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Microplate library for parsing wet lab data.
/**
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
* KIND, either express or implied. See the License for the
* specific language governing permissions and limitations
* under the License.
*/
/*--------------------------- Package Declaration ----------------------------*/
package com.github.jessemull.microflex.bigintegerflex.io;
/*------------------------------- Dependencies -------------------------------*/
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.OutputStream;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.io.UnsupportedEncodingException;
import java.io.Writer;
import java.math.BigInteger;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.github.jessemull.microflex.bigintegerflex.plate.PlateBigInteger;
import com.github.jessemull.microflex.bigintegerflex.plate.StackBigInteger;
import com.github.jessemull.microflex.bigintegerflex.plate.WellBigInteger;
import com.github.jessemull.microflex.bigintegerflex.plate.WellSetBigInteger;
/**
* 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
* 9.114
* 2.667
* 4.214
* 5.154
* 1.293
* 7.882
*
*
* B
* 8.953
* 4.827
* 5.149
* 9.792
* 2.514
* 6.448
*
*
* C
* 6.328
* 4.896
* 5.130
* 9.655
* 5.120
* 1.485
*
*
* D
* 2.661
* 5.290
* 4.057
* 2.374
* 1.200
* 2.724
*
*
*
*
* Example Result Table:
*
*
* Result
*
*
* Index
* Value
*
*
* A1
* 48.77
*
*
* A2
* 50.32
*
*
* A3
* 67.23
*
*
* B1
* 49.81
*
*
*
*
* Example Result JSON:
*
* {
* "results" : [ {
* "type" : "Double",
* "label" : "Example Result",
* "size" : 10,
* "wells" : {
* "A11" : 56.455852093078924,
* "A2" : 61.49253731775972,
* "A5" : 58.462812164254956,
* "D10" : 58.957595115303654,
* "D2" : 54.5241886265687,
* "E4" : 56.821464250881434,
* "E8" : 61.16876436088828,
* "E9" : 49.45000301303015,
* "G6" : 58.74507294128508,
* "H1" : 49.115877056175314
* }
* } ]
* }
*
*
*
* 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>55.873951592640616</value>
* </well>
* <well>
* <index>A3</index>
* <value>53.03191840271489</value>
* </well>
* <well>
* <index>A4</index>
* <value>49.02962476222037</value>
* </well>
* </wells>
* </result>
* </results>
*
*
*
*
*
* Example Well JSON:
*
* {
* "wells" : [ {
* "type" : "Double",
* "index" : "F8",
* "size" : 24,
* "values" : [ 15.11, 28.82, 52.54 ]
* } ]
* }
*
*
*
* Example Well Set JSON:
*
* {
* "wellsets" : [ {
* "type" : "Double",
* "label" : "Example Well Set",
* "size" : 1,
* "wells" : [ {
* "index" : "A3",
* "values" : [ 44.70, 91.16, 52.15 ]
* } ]
* } ]
* }
*
*
*
* Example Plate JSON:
*
* {
* "plates" : [ {
* "type" : "Double",
* "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" : [ 44.51, 34.53, 55.92 ]
* } ]
* } ]
* }
*
*
*
* Example Stack JSON:
*
* {
* "stacks" : [ {
* "type" : "Double",
* "label" : "Example Stack",
* "rows" : 8,
* "columns" : 12,
* "size" : 1,
* "plates" : [ {
* "type" : "Double",
* "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" : [ 35.94, 28.17, 21.00 ]
* } ]
* } ]
* } ]
* }
*
*
*
*
*
* Example Well XML:
*
* <wells>
* <well>
* <type>Double</type>
* <index>H8</index>
* <size>24</size>
* <values>
* <value>78.70</value>
* <value>72.96</value>
* <value>38.98</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>17.39</value>
* <value>54.65</value>
* <value>54.12</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>13.89</value>
* <value>92.46</value>
* <value>19.48</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>13.03</value>
* <value>53.21</value>
* <value>28.08</value>
* </values>
* </well>
* </wells>
* </plate>
* </plates>
* </stack>
* </stacks>
*
*
*
*
* @author Jesse L. Mull
* @update Updated Oct 17, 2016
* @address http://www.jessemull.com
* @email [email protected]
*/
public class PlateWriterBigInteger extends PrintWriter {
/*---------------------------- Private Fields ----------------------------*/
/* Number of character types available for the row ID */
private int ALPHA_BASE = 26;
/* The delimiter for delimiter separated values */
private String delimiter = "\t";
/*------------------------------ Constructors ----------------------------*/
/**
* Creates a new PlateWriterBigInteger without automatic line flushing using
* the specified file.
