SampleInfo (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

All Implemented Interfaces:: Comparable<SampleInfo>

public class SampleInfo
extends Object
implements Comparable<SampleInfo>

Author:: mtaschuk

Constructor Summary

Constructors
Constructor and Description

SampleInfo()

Constructors
Constructor and Description
`SampleInfo()`

Method Summary

Methods
Modifier and Type	Method and Description
`int`	`compareTo(SampleInfo otherSample)`
`String`	`getBarcode()` Get the value of barcode
`String`	`getIndividualNumber()`
`Set<TagValueUnit>`	`getIusAttributes()` Get the value of iusAttributes
`String`	`getIusDescription()` Get the value of iusDescription
`String`	`getIusName()` Get the value of iusName
`boolean`	`getIusSkip()` Get the value of iusSkip
`String`	`getLibrarySizeCode()`
`String`	`getLibrarySourceTemplateType()` Get the value of librarySourceTemplateType
`String`	`getLibraryType()`
`String`	`getName()` Get the value of name
`String`	`getOrganismId()`
`Boolean`	`getPairedEnd()`
`String`	`getParentSample()` Get the value of parentSample
`String`	`getProjectCode()`
`Set<TagValueUnit>`	`getSampleAttributes()` Get the value of sampleAttributes
`String`	`getSampleDescription()` Get the value of sampleDescription
`String`	`getTargetedResequencing()` Get the value of targetedResequencing
`String`	`getTissueOrigin()` Get the value of tissueOrigin
`String`	`getTissuePreparation()` Get the value of tissuePreparation
`String`	`getTissueType()` Get the value of tissueType
`void`	`print(Appendable writer, Metadata metadata)`
`void`	`setBarcode(String barcode)` Set the value of barcode
`void`	`setIndividualNumber(String individualNumber)`
`void`	`setIusAttribute(String tag, String value)` Adds a new ius attribute if the tag does not exist for this ius, or changes the value of an existing ius attribute.
`void`	`setIusAttributes(Set<TagValueUnit> iusAttributes)` Set the value of iusAttributes
`void`	`setIusDescription(String iusDescription)` Set the value of iusDescription
`void`	`setIusName(String iusName)` Set the value of iusName
`void`	`setIusSkip(boolean iusSkip)` Set the value of iusSkip
`void`	`setLibrarySizeCode(String librarySizeCode)` Sets the library size code and sets the 'geo_library_size_code' attribute.
`void`	`setLibrarySourceTemplateType(String librarySourceTemplateType)` Set the value of librarySourceTemplateType sets the 'geo_library_source_template_type' attribute.
`void`	`setLibraryType(String libraryType)` Sets the library type and sets the 'geo_library_type' attribute .
`void`	`setName(String name)` Set the value of name
`void`	`setOrganismId(int organismId)` Sets the organismId, as long as the organism id is over 0.
`void`	`setPairedEnd(Boolean pairedEnd)`
`void`	`setProjectCode(String projectName)`
`void`	`setSampleAttribute(String tag, String value)` Adds a new sample attribute if the tag does not exist for this sample, or changes the value of an existing sample attribute.
`void`	`setSampleAttributes(Set<TagValueUnit> sampleAttributes)` Set the value of sampleAttributes
`void`	`setSampleDescription(String sampleDescription)` Set the value of sampleDescription
`void`	`setTargetedResequencing(String targetedResequencing)` Set the value of targetedResequencing and sets the 'geo_targeted_resequencing' attribute.
`void`	`setTissueOrigin(String tissueOrigin)` Set the value of tissueOrigin and sets the 'geo_tissue_origin' attribute.
`void`	`setTissuePreparation(String tissuePreparation)` Set the value of tissuePreparation, and sets the 'geo_tissue_preparation' attribute.
`void`	`setTissueType(String tissueType)` Set the value of tissueType and sets the 'geo_tissue_type' attribute.
`String`	`toString()`

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

- Constructor Detail
  - SampleInfo
```
public SampleInfo()
```
- Method Detail
  - getIndividualNumber
```
public String getIndividualNumber()
```
  - setIndividualNumber
```
public void setIndividualNumber(String individualNumber)
```
  - getProjectCode
```
public String getProjectCode()
```
  - setProjectCode
```
public void setProjectCode(String projectName)
```
  - getIusSkip
```
public boolean getIusSkip()
```
    Get the value of iusSkip
    
    Returns:
    the value of iusSkip
  - setIusSkip
```
public void setIusSkip(boolean iusSkip)
```
    Set the value of iusSkip
    
    Parameters:
    iusSkip - new value of iusSkip
  - getIusDescription
```
public String getIusDescription()
```
    Get the value of iusDescription
    
    Returns:
    the value of iusDescription
  - setIusDescription
```
public void setIusDescription(String iusDescription)
```
    Set the value of iusDescription
    
    Parameters:
    iusDescription - new value of iusDescription
  - getIusName
```
public String getIusName()
```
    Get the value of iusName
    
    Returns:
    the value of iusName
  - setIusName
```
public void setIusName(String iusName)
```
    Set the value of iusName
    
    Parameters:
    iusName - new value of iusName
  - getSampleDescription
```
public String getSampleDescription()
```
    Get the value of sampleDescription
    
    Returns:
    the value of sampleDescription
  - setSampleDescription
```
public void setSampleDescription(String sampleDescription)
```
    Set the value of sampleDescription
    
    Parameters:
    sampleDescription - new value of sampleDescription
  - getLibrarySourceTemplateType
```
public String getLibrarySourceTemplateType()
```
    Get the value of librarySourceTemplateType
    
    Returns:
    the value of librarySourceTemplateType
  - setLibrarySourceTemplateType
```
public void setLibrarySourceTemplateType(String librarySourceTemplateType)
```
    Set the value of librarySourceTemplateType sets the 'geo_library_source_template_type' attribute.
    
    Parameters:
    librarySourceTemplateType - new value of librarySourceTemplateType
  - getLibrarySizeCode
```
public String getLibrarySizeCode()
```
  - setLibrarySizeCode
```
public void setLibrarySizeCode(String librarySizeCode)
```
    Sets the library size code and sets the 'geo_library_size_code' attribute.
    
    Parameters:
    librarySizeCode -
  - getLibraryType
```
public String getLibraryType()
```
  - setLibraryType
```
public void setLibraryType(String libraryType)
```
    Sets the library type and sets the 'geo_library_type' attribute .
    
    Parameters:
    libraryType -
  - getOrganismId
```
public String getOrganismId()
```
  - setOrganismId
```
public void setOrganismId(int organismId)
```
    Sets the organismId, as long as the organism id is over 0.
    
    Parameters:
    organismId -
  - getPairedEnd
```
public Boolean getPairedEnd()
```
  - setPairedEnd
```
public void setPairedEnd(Boolean pairedEnd)
```
  - getIusAttributes
```
public Set<TagValueUnit> getIusAttributes()
```
    Get the value of iusAttributes
    
    Returns:
    the value of iusAttributes
  - setIusAttribute
```
public void setIusAttribute(String tag,
                   String value)
```
    Adds a new ius attribute if the tag does not exist for this ius, or changes the value of an existing ius attribute.
    
    Parameters:
    tag - the key of the attribute
    value - the value of the attribute
  - setIusAttributes
```
public void setIusAttributes(Set<TagValueUnit> iusAttributes)
```
    Set the value of iusAttributes
    
    Parameters:
    iusAttributes - new value of iusAttributes
  - getSampleAttributes
```
public Set<TagValueUnit> getSampleAttributes()
```
    Get the value of sampleAttributes
    
    Returns:
    the value of sampleAttributes
  - setSampleAttribute
```
public void setSampleAttribute(String tag,
                      String value)
```
    Adds a new sample attribute if the tag does not exist for this sample, or changes the value of an existing sample attribute.
    
    Parameters:
    tag - the key of the attribute
    value - the value of the attribute
  - setSampleAttributes
```
public void setSampleAttributes(Set<TagValueUnit> sampleAttributes)
```
    Set the value of sampleAttributes
    
    Parameters:
    sampleAttributes - new value of sampleAttributes
  - getParentSample
```
public String getParentSample()
```
    Get the value of parentSample
    
    Returns:
    the value of parentSample
  - getBarcode
```
public String getBarcode()
```
    Get the value of barcode
    
    Returns:
    the value of barcode
  - setBarcode
```
public void setBarcode(String barcode)
```
    Set the value of barcode
    
    Parameters:
    barcode - new value of barcode
  - getTargetedResequencing
```
public String getTargetedResequencing()
```
    Get the value of targetedResequencing
    
    Returns:
    the value of targetedResequencing
  - setTargetedResequencing
```
public void setTargetedResequencing(String targetedResequencing)
```
    Set the value of targetedResequencing and sets the 'geo_targeted_resequencing' attribute.
    
    Parameters:
    targetedResequencing - new value of targetedResequencing
  - getTissuePreparation
```
public String getTissuePreparation()
```
    Get the value of tissuePreparation
    
    Returns:
    the value of tissuePreparation
  - setTissuePreparation
```
public void setTissuePreparation(String tissuePreparation)
```
    Set the value of tissuePreparation, and sets the 'geo_tissue_preparation' attribute.
    
    Parameters:
    tissuePreparation - new value of tissuePreparation
  - getTissueOrigin
```
public String getTissueOrigin()
```
    Get the value of tissueOrigin
    
    Returns:
    the value of tissueOrigin
  - setTissueOrigin
```
public void setTissueOrigin(String tissueOrigin)
```
    Set the value of tissueOrigin and sets the 'geo_tissue_origin' attribute.
    
    Parameters:
    tissueOrigin - new value of tissueOrigin
  - getTissueType
```
public String getTissueType()
```
    Get the value of tissueType
    
    Returns:
    the value of tissueType
  - setTissueType
```
public void setTissueType(String tissueType)
```
    Set the value of tissueType and sets the 'geo_tissue_type' attribute.
    
    Parameters:
    tissueType - new value of tissueType
  - getName
```
public String getName()
```
    Get the value of name
    
    Returns:
    the value of name
  - setName
```
public void setName(String name)
```
    Set the value of name
    
    Parameters:
    name - new value of name
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - print
```
public void print(Appendable writer,
         Metadata metadata)
           throws IOException
```
    Throws:
    
    IOException
  - compareTo
```
public int compareTo(SampleInfo otherSample)
```
    Specified by:
    
    compareTo in interface Comparable<SampleInfo>

Class SampleInfo

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SampleInfo

Method Detail

getIndividualNumber

setIndividualNumber

getProjectCode

setProjectCode

getIusSkip

setIusSkip

getIusDescription

setIusDescription

getIusName

setIusName

getSampleDescription

setSampleDescription

getLibrarySourceTemplateType

setLibrarySourceTemplateType

getLibrarySizeCode

setLibrarySizeCode

getLibraryType

setLibraryType

getOrganismId

setOrganismId

getPairedEnd

setPairedEnd

getIusAttributes

setIusAttribute

setIusAttributes

getSampleAttributes

setSampleAttribute

setSampleAttributes

getParentSample

getBarcode

setBarcode

getTargetedResequencing

setTargetedResequencing

getTissuePreparation

setTissuePreparation

getTissueOrigin

setTissueOrigin

getTissueType

setTissueType

getName

setName

toString

print

compareTo