com.github.jessemull.microflexinteger.io

Class PlateWriter

java.lang.Object

java.io.Writer

java.io.PrintWriter

com.github.jessemull.microflexinteger.io.PlateWriter

All Implemented Interfaces:

Closeable, Flushable, Appendable, AutoCloseable

public class PlateWriter
extends PrintWriter

Formats and writes stacks, plates, well sets and wells to an output stream or string. Supports the following formats:

Formats
Plate Map
Result Table
JSON
XML

Result tables and maps are separated using a user defined delimiter or the default tab delimiter.

Example Result Plate Map:

Result
	1	2	3	4	5	6
A	9114	2667	4214	5154	1293	7882
B	8953	4827	5149	9792	2514	6448
C	6328	4896	5130	9655	5120	1485
D	2661	5290	4057	2374	1200	2724

Example Result Table:

Result
Index	Value
A1	4877
A2	5032
A3	6723
B1	4981

Example Result JSON:

  {
   "results" : [ {
     "type" : "Integer",
     "label" : "Example Result",
     "size" : 10,
     "wells" : {
       "A11" : 5645,
       "A2" : 6149,
       "A5" : 5846,
       "D10" : 5895,
       "D2" : 5452,
       "E4" : 5682,
       "E8" : 6116,
       "E9" : 4945,
       "G6" : 5874,
       "H1" : 4911
     }
   } ]
  }
       

Example Result XML:

  <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
  <results>
     <result>
         <type>Double</type>
         <label>Example Result</label>
         <size>3</size>
         <wells>
             <well>
                 <index>A2</index>
                 <value>55873951592640616</value>
             </well>
             <well>
                 <index>A3</index>
                 <value>5303191840271489</value>
             </well>
             <well>
                 <index>A4</index>
                 <value>4902962476222037</value>
             </well>
         </wells>
     </result>
  </results>
       

Example Well JSON:

  {
    "wells" : [ {
      "type" : "Integer",
      "index" : "F8",
      "size" : 24,
      "values" : [ 1511, 2882, 5254 ]
    } ]
  }
        

Example Well Set JSON:

  {
    "wellsets" : [ {
      "type" : "Integer",
      "label" : "Example Well Set",
      "size" : 1,
      "wells" : [ {
        "index" : "A3",
        "values" : [ 4470, 9116, 5215 ]
      } ]
    } ]
  }
        

Example Plate JSON:

  {
    "plates" : [ {
      "type" : "Integer",
      "label" : "Example Plate",
      "descriptor" : "96-Well",
      "rows" : 8,
      "columns" : 12,
      "size" : 1,
      "wellsets" : [ {
        "label" : "Example Well Set",
        "size" : 3,
        "wells" : [ "C5", "D4", "F7" ]
      } ],
      "wells" : [ {
        "index" : "A7",
        "values" : [ 4451, 3453, 5592 ]
      } ]
    } ]
  }
        

Example Stack JSON:

  {
    "stacks" : [ {
      "type" : "Integer",
      "label" : "Example Stack",
      "rows" : 8,
      "columns" : 12,
      "size" : 1,
      "plates" : [ {
        "type" : "Integer",
        "label" : "Example Plate",
        "descriptor" : "96-Well",
        "rows" : 8,
        "columns" : 12,
        "size" : 1,
        "wellsets" : [ {
          "label" : "Example Well Set",
          "size" : 3,
          "wells" : [ "B6", "G1", "G12" ]
        } ],
        "wells" : [ {
          "index" : "A2",
          "values" : [ 3594, 2817, 2100 ]
        } ]
      } ]
    } ]
  }
        

Example Well XML:

  <wells>
     <well>
         <type>Double</type>
         <index>H8</index>
         <size>24</size>
         <values>
             <value>7870</value>
             <value>7296</value>
             <value>3898</value>
         </values>
     </well>
  </wells>
       

Example Well Set XML:

  <wellsets>
     <wellset>
         <type>Double</type>
         <label>Example Well Set</label>
         <size>1</size>
         <wells>
             <well>
                 <index>A11</index>
                 <values>
                     <value>1739</value>
                     <value>5465</value>
                     <value>5412</value>
                 </values>
             </well>
         </wells>
     </wellset>
  </wellsets>
       

Example Plate XML:

  <plates>
     <plate>
         <type>Double</type>
         <label>Example Plate</label>
         <descriptor>96-Well</descriptor>
         <rows>8</rows>
         <columns>12</columns>
         <size>1</size>
         <wellsets>
             <wellset>
                 <label>Example Well Set</label>
                 <size>3</size>
                 <wells>
                     <well>B12</well>
                     <well>E2</well>
                     <well>H8</well>
                 </wells>
             </wellset>
         </wellsets>
         <wells>
             <well>
                 <index>A5</index>
                 <values>
                     <value>1389</value>
                     <value>9246</value>
                     <value>1948</value>
                 </values>
             </well>
         </wells>
     </plate>
  </plates>
       

Example Stack XML:

  <stacks>
     <stack>
         <type>Double</type>
         <label>Example Stack</label>
         <rows>8</rows>
         <columns>12</columns>
         <size>1</size>
         <plates>
             <plate>
                 <type>Double</type>
                 <label>Example Plate</label>
                 <descriptor>96-Well</descriptor>
                 <rows>8</rows>
                 <columns>12</columns>
                 <size>1</size>
                 <wellsets>
                     <wellset>
                         <label>Example Well Set</label>
                         <size>3</size>
                         <wells>
                             <well>B7</well>
                             <well>H2</well>
                             <well>H3</well>
                         </wells>
                     </wellset>
                 </wellsets>
                 <wells>
                     <well>
                         <index>A2</index>
                         <values>
                             <value>1303</value>
                             <value>5321</value>
                             <value>2808</value>
                         </values>
                     </well>
                 </wells>
             </plate>
         </plates>
     </stack>
  </stacks>
       

Author:

Jesse L. Mull

Field Summary

Fields inherited from class java.io.PrintWriter

out

Fields inherited from class java.io.Writer

lock

Constructor Summary

Constructors

Constructor and Description
PlateWriter(File file) Creates a new PlateWriterInteger without automatic line flushing using the specified file.
PlateWriter(File file, String csn) Creates a new PlateWriterInteger without automatic line flushing using the specified file and character set.
PlateWriter(OutputStream out) Creates a new PlateWriterInteger, without automatic line flushing using the OutputStream.
PlateWriter(OutputStream out, boolean autoFlush) Creates a new PlateWriterInteger with automatic line flushing, using the OutputStream.
PlateWriter(String fileName) Creates a new PlateWriterInteger without automatic line flushing using the specified file name.
PlateWriter(String fileName, String csn) Creates a new PlateWriterInteger without automatic line flushing using the specified file name and character set.
PlateWriter(Writer out) Creates a new PlateWriterInteger without automatic line flushing using the writer.
PlateWriter(Writer out, boolean autoFlush) Creates a new PlateWriterInteger with automatic line flushing using the writer.

Method Summary

Modifier and Type	Method and Description
String	getDelimiter() Returns the delimiter.
void	plateToJSON(Collection<Plate> collection) Prints the collection of plates in a JSON format.
void	plateToJSON(Plate plate) Prints the plate values in a JSON format.
void	plateToJSON(Plate[] array) Prints the array of plates in a JSON format.
String	plateToJSONAsString(Collection<Plate> collection) Returns a string containing the collection of plates in a JSON format.
String	plateToJSONAsString(Plate plate) Returns a string containing the plate values in a JSON format.
String	plateToJSONAsString(Plate[] array) Returns a string containing the array of plates in a JSON format.
void	plateToXML(Collection<Plate> collection) Prints the collection of plates in an XML format.
void	plateToXML(Plate plate) Prints the plate values in an XML format.
void	plateToXML(Plate[] array) Prints the array of plates in an XML format.
String	plateToXMLAsString(Collection<Plate> collection) Returns a string containing the collection of plates in an XML format.
String	plateToXMLAsString(Plate plate) Returns a string containing the plate values in an XML format.
String	plateToXMLAsString(Plate[] array) Returns a string containing the array of plates in an XML format.
void	printMapResult(Map<Well,Integer> data, int rows, int columns, String label) Prints the plate map.
String	printMapResultAsString(Map<Well,Integer> data, int rows, int columns, String label) Returns a string containing the plate map.
void	printTableResult(Map<Well,Integer> data, String label) Prints the well value pairs as a delimiter separated table.
String	printTableResultAsString(Map<Well,Integer> data, String label) Resturns a string holding the well value pairs as a delimiter separated table.
void	printXMLStack(StackListXML stackList) Prints the stack as an XML object.
String	printXMLStackAsString(StackListXML stackList) Returns a string containing the stack list as an XML object.
void	resultToJSON(List<Map<Well,Integer>> data) Prints the well value pairs in a JSON format for each data set.
void	resultToJSON(List<Map<Well,Integer>> data, List<String> labels) Prints the well value pairs in a JSON format for each data set using the specified labels.
void	resultToJSON(Map<Well,Integer> data) Prints the well value pairs in a JSON format.
void	resultToJSON(Map<Well,Integer> data, String label) Prints the well value pairs in a JSON format using the label.
String	resultToJSONAsString(List<Map<Well,Integer>> data) Returns a string containing the well value pairs in a JSON format for each data set.
String	resultToJSONAsString(List<Map<Well,Integer>> data, List<String> labels) Returns a string containing the well value pairs in a JSON format for each data set using the specified labels.
String	resultToJSONAsString(Map<Well,Integer> data) Returns a string containing the well value pairs in a JSON format.
String	resultToJSONAsString(Map<Well,Integer> data, String label) Returns a string containing the well value pairs in a JSON format using the label.
void	resultToPlateMap(List<Map<Well,Integer>> data, int type) Prints the plate map for each data set in the list.
void	resultToPlateMap(List<Map<Well,Integer>> data, int rows, int columns) Prints the plate map for each data set in the list.
void	resultToPlateMap(List<Map<Well,Integer>> data, int rows, int columns, List<String> labels) Prints the plate map for each data set in the list.
void	resultToPlateMap(List<Map<Well,Integer>> data, int type, List<String> labels) Prints the plate map for each data set in the list.
void	resultToPlateMap(Map<Well,Integer> data, int type) Prints the plate map.
void	resultToPlateMap(Map<Well,Integer> data, int rows, int columns) Prints the plate map.
void	resultToPlateMap(Map<Well,Integer> data, int rows, int columns, String label) Prints the plate map.
void	resultToPlateMap(Map<Well,Integer> data, int type, String label) Prints the plate map.
String	resultToPlateMapAsString(List<Map<Well,Integer>> data, int type) Returns a string holding the plate map for each data set in the list.
String	resultToPlateMapAsString(List<Map<Well,Integer>> data, int rows, int columns) Returns a string holding the plate map for each data set in the list.
String	resultToPlateMapAsString(List<Map<Well,Integer>> data, int rows, int columns, List<String> labels) Returns a string containing the plate map for each data set in the list.
String	resultToPlateMapAsString(List<Map<Well,Integer>> data, int type, List<String> labels) Returns a string containing the plate map for each data set in the list.
String	resultToPlateMapAsString(Map<Well,Integer> data, int type) Returns a string containing the plate map.
String	resultToPlateMapAsString(Map<Well,Integer> data, int rows, int columns) Returns a string holding the plate map.
String	resultToPlateMapAsString(Map<Well,Integer> data, int rows, int columns, String label) Returns a string containing the plate map.
String	resultToPlateMapAsString(Map<Well,Integer> data, int type, String label) Returns a string holding the plate map.
void	resultToTable(List<Map<Well,Integer>> data) Prints each set of well value pairs as a delimiter separated table.
void	resultToTable(List<Map<Well,Integer>> data, List<String> labels) Prints the well value pairs as a delimiter separated table.
void	resultToTable(Map<Well,Integer> data) Prints the well value pairs as a delimiter separated table.
void	resultToTable(Map<Well,Integer> data, String label) Prints the well value pairs as a delimiter separated table.
String	resultToTableAsString(List<Map<Well,Integer>> data) Returns a string containing each set of well value pairs as a delimiter separated table.
String	resultToTableAsString(List<Map<Well,Integer>> data, List<String> labels) Returns a string containing the well value pairs as a delimiter separated table.
String	resultToTableAsString(Map<Well,Integer> data) Returns a string containing the well value pairs as a delimiter separated table.
String	resultToTableAsString(Map<Well,Integer> data, String label) Returns a string containing the well value pairs as a delimiter separated table.
void	resultToXML(Collection<Map<Well,Integer>> collection) Prints the collection of result values in an XML format.
void	resultToXML(Collection<Map<Well,Integer>> collection, List<String> labels) Prints the collection of result values in an XML format.
void	resultToXML(Map<Well,Integer> map) Prints the well result values in an XML format.
void	resultToXML(Map<Well,Integer> map, String label) Prints the well result values in an XML format.
String	resultToXMLAsString(Collection<Map<Well,Integer>> collection) Returns a string containing the collection of result values in an XML format.
String	resultToXMLAsString(Collection<Map<Well,Integer>> collection, List<String> labels) Returns a string containing the collection of result values in an XML format.
String	resultToXMLAsString(Map<Well,Integer> map) Returns a string containing the result values in an XML format.
String	resultToXMLAsString(Map<Well,Integer> map, String label) Returns a string containing the result values in an XML format.
void	setDelimiter(String delimiter) Sets the delimiter for the plate writer.
void	setToJSON(Collection<WellSet> collection) Prints the collection of well sets in a JSON format.
void	setToJSON(WellSet set) Prints the well set values in a JSON format.
void	setToJSON(WellSet[] array) Prints the well set values in a JSON format.
String	setToJSONAsString(Collection<WellSet> collection) Returns a string containing the collection of well sets in a JSON format.
String	setToJSONAsString(WellSet set) Returns a string containing the well set values in a JSON format.
String	setToJSONAsString(WellSet[] array) Returns a string containing the well set values in a JSON format.
void	setToXML(Collection<WellSet> collection) Prints the collection of well sets in an XML format.
void	setToXML(WellSet set) Prints the well set values in an XML format.
void	setToXML(WellSet[] array) Prints the well set values in an XML format.
String	setToXMLAsString(Collection<WellSet> collection) Returns a string containing the collection of well sets in an XML format.
String	setToXMLAsString(WellSet set) Returns a string containing the well set values in an XML format.
String	setToXMLAsString(WellSet[] array) Returns a string containing the well set values in an XML format.
void	stackToJSON(Collection<Stack> collection) Prints the collection of plate stacks in a JSON format.
void	stackToJSON(Stack stack) Prints the plate stack in a JSON format.
void	stackToJSON(Stack[] array) Prints the array of plate stacks in a JSON format.
String	stackToJSONAsString(Collection<Stack> collection) Returns a string containing the collection of plate stacks in a JSON format.
String	stackToJSONAsString(Stack stack) Returns a string containing the plate stack in a JSON format.
String	stackToJSONAsString(Stack[] array) Prints the array of plate stacks in a JSON format.
void	stackToXML(Collection<Stack> collection) Prints the collection of plate stacks in an XML format.
void	stackToXML(Stack stack) Prints the plate stack in an XML format.
void	stackToXML(Stack[] array) Prints the array of plate stacks in an XML format.
String	stackToXMLAsString(Collection<Stack> collection) Returns a string containing the collection of plate stacks in an XML format.
String	stackToXMLAsString(Stack stack) Returns a string containing the plate stack in an XML format.
String	stackToXMLAsString(Stack[] array) Returns a string containing the array of plate stacks in an XML format.
void	wellToJSON(Collection<Well> collection) Prints the collection of wells in a JSON format.
void	wellToJSON(Well well) Prints the well values in a JSON format.
void	wellToJSON(Well[] array) Prints the wells values in the array in a JSON format.
String	wellToJSONAsString(Collection<Well> collection) Returns a string containing the collection of wells in a JSON format.
String	wellToJSONAsString(Well well) Returns a string containing the well values in a JSON format.
String	wellToJSONAsString(Well[] array) Returns a string containing the well values in the array in a JSON format.
void	wellToXML(Collection<Well> collection) Prints the collection of well values in an XML format.
void	wellToXML(Well well) Prints the well values in an XML format.
void	wellToXML(Well[] array) Prints the well values in the array in an XML format.
String	wellToXMLAsString(Collection<Well> collection) Returns a string containing the collection of well values in an XML format.
String	wellToXMLAsString(Well well) Returns a string containing the well values in an XML format.
String	wellToXMLAsString(Well[] array) Prints the well values in the array in an XML format.

Methods inherited from class java.io.PrintWriter

append, append, append, checkError, clearError, close, flush, format, format, print, print, print, print, print, print, print, print, print, printf, printf, println, println, println, println, println, println, println, println, println, println, setError, write, write, write, write, write

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PlateWriter

public PlateWriter(File file)
            throws FileNotFoundException

Creates a new PlateWriterInteger without automatic line flushing using the specified file.

Parameters:

File - the output file

Throws:

FileNotFoundException

PlateWriter

public PlateWriter(File file,
                   String csn)
            throws FileNotFoundException,
                   UnsupportedEncodingException

Creates a new PlateWriterInteger without automatic line flushing using the specified file and character set.

Parameters:

File - the output file

String - the character set

Throws:

UnsupportedEncodingException

FileNotFoundException

PlateWriter

public PlateWriter(OutputStream out)

Creates a new PlateWriterInteger, without automatic line flushing using the OutputStream.

Parameters:

OutputStream - the output stream

PlateWriter

public PlateWriter(OutputStream out,
                   boolean autoFlush)

Creates a new PlateWriterInteger with automatic line flushing, using the OutputStream.

Parameters:

OutputStream - the output stream

boolean - sets automatic flush when true

PlateWriter

public PlateWriter(String fileName)
            throws FileNotFoundException

Creates a new PlateWriterInteger without automatic line flushing using the specified file name.

Parameters:

String - the file name

Throws:

FileNotFoundException

PlateWriter

public PlateWriter(String fileName,
                   String csn)
            throws FileNotFoundException,
                   UnsupportedEncodingException

Creates a new PlateWriterInteger without automatic line flushing using the specified file name and character set.

Parameters:

String - the file name

String - the character set

Throws:

UnsupportedEncodingException

FileNotFoundException

PlateWriter

public PlateWriter(Writer out)

Creates a new PlateWriterInteger without automatic line flushing using the writer.

Parameters:

Writer - the writer

PlateWriter

public PlateWriter(Writer out,
                   boolean autoFlush)

Creates a new PlateWriterInteger with automatic line flushing using the writer.

Parameters:

Writer - the writer

boolean - sets auto flush when true

Method Detail

resultToPlateMap

public void resultToPlateMap(Map<Well,Integer> data,
                             int type)
                      throws FileNotFoundException,
                             UnsupportedEncodingException

Prints the plate map.

Parameters:

Map - Integer> the data set

int - the plate type

Throws:

UnsupportedEncodingException

FileNotFoundException

resultToPlateMapAsString

public String resultToPlateMapAsString(Map<Well,Integer> data,
                                       int type)

Returns a string containing the plate map.

Parameters:

Map - Integer> the data set

int - the plate type

resultToPlateMap

public void resultToPlateMap(List<Map<Well,Integer>> data,
                             int type)
                      throws FileNotFoundException,
                             UnsupportedEncodingException

Prints the plate map for each data set in the list.

Parameters:

List - Integer>> list of data sets

int - the plate type

Throws:

UnsupportedEncodingException

FileNotFoundException

resultToPlateMapAsString

public String resultToPlateMapAsString(List<Map<Well,Integer>> data,
                                       int type)

Returns a string holding the plate map for each data set in the list.

Parameters:

List - Integer>> list of data sets

int - the plate type

Returns:

the plate maps

resultToPlateMap

public void resultToPlateMap(Map<Well,Integer> data,
                             int rows,
                             int columns)
                      throws FileNotFoundException,
                             UnsupportedEncodingException

Prints the plate map.

Parameters:

Map - Integer> the data set

int - number of rows

int - number of columns

Throws:

UnsupportedEncodingException

FileNotFoundException

resultToPlateMapAsString

public String resultToPlateMapAsString(Map<Well,Integer> data,
                                       int rows,
                                       int columns)

Returns a string holding the plate map.

Parameters:

Map - Integer> the data set

int - number of rows

int - number of columns

Returns:

the plate map

resultToPlateMap

public void resultToPlateMap(List<Map<Well,Integer>> data,
                             int rows,
                             int columns)
                      throws FileNotFoundException,
                             UnsupportedEncodingException

Prints the plate map for each data set in the list.

Parameters:

List - Integer>> list of data sets

int - number of rows

int - number of columns

Throws:

UnsupportedEncodingException

FileNotFoundException

resultToPlateMapAsString

public String resultToPlateMapAsString(List<Map<Well,Integer>> data,
                                       int rows,
                                       int columns)

Returns a string holding the plate map for each data set in the list.

Parameters:

List - Integer>> list of data sets

int - number of rows

int - number of columns

Returns:

the plate maps

resultToPlateMap

public void resultToPlateMap(Map<Well,Integer> data,
                             int type,
                             String label)
                      throws FileNotFoundException,
                             UnsupportedEncodingException

Prints the plate map.

Parameters:

Map - Integer> the data set

int - the plate type

String - the data set label

Throws:

UnsupportedEncodingException

FileNotFoundException

resultToPlateMapAsString

public String resultToPlateMapAsString(Map<Well,Integer> data,
                                       int type,
                                       String label)

Returns a string holding the plate map.

Parameters:

Map - Integer> the data set

int - the plate type

String - the data set label

Returns:

the plate map

resultToPlateMap

public void resultToPlateMap(List<Map<Well,Integer>> data,
                             int type,
                             List<String> labels)
                      throws FileNotFoundException,
                             UnsupportedEncodingException

Prints the plate map for each data set in the list.

Parameters:

List - Integer>> list of data sets

int - the plate type

List - list of data set labels

Throws:

UnsupportedEncodingException

FileNotFoundException

resultToPlateMapAsString

public String resultToPlateMapAsString(List<Map<Well,Integer>> data,
                                       int type,
                                       List<String> labels)

Returns a string containing the plate map for each data set in the list.

Parameters:

List - Integer>> list of data sets

int - the plate type

List - list of data set labels

Returns:

the plate maps

resultToPlateMap

public void resultToPlateMap(Map<Well,Integer> data,
                             int rows,
                             int columns,
                             String label)
                      throws FileNotFoundException,
                             UnsupportedEncodingException

Prints the plate map.

Parameters:

Map - Integer> the data set

int - number of rows

int - number of columns

String - the data set label

Throws:

UnsupportedEncodingException

FileNotFoundException

resultToPlateMapAsString

public String resultToPlateMapAsString(Map<Well,Integer> data,
                                       int rows,
                                       int columns,
                                       String label)

Returns a string containing the plate map.

Parameters:

Map - Integer> the data set

int - number of rows

int - number of columns

String - the data set label

Returns:

the plate map

resultToPlateMap

public void resultToPlateMap(List<Map<Well,Integer>> data,
                             int rows,
                             int columns,
                             List<String> labels)
                      throws FileNotFoundException,
                             UnsupportedEncodingException

Prints the plate map for each data set in the list.

Parameters:

List - Integer>> list of data sets

int - number of rows

int - number of columns

List - list of data set labels

Throws:

UnsupportedEncodingException

FileNotFoundException

resultToPlateMapAsString

public String resultToPlateMapAsString(List<Map<Well,Integer>> data,
                                       int rows,
                                       int columns,
                                       List<String> labels)

Returns a string containing the plate map for each data set in the list.

Parameters:

List - Integer>> list of data sets

int - number of rows

int - number of columns

List - list of data set labels

Returns:

the plate maps

printMapResult

public void printMapResult(Map<Well,Integer> data,
                           int rows,
                           int columns,
                           String label)
                    throws FileNotFoundException,
                           UnsupportedEncodingException

Prints the plate map.

Parameters:

Map - Integer> the data set

int - number of rows

int - number of columns

String - the data set label

Throws:

FileNotFoundException

UnsupportedEncodingException

printMapResultAsString

public String printMapResultAsString(Map<Well,Integer> data,
                                     int rows,
                                     int columns,
                                     String label)

Returns a string containing the plate map.

Parameters:

Map - Integer> the data set

int - number of rows

int - number of columns

String - the data set label

Returns:

the plate map

resultToTable

public void resultToTable(Map<Well,Integer> data)
                   throws FileNotFoundException,
                          UnsupportedEncodingException

Prints the well value pairs as a delimiter separated table.

Parameters:

Map - Integer> the data set

Throws:

UnsupportedEncodingException

FileNotFoundException

resultToTableAsString

public String resultToTableAsString(Map<Well,Integer> data)

Returns a string containing the well value pairs as a delimiter separated table.

Parameters:

Map - Integer> the data set

Returns:

the table

resultToTable

public void resultToTable(List<Map<Well,Integer>> data)
                   throws FileNotFoundException,
                          UnsupportedEncodingException

Prints each set of well value pairs as a delimiter separated table.

Parameters:

List - Integer>> list of data sets

Throws:

UnsupportedEncodingException

FileNotFoundException

resultToTableAsString

public String resultToTableAsString(List<Map<Well,Integer>> data)

Returns a string containing each set of well value pairs as a delimiter separated table.

Parameters:

List - Integer>> list of data sets

Returns:

the tables

resultToTable

public void resultToTable(Map<Well,Integer> data,
                          String label)
                   throws FileNotFoundException,
                          UnsupportedEncodingException

Prints the well value pairs as a delimiter separated table.

Parameters:

Map - Integer> the data set

String - the data set label

Throws:

UnsupportedEncodingException

FileNotFoundException

resultToTableAsString

public String resultToTableAsString(Map<Well,Integer> data,
                                    String label)

Returns a string containing the well value pairs as a delimiter separated table.

Parameters:

Map - Integer> the data set

String - the data set label

Returns:

the table

resultToTable

public void resultToTable(List<Map<Well,Integer>> data,
                          List<String> labels)
                   throws FileNotFoundException,
                          UnsupportedEncodingException

Prints the well value pairs as a delimiter separated table.

Parameters:

List - Integer>> list of data sets

List - list of data set labels

Throws:

UnsupportedEncodingException

FileNotFoundException

resultToTableAsString

public String resultToTableAsString(List<Map<Well,Integer>> data,
                                    List<String> labels)

Returns a string containing the well value pairs as a delimiter separated table.

Parameters:

List - Integer>> list of data sets

List - list of data set labels

Returns:

the tables

printTableResult

public void printTableResult(Map<Well,Integer> data,
                             String label)
                      throws FileNotFoundException,
                             UnsupportedEncodingException

Prints the well value pairs as a delimiter separated table.

Parameters:

Map - Integer> the data set

String - the data set label

Throws:

UnsupportedEncodingException

FileNotFoundException

printTableResultAsString

public String printTableResultAsString(Map<Well,Integer> data,
                                       String label)

Resturns a string holding the well value pairs as a delimiter separated table.

Parameters:

Map - Integer> the data set

String - the data set label

Returns:

the table string

resultToJSON

public void resultToJSON(Map<Well,Integer> data)
                  throws IOException

Prints the well value pairs in a JSON format.

Parameters:

Map - Integer> the data set

Throws:

IOException

resultToJSONAsString

public String resultToJSONAsString(Map<Well,Integer> data)
                            throws com.fasterxml.jackson.core.JsonProcessingException

Returns a string containing the well value pairs in a JSON format.

Parameters:

Map - Integer> the data set

Returns:

the JSON formatted result

Throws:

com.fasterxml.jackson.core.JsonProcessingException

resultToJSON

public void resultToJSON(List<Map<Well,Integer>> data)
                  throws IOException

Prints the well value pairs in a JSON format for each data set.

Parameters:

List - Integer>> the list of data sets

Throws:

IOException

resultToJSONAsString

public String resultToJSONAsString(List<Map<Well,Integer>> data)
                            throws com.fasterxml.jackson.core.JsonProcessingException

Returns a string containing the well value pairs in a JSON format for each data set.

Parameters:

List - Integer>> the list of data sets

Returns:

the JSON formatted results

Throws:

com.fasterxml.jackson.core.JsonProcessingException

resultToJSON

public void resultToJSON(Map<Well,Integer> data,
                         String label)
                  throws IOException

Prints the well value pairs in a JSON format using the label.

Parameters:

Map - Integer> the data set

String - the data set label

Throws:

IOException

resultToJSONAsString

public String resultToJSONAsString(Map<Well,Integer> data,
                                   String label)
                            throws IOException

Returns a string containing the well value pairs in a JSON format using the label.

Parameters:

Map - Integer> the data set

String - the data set label

Returns:

the JSON formatted result

Throws:

IOException

resultToJSON

public void resultToJSON(List<Map<Well,Integer>> data,
                         List<String> labels)
                  throws IOException

Prints the well value pairs in a JSON format for each data set using the specified labels.

Parameters:

List - Integer>> the list of data sets

List - the list of data set labels

Throws:

IOException

resultToJSONAsString

public String resultToJSONAsString(List<Map<Well,Integer>> data,
                                   List<String> labels)
                            throws com.fasterxml.jackson.core.JsonProcessingException

Returns a string containing the well value pairs in a JSON format for each data set using the specified labels.

Parameters:

List - Integer>> the list of data sets

List - the list of data set labels

Returns:

the JSON formatted results

Throws:

com.fasterxml.jackson.core.JsonProcessingException

wellToJSON

public void wellToJSON(Well well)
                throws IOException

Prints the well values in a JSON format.

Parameters:

Well - the well

Throws:

IOException

wellToJSONAsString

public String wellToJSONAsString(Well well)
                          throws com.fasterxml.jackson.core.JsonProcessingException

Returns a string containing the well values in a JSON format.

Parameters:

Well - the well

Returns:

the JSON formatted well

Throws:

com.fasterxml.jackson.core.JsonProcessingException

wellToJSON

public void wellToJSON(Collection<Well> collection)
                throws IOException

Prints the collection of wells in a JSON format.

Parameters:

Collection - the collection of wells

Throws:

IOException

wellToJSONAsString

public String wellToJSONAsString(Collection<Well> collection)
                          throws com.fasterxml.jackson.core.JsonProcessingException

Returns a string containing the collection of wells in a JSON format.

Parameters:

Collection - the collection of wells

Returns:

the JSON formatted wells

Throws:

com.fasterxml.jackson.core.JsonProcessingException

wellToJSON

public void wellToJSON(Well[] array)
                throws IOException

Prints the wells values in the array in a JSON format.

Parameters:

WellInteger[] - the array of wells

Throws:

IOException

wellToJSONAsString

public String wellToJSONAsString(Well[] array)
                          throws com.fasterxml.jackson.core.JsonProcessingException

Returns a string containing the well values in the array in a JSON format.

Parameters:

WellInteger[] - the array of wells

Returns:

the JSON formatted wells

Throws:

com.fasterxml.jackson.core.JsonProcessingException

setToJSON

public void setToJSON(WellSet set)
               throws IOException

Prints the well set values in a JSON format.

Parameters:

WellSet - the well set

Throws:

IOException

setToJSONAsString

public String setToJSONAsString(WellSet set)
                         throws com.fasterxml.jackson.core.JsonProcessingException

Returns a string containing the well set values in a JSON format.

Parameters:

WellSet - the well set

Returns:

the JSON formatted set

Throws:

com.fasterxml.jackson.core.JsonProcessingException

setToJSON

public void setToJSON(Collection<WellSet> collection)
               throws IOException

Prints the collection of well sets in a JSON format.

Parameters:

Collection - the collection of well sets

Throws:

IOException

setToJSONAsString

public String setToJSONAsString(Collection<WellSet> collection)
                         throws com.fasterxml.jackson.core.JsonProcessingException

Returns a string containing the collection of well sets in a JSON format.

Parameters:

Collection - the collection of well sets

Returns:

the JSON formatted set

Throws:

com.fasterxml.jackson.core.JsonProcessingException

setToJSON

public void setToJSON(WellSet[] array)
               throws IOException

Prints the well set values in a JSON format.

Parameters:

WellSetInteger[] - the array of well sets

Throws:

IOException

setToJSONAsString

public String setToJSONAsString(WellSet[] array)
                         throws com.fasterxml.jackson.core.JsonProcessingException

Returns a string containing the well set values in a JSON format.

Parameters:

WellSetInteger[] - the array of well sets

Returns:

the JSON formatted set

Throws:

com.fasterxml.jackson.core.JsonProcessingException

plateToJSON

public void plateToJSON(Plate plate)
                 throws IOException

Prints the plate values in a JSON format.

Parameters:

Plate - the plate

Throws:

IOException

plateToJSONAsString

public String plateToJSONAsString(Plate plate)
                           throws com.fasterxml.jackson.core.JsonProcessingException

Returns a string containing the plate values in a JSON format.

Parameters:

Plate - the plate

Returns:

the JSON formatted plate

Throws:

com.fasterxml.jackson.core.JsonProcessingException

plateToJSON

public void plateToJSON(Collection<Plate> collection)
                 throws IOException

Prints the collection of plates in a JSON format.

Parameters:

Collection - the collection of plates

Throws:

IOException

plateToJSONAsString

public String plateToJSONAsString(Collection<Plate> collection)
                           throws com.fasterxml.jackson.core.JsonProcessingException

Returns a string containing the collection of plates in a JSON format.

Parameters:

Collection - the collection of plates

Returns:

the JSON formatted plates

Throws:

com.fasterxml.jackson.core.JsonProcessingException

plateToJSON

public void plateToJSON(Plate[] array)
                 throws IOException

Prints the array of plates in a JSON format.

Parameters:

PlateInteger[] - the array of plates

Throws:

IOException

plateToJSONAsString

public String plateToJSONAsString(Plate[] array)
                           throws com.fasterxml.jackson.core.JsonProcessingException

Returns a string containing the array of plates in a JSON format.

Parameters:

PlateInteger[] - the array of plates

Throws:

com.fasterxml.jackson.core.JsonProcessingException

stackToJSON

public void stackToJSON(Stack stack)
                 throws IOException

Prints the plate stack in a JSON format.

Parameters:

Stack - the plate stack

Throws:

IOException

stackToJSONAsString

public String stackToJSONAsString(Stack stack)
                           throws com.fasterxml.jackson.core.JsonProcessingException

Returns a string containing the plate stack in a JSON format.

Parameters:

Stack - the plate stack

Returns:

the JSON formatted stack

Throws:

com.fasterxml.jackson.core.JsonProcessingException

stackToJSON

public void stackToJSON(Collection<Stack> collection)
                 throws IOException

Prints the collection of plate stacks in a JSON format.

Parameters:

Collection - the collection of plate stacks

Throws:

IOException

stackToJSONAsString

public String stackToJSONAsString(Collection<Stack> collection)
                           throws com.fasterxml.jackson.core.JsonProcessingException

Returns a string containing the collection of plate stacks in a JSON format.

Parameters:

Collection - the collection of plate stacks

Returns:

the JSON formatted stacks

Throws:

com.fasterxml.jackson.core.JsonProcessingException

stackToJSON

public void stackToJSON(Stack[] array)
                 throws IOException

Prints the array of plate stacks in a JSON format.

Parameters:

StackInteger[] - the array of plate stacks

Throws:

IOException

stackToJSONAsString

public String stackToJSONAsString(Stack[] array)
                           throws com.fasterxml.jackson.core.JsonProcessingException

Prints the array of plate stacks in a JSON format.

Parameters:

StackInteger[] - the array of plate stacks

Returns:

the JSON formatted stacks

Throws:

com.fasterxml.jackson.core.JsonProcessingException

resultToXML

public void resultToXML(Map<Well,Integer> map)
                 throws IOException,
                        ParserConfigurationException,
                        TransformerException

Prints the well result values in an XML format.

Parameters:

Map - Integer> the result map

Throws:

IOException

ParserConfigurationException

TransformerException

resultToXMLAsString

public String resultToXMLAsString(Map<Well,Integer> map)

Returns a string containing the result values in an XML format.

Parameters:

Map - Integer> the result map

Returns:

the XML formatted result

resultToXML

public void resultToXML(Map<Well,Integer> map,
                        String label)
                 throws IOException,
                        ParserConfigurationException,
                        TransformerException

Prints the well result values in an XML format.

Parameters:

Map - Integer> the result map

String - the label

Throws:

IOException

ParserConfigurationException

TransformerException

resultToXMLAsString

public String resultToXMLAsString(Map<Well,Integer> map,
                                  String label)

Returns a string containing the result values in an XML format.

Parameters:

Map - Integer> the result map

String - the label

Returns:

the XML formatted result values

resultToXML

public void resultToXML(Collection<Map<Well,Integer>> collection)
                 throws IOException,
                        TransformerException,
                        ParserConfigurationException

Prints the collection of result values in an XML format.

Parameters:

Collection - the collection of well sets

Throws:

IOException

TransformerException

ParserConfigurationException

resultToXMLAsString

public String resultToXMLAsString(Collection<Map<Well,Integer>> collection)

Returns a string containing the collection of result values in an XML format.

Parameters:

Collection - the collection of well sets

Returns:

the XML formatted result values

resultToXML

public void resultToXML(Collection<Map<Well,Integer>> collection,
                        List<String> labels)
                 throws IOException,
                        TransformerException,
                        ParserConfigurationException

Prints the collection of result values in an XML format.

Parameters:

Collection - the collection of well sets

List - result labels

Throws:

IOException

TransformerException

ParserConfigurationException

resultToXMLAsString

public String resultToXMLAsString(Collection<Map<Well,Integer>> collection,
                                  List<String> labels)

Returns a string containing the collection of result values in an XML format.

Parameters:

Collection - the collection of well sets

List - result labels

Returns:

the XML formatted result values

wellToXML

public void wellToXML(Well well)
               throws IOException,
                      ParserConfigurationException,
                      TransformerException

Prints the well values in an XML format.

Parameters:

Well - the set

Throws:

IOException

ParserConfigurationException

TransformerException

wellToXMLAsString

public String wellToXMLAsString(Well well)

Returns a string containing the well values in an XML format.

Parameters:

Well - the set

Returns:

the XML formatted well values

wellToXML

public void wellToXML(Collection<Well> collection)
               throws IOException,
                      TransformerException,
                      ParserConfigurationException

Prints the collection of well values in an XML format.

Parameters:

Collection - the collection of wells

Throws:

IOException

TransformerException

ParserConfigurationException

wellToXMLAsString

public String wellToXMLAsString(Collection<Well> collection)
                         throws IOException,
                                TransformerException,
                                ParserConfigurationException

Returns a string containing the collection of well values in an XML format.

Parameters:

Collection - the collection of wells

Returns:

the XML formatted wells

Throws:

IOException

TransformerException

ParserConfigurationException

wellToXML

public void wellToXML(Well[] array)
               throws IOException,
                      ParserConfigurationException,
                      TransformerException

Prints the well values in the array in an XML format.

Parameters:

WellInteger[] - the array of wells

Throws:

IOException

ParserConfigurationException

TransformerException

wellToXMLAsString

public String wellToXMLAsString(Well[] array)
                         throws IOException,
                                ParserConfigurationException,
                                TransformerException

Prints the well values in the array in an XML format.

Parameters:

WellInteger[] - the array of wells

Returns:

the XML formatted wells

Throws:

IOException

ParserConfigurationException

TransformerException

setToXML

public void setToXML(WellSet set)
              throws IOException,
                     ParserConfigurationException,
                     TransformerException

Prints the well set values in an XML format.

Parameters:

WellSet - the well set

Throws:

IOException

ParserConfigurationException

TransformerException

setToXMLAsString

public String setToXMLAsString(WellSet set)

Returns a string containing the well set values in an XML format.

Parameters:

WellSet - the well set

Returns:

the XML formatted well sets

setToXML

public void setToXML(Collection<WellSet> collection)
              throws IOException,
                     TransformerException,
                     ParserConfigurationException

Prints the collection of well sets in an XML format.

Parameters:

Collection - the collection of well sets

Throws:

IOException

TransformerException

ParserConfigurationException

setToXMLAsString

public String setToXMLAsString(Collection<WellSet> collection)

Returns a string containing the collection of well sets in an XML format.

Parameters:

Collection - the collection of well sets

Returns:

the XML formatted well sets

setToXML

public void setToXML(WellSet[] array)
              throws IOException,
                     ParserConfigurationException,
                     TransformerException

Prints the well set values in an XML format.

Parameters:

WellSetInteger[] - the array of well sets

Throws:

IOException

ParserConfigurationException

TransformerException

setToXMLAsString

public String setToXMLAsString(WellSet[] array)

Returns a string containing the well set values in an XML format.

Parameters:

WellSetInteger[] - the array of well sets

Returns:

the XML formatted well sets

plateToXML

public void plateToXML(Plate plate)
                throws IOException,
                       TransformerException,
                       ParserConfigurationException

Prints the plate values in an XML format.

Parameters:

Plate - the plate

Throws:

IOException

TransformerException

ParserConfigurationException

plateToXMLAsString

public String plateToXMLAsString(Plate plate)

Returns a string containing the plate values in an XML format.

Parameters:

Plate - the plate

Returns:

the XML formatted plates

plateToXML

public void plateToXML(Collection<Plate> collection)
                throws IOException,
                       TransformerException,
                       ParserConfigurationException

Prints the collection of plates in an XML format.

Parameters:

Collection - the collection of plates

Throws:

IOException

TransformerException

ParserConfigurationException

plateToXMLAsString

public String plateToXMLAsString(Collection<Plate> collection)

Returns a string containing the collection of plates in an XML format.

Parameters:

Collection - the collection of plates

Returns:

the XML formatted plates

plateToXML

public void plateToXML(Plate[] array)
                throws IOException,
                       ParserConfigurationException,
                       TransformerException

Prints the array of plates in an XML format.

Parameters:

PlateInteger[] - the array of plates

Throws:

IOException

ParserConfigurationException

TransformerException

plateToXMLAsString

public String plateToXMLAsString(Plate[] array)

Returns a string containing the array of plates in an XML format.

Parameters:

PlateInteger[] - the array of plates

Returns:

the XML formatted plates

stackToXML

public void stackToXML(Stack stack)
                throws IOException,
                       TransformerException,
                       ParserConfigurationException

Prints the plate stack in an XML format.

Parameters:

Stack - the plate stack

Throws:

IOException

TransformerException

ParserConfigurationException

stackToXMLAsString

public String stackToXMLAsString(Stack stack)

Returns a string containing the plate stack in an XML format.

Parameters:

Stack - the plate stack

Returns:

the XML formatted stacks

stackToXML

public void stackToXML(Collection<Stack> collection)
                throws IOException,
                       ParserConfigurationException,
                       TransformerException

Prints the collection of plate stacks in an XML format.

Parameters:

Collection - the collection of plate stacks

Throws:

IOException

ParserConfigurationException

TransformerException

stackToXMLAsString

public String stackToXMLAsString(Collection<Stack> collection)

Returns a string containing the collection of plate stacks in an XML format.

Parameters:

Collection - the collection of plate stacks

Returns:

the XML formatted stacks

stackToXML

public void stackToXML(Stack[] array)
                throws IOException,
                       ParserConfigurationException,
                       TransformerException

Prints the array of plate stacks in an XML format.

Parameters:

StackInteger[] - the array of plate stacks

Throws:

IOException

ParserConfigurationException

TransformerException

stackToXMLAsString

public String stackToXMLAsString(Stack[] array)

Returns a string containing the array of plate stacks in an XML format.

Parameters:

StackInteger[] - the array of plate stacks

Returns:

the XML formatted stacks

printXMLStack

public void printXMLStack(StackListXML stackList)
                   throws IOException,
                          TransformerException

Prints the stack as an XML object.

Parameters:

StackListXML - the stack list

Throws:

IOException

TransformerException

printXMLStackAsString

public String printXMLStackAsString(StackListXML stackList)

Returns a string containing the stack list as an XML object.

Parameters:

StackListXML - the stack list

Returns:

the XML formatted stack list

setDelimiter

public void setDelimiter(String delimiter)

Sets the delimiter for the plate writer.

Parameters:

String - the delimiter

getDelimiter

public String getDelimiter()

Returns the delimiter.

Returns:

the delimiter