* @param File file the output file
* @throws FileNotFoundException
*/
public PlateWriterBigInteger(File file) throws FileNotFoundException {
super(file);
}
/**
* Creates a new PlateWriterBigInteger without automatic line flushing using
* the specified file and character set.
* @param File file the output file
* @param String csn the character set
* @throws UnsupportedEncodingException
* @throws FileNotFoundException
*/
public PlateWriterBigInteger(File file, String csn) throws FileNotFoundException,
UnsupportedEncodingException {
super(file, csn);
}
/**
* Creates a new PlateWriterBigInteger, without automatic line flushing using
* the OutputStream.
* @param OutputStream out the output stream
*/
public PlateWriterBigInteger(OutputStream out) {
super(out);
}
/**
* Creates a new PlateWriterBigInteger with automatic line flushing, using the
* OutputStream.
* @param OutputStream out the output stream
* @param boolean autoFlush sets automatic flush when true
*/
public PlateWriterBigInteger(OutputStream out, boolean autoFlush) {
super(out, autoFlush);
}
/**
* Creates a new PlateWriterBigInteger without automatic line flushing using the
* specified file name.
* @param String fileName the file name
* @throws FileNotFoundException
*/
public PlateWriterBigInteger(String fileName) throws FileNotFoundException {
super(fileName);
}
/**
* Creates a new PlateWriterBigInteger without automatic line flushing using the
* specified file name and character set.
* @param String fileName the file name
* @param String csn the character set
* @throws UnsupportedEncodingException
* @throws FileNotFoundException
*/
public PlateWriterBigInteger(String fileName, String csn) throws FileNotFoundException,
UnsupportedEncodingException {
super(fileName, csn);
}
/**
* Creates a new PlateWriterBigInteger without automatic line flushing using the
* writer.
* @param Writer out the writer
*/
public PlateWriterBigInteger(Writer out) {
super(out);
}
/**
* Creates a new PlateWriterBigInteger with automatic line flushing using the
* writer.
* @param Writer out the writer
* @param boolean autoFlush sets auto flush when true
*/
public PlateWriterBigInteger(Writer out, boolean autoFlush) {
super(out, autoFlush);
}
/*--------------------- Methods for Plate Map Output ---------------------*/
/**
* Prints the plate map.
* @param Map data the data set
* @param int type the plate type
* @throws UnsupportedEncodingException
* @throws FileNotFoundException
*/
public void resultToPlateMap(Map data, int type)
throws FileNotFoundException, UnsupportedEncodingException {
int rows = parseRows(type);
int columns = parseColumns(type);
TreeMap sorted = new TreeMap(data);
this.printMapResult(sorted, rows, columns, "Result");
this.flush();
}
/**
* Returns a string containing the plate map.
* @param Map data the data set
* @param int type the plate type
*/
public String resultToPlateMapAsString(Map data, int type) {
int rows = parseRows(type);
int columns = parseColumns(type);
TreeMap sorted = new TreeMap(data);
return this.printMapResultAsString(sorted, rows, columns, "Result");
}
/**
* Prints the plate map for each data set in the list.
* @param List> data list of data sets
* @param int type the plate type
* @throws UnsupportedEncodingException
* @throws FileNotFoundException
*/
public void resultToPlateMap(List> data,
int type) throws FileNotFoundException, UnsupportedEncodingException {
int rows = parseRows(type);
int columns = parseColumns(type);
for(Map map : data) {
TreeMap sorted = new TreeMap(map);
this.printMapResult(sorted, rows, columns, "Result");
this.println();
}
this.flush();
}
/**
* Returns a string holding the plate map for each data set in the list.
* @param List> data list of data sets
* @param int type the plate type
* @return String the plate maps
*/
public String resultToPlateMapAsString(List> data, int type) {
String result = "";
int rows = parseRows(type);
int columns = parseColumns(type);
for(Map map : data) {
TreeMap sorted = new TreeMap(map);
result += this.printMapResultAsString(sorted, rows, columns, "Result");
result += "\n";
}
return result;
}
/**
* Prints the plate map.
* @param Map data the data set
* @param int rows number of rows
* @param int columns number of columns
* @throws UnsupportedEncodingException
* @throws FileNotFoundException
*/
public void resultToPlateMap(Map data, int rows, int columns)
throws FileNotFoundException, UnsupportedEncodingException {
TreeMap sorted = new TreeMap(data);
this.printMapResult(sorted, rows, columns, "Result");
this.flush();
}
/**
* Returns a string holding the plate map.
* @param Map data the data set
* @param int rows number of rows
* @param int columns number of columns
* @return String the plate map
*/
public String resultToPlateMapAsString(Map data,
int rows, int columns) {
TreeMap sorted = new TreeMap(data);
return this.printMapResultAsString(sorted, rows, columns, "Result");
}
/**
* Prints the plate map for each data set in the list.
* @param List> data list of data sets
* @param int rows number of rows
* @param int columns number of columns
* @throws UnsupportedEncodingException
* @throws FileNotFoundException
*/
public void resultToPlateMap(List> data, int rows, int columns)
throws FileNotFoundException, UnsupportedEncodingException {
for(Map map : data) {
TreeMap sorted = new TreeMap(map);
this.printMapResult(sorted, rows, columns, "Result");
this.println();
}
this.flush();
}
/**
* Returns a string holding the plate map for each data set in the list.
* @param List> data list of data sets
* @param int rows number of rows
* @param int columns number of columns
* @return String the plate maps
*/
public String resultToPlateMapAsString(List> data,
int rows, int columns) {
String result = "";
for(Map map : data) {
TreeMap sorted = new TreeMap(map);
result += this.printMapResultAsString(sorted, rows, columns, "Result");
result += "\n";
}
return result;
}
/**
* Prints the plate map.
* @param Map data the data set
* @param int type the plate type
* @param String label the data set label
* @throws UnsupportedEncodingException
* @throws FileNotFoundException
*/
public void resultToPlateMap(Map data, int type,
String label) throws FileNotFoundException, UnsupportedEncodingException {
int rows = parseRows(type);
int columns = parseColumns(type);
TreeMap sorted = new TreeMap(data);
this.printMapResult(sorted, rows, columns, label);
this.flush();
}
/**
* Returns a string holding the plate map.
* @param Map data the data set
* @param int type the plate type
* @param String label the data set label
* @return String the plate map
*/
public String resultToPlateMapAsString(Map data,
int type, String label) {
int rows = parseRows(type);
int columns = parseColumns(type);
TreeMap sorted = new TreeMap(data);
return this.printMapResultAsString(sorted, rows, columns, label);
}
/**
* Prints the plate map for each data set in the list.
* @param List> data list of data sets
* @param int type the plate type
* @param List label list of data set labels
* @throws UnsupportedEncodingException
* @throws FileNotFoundException
*/
public void resultToPlateMap(List> data, int type,
List labels) throws FileNotFoundException, UnsupportedEncodingException {
int rows = parseRows(type);
int columns = parseColumns(type);
for(int i = 0; i < data.size(); i++) {
TreeMap sorted = new TreeMap(data.get(i));
String label = i > labels.size() ? "Result" : labels.get(i);
this.printMapResult(sorted, rows, columns, label);
this.println();
}
this.flush();
}
/**
* Returns a string containing the plate map for each data set in the list.
* @param List> data list of data sets
* @param int type the plate type
* @param List label list of data set labels
* @return String the plate maps
*/
public String resultToPlateMapAsString(List> data,
int type, List labels) {
String result = "";
int rows = parseRows(type);
int columns = parseColumns(type);
for(int i = 0; i < data.size(); i++) {
TreeMap sorted = new TreeMap(data.get(i));
String label = i > labels.size() ? "Result" : labels.get(i);
result += this.printMapResultAsString(sorted, rows, columns, label);
result += "\n";
}
return result;
}
/**
* Prints the plate map.
* @param Map data the data set
* @param int rows number of rows
* @param int columns number of columns
* @param String label the data set label
* @throws UnsupportedEncodingException
* @throws FileNotFoundException
*/
public void resultToPlateMap(Map data, int rows, int columns,
String label) throws FileNotFoundException, UnsupportedEncodingException {
TreeMap sorted = new TreeMap(data);
this.printMapResult(sorted, rows, columns, label);
this.flush();
}
/**
* Returns a string containing the plate map.
* @param Map data the data set
* @param int rows number of rows
* @param int columns number of columns
* @param String label the data set label
* @return String the plate map
*/
public String resultToPlateMapAsString(Map data, int rows, int columns,
String label) {
TreeMap sorted = new TreeMap(data);
return this.printMapResultAsString(sorted, rows, columns, label);
}
/**
* Prints the plate map for each data set in the list.
* @param List> data list of data sets
* @param int rows number of rows
* @param int columns number of columns
* @param List label list of data set labels
* @throws UnsupportedEncodingException
* @throws FileNotFoundException
*/
public void resultToPlateMap(List> data, int rows, int columns,
List labels) throws FileNotFoundException, UnsupportedEncodingException {
for(int i = 0; i < data.size(); i++) {
TreeMap sorted = new TreeMap(data.get(i));
String label = i > labels.size() ? "Result" : labels.get(i);
this.printMapResult(sorted, rows, columns, label);
this.println();
}
this.flush();
}
/**
* Returns a string containing the plate map for each data set in the list.
* @param List> data list of data sets
* @param int rows number of rows
* @param int columns number of columns
* @param List label list of data set labels
* @return String the plate maps
*/
public String resultToPlateMapAsString(List> data,
int rows, int columns, List labels) {
String result = "";
for(int i = 0; i < data.size(); i++) {
TreeMap sorted = new TreeMap(data.get(i));
String label = i > labels.size() ? "Result" : labels.get(i);
result += this.printMapResultAsString(sorted, rows, columns, label);
result += "\n";
}
return result;
}
/**
* Prints the plate map.
* @param Map data the data set
* @param int rows number of rows
* @param int columns number of columns
* @param String label the data set label
* @throws FileNotFoundException
* @throws UnsupportedEncodingException
*/
public void printMapResult(Map data, int rows,
int columns, String label) throws FileNotFoundException, UnsupportedEncodingException {
this.println(label);
this.print(delimiter);
for(int k = 0; k < columns; k++) {
this.print((k + 1) + delimiter);
}
this.println();
for(int i = 0; i < rows; i++) {
this.print(this.rowString(i) + delimiter);
for(int j = 1; j < columns + 1; j++) {
WellBigInteger well = new WellBigInteger(i, j);
if(data.containsKey(well)) {
this.print(data.get(well) + delimiter);
} else {
this.print("Null" + delimiter);
}
}
this.println();
}
this.println();
}
/**
* Returns a string containing the plate map.
* @param Map data the data set
* @param int rows number of rows
* @param int columns number of columns
* @param String label the data set label
* @return String the plate map
*/
public String printMapResultAsString(Map data,
int rows, int columns, String label) {
String result = label + "\n";
result += this.delimiter;
for(int k = 0; k < columns; k++) {
result += (k + 1) + delimiter;
}
result += "\n";
for(int i = 0; i < rows; i++) {
result += this.rowString(i) + delimiter;
for(int j = 1; j < columns + 1; j++) {
WellBigInteger well = new WellBigInteger(i, j);
if(data.containsKey(well)) {
result += data.get(well) + delimiter;
} else {
result += "Null" + delimiter;
}
}
result += "\n";;
}
return result;
}
/*----------------------- Methods for Table Output -----------------------*/
/**
* Prints the well value pairs as a delimiter separated table.
* @param Map data the data set
* @throws UnsupportedEncodingException
* @throws FileNotFoundException
*/
public void resultToTable(Map data)
throws FileNotFoundException, UnsupportedEncodingException {
TreeMap sorted = new TreeMap(data);
this.printTableResult(sorted, "Result");
this.flush();
}
/**
* Returns a string containing the well value pairs as a delimiter separated
* table.
* @param Map data the data set
* @return String the table
*/
public String resultToTableAsString(Map data) {
TreeMap sorted = new TreeMap(data);
return this.printTableResultAsString(sorted, "Result");
}
/**
* Prints each set of well value pairs as a delimiter separated table.
* @param List> data list of data sets
* @throws UnsupportedEncodingException
* @throws FileNotFoundException
*/
public void resultToTable(List> data)
throws FileNotFoundException, UnsupportedEncodingException {
for(Map map : data) {
TreeMap sorted = new TreeMap(map);
this.printTableResult(sorted, "Result");
this.print("\n");
}
this.flush();
}
/**
* Returns a string containing each set of well value pairs as a delimiter
* separated table.
* @param List> data list of data sets
* @return String the tables
*/
public String resultToTableAsString(List> data) {
String result = "";
for(Map map : data) {
TreeMap sorted = new TreeMap(map);
result += this.printTableResultAsString(sorted, "Result");
result += "\n";
}
return result;
}
/**
* Prints the well value pairs as a delimiter separated table.
* @param Map data the data set
* @param String label the data set label
* @throws UnsupportedEncodingException
* @throws FileNotFoundException
*/
public void resultToTable(Map data, String label)
throws FileNotFoundException, UnsupportedEncodingException {
TreeMap sorted = new TreeMap(data);
this.printTableResult(sorted, label);
this.flush();
}
/**
* Returns a string containing the well value pairs as a delimiter separated
* table.
* @param Map data the data set
* @param String label the data set label
* @return String the table
*/
public String resultToTableAsString(Map data, String label) {
TreeMap sorted = new TreeMap(data);
return this.printTableResultAsString(sorted, label);
}
/**
* Prints the well value pairs as a delimiter separated table.
* @param List> data list of data sets
* @param List label list of data set labels
* @throws UnsupportedEncodingException
* @throws FileNotFoundException
*/
public void resultToTable(List> data, List labels)
throws FileNotFoundException, UnsupportedEncodingException {
for(int i = 0; i < data.size(); i++) {
TreeMap sorted = new TreeMap(data.get(i));
String label = i > labels.size() ? "Result" : labels.get(i);
this.printTableResult(sorted, label);
this.print("\n");
}
this.flush();
}
/**
* Returns a string containing the well value pairs as a delimiter separated
* table.
* @param List> data list of data sets
* @param List label list of data set labels
* @return String the tables
*/
public String resultToTableAsString(List> data, List labels) {
String result = "";
for(int i = 0; i < data.size(); i++) {
TreeMap sorted = new TreeMap(data.get(i));
String label = i > labels.size() ? "Result" : labels.get(i);
result += this.printTableResultAsString(sorted, label);
result += "\n";
}
return result;
}
/**
* Prints the well value pairs as a delimiter separated table.
* @param Map data the data set
* @param String label the data set label
* @throws UnsupportedEncodingException
* @throws FileNotFoundException
*/
public void printTableResult(Map data, String label) throws FileNotFoundException, UnsupportedEncodingException {
this.println(label);
this.println("Index" + this.delimiter + "Value");
for (Map.Entry entry : data.entrySet()) {
this.println(entry.getKey().index() + this.delimiter + entry.getValue());
}
this.println();
}
/**
* Resturns a string holding the well value pairs as a delimiter separated table.
* @param Map data the data set
* @param String label the data set label
* @return String the table string
*/
public String printTableResultAsString(Map data, String label) {
String result = label + "\n";
result += "Index" + this.delimiter + "Value\n";
for (Map.Entry entry : data.entrySet()) {
result += entry.getKey().index() + this.delimiter + entry.getValue();
result += "\n";
}
result += "\n";
return result;
}
/*------------------- Methods for Data Set JSON Output -------------------*/
/**
* Prints the well value pairs in a JSON format.
* @param Map data the data set
* @throws IOException
*/
public void resultToJSON(Map data) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new ResultListPOJOBigInteger(data));
}
/**
* Returns a string containing the well value pairs in a JSON format.
* @param Map data the data set
* @return String the JSON formatted result
* @throws JsonProcessingException
*/
public String resultToJSONAsString(Map data) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new ResultListPOJOBigInteger(data));
}
/**
* Prints the well value pairs in a JSON format for each data set.
* @param List> data the list of data sets
* @throws IOException
*/
public void resultToJSON(List> data) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new ResultListPOJOBigInteger(data));
}
/**
* Returns a string containing the well value pairs in a JSON format for each data set.
* @param List> data the list of data sets
* @return String the JSON formatted results
* @throws JsonProcessingException
*/
public String resultToJSONAsString(List> data) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new ResultListPOJOBigInteger(data));
}
/**
* Prints the well value pairs in a JSON format using the label.
* @param