
    Overrides:
    
    getDomain in class DomainArchitecture
  - getDomains
```
public java.util.SortedMap<java.math.BigDecimal,ProteinDomain> getDomains()
```
    Overrides:
    
    getDomains in class DomainArchitecture
  - getNumberOfDomains
```
public int getNumberOfDomains()
```
    Overrides:
    
    getNumberOfDomains in class DomainArchitecture
  - getOriginalSize
```
public java.awt.Dimension getOriginalSize()
```
    Specified by:
    
    getOriginalSize in interface RenderablePhylogenyData
  - getParameter
```
public java.lang.Object getParameter()
```
    Specified by:
    
    getParameter in interface RenderablePhylogenyData
  - getRenderingFactorWidth
```
public float getRenderingFactorWidth()
```
  - getRenderingSize
```
public java.awt.Dimension getRenderingSize()
```
    Specified by:
    
    getRenderingSize in interface RenderablePhylogenyData
  - getTotalLength
```
public int getTotalLength()
```
    Overrides:
    
    getTotalLength in class DomainArchitecture
  - isEqual
```
public boolean isEqual(PhylogenyData data)
```
    Description copied from class: DomainArchitecture
    
    Returns true if the names and the order of the domains match (domain and linker lengths are ignored).
    
    Specified by:
    
    isEqual in interface PhylogenyData
    
    Overrides:
    
    isEqual in class DomainArchitecture
    
    Returns:
    
    in general, true if and only if all fiels are exactly identical, false otherwise
  - render
```
public void render(float x1,
                   float y1,
                   java.awt.Graphics2D g,
                   TreePanel tree_panel,
                   boolean to_pdf)
```
    Description copied from interface: RenderablePhylogenyData
    
    This can be used to render phylogeny data as graphics (for example, display of the domain structure). In most Renderable implementations this will do nothing (i.e. just return).
    
    Specified by:
    
    render in interface RenderablePhylogenyData
    
    g - the Graphics to render to
  - setParameter
```
public void setParameter(double e_value_threshold_exp)
```
    Specified by:
    
    setParameter in interface RenderablePhylogenyData
  - setRenderingFactorWidth
```
public void setRenderingFactorWidth(float rendering_factor_width)
```
  - setRenderingHeight
```
public void setRenderingHeight(float rendering_height)
```
    Specified by:
    
    setRenderingHeight in interface RenderablePhylogenyData
  - toNHX
```
public java.lang.StringBuffer toNHX()
```
    Specified by:
    
    toNHX in interface PhylogenyData
    
    Overrides:
    
    toNHX in class DomainArchitecture
  - toPhyloXML
```
public void toPhyloXML(java.io.Writer writer,
                       int level,
                       java.lang.String indentation)
                throws java.io.IOException
```
    Description copied from interface: PhylogenyData
    
    Writes a phyloXML representation of this phylogeny data.
    
    Specified by:
    
    toPhyloXML in interface PhylogenyData
    
    Overrides:
    
    toPhyloXML in class DomainArchitecture
    
    Throws:
    
    java.io.IOException

Class RenderableDomainArchitecture

Field Summary

Fields inherited from class org.forester.phylogeny.data.DomainArchitecture

Constructor Summary

Method Summary

Methods inherited from class org.forester.phylogeny.data.DomainArchitecture

Methods inherited from class java.lang.Object

Constructor Detail

RenderableDomainArchitecture

RenderableDomainArchitecture

Method Detail

setColorMap

asSimpleText

asText

copy

getDomain

getDomains

getNumberOfDomains

getOriginalSize

getParameter

getRenderingFactorWidth

getRenderingSize

getTotalLength

isEqual

render

setParameter

setRenderingFactorWidth

setRenderingHeight

toNHX

toPhyloXML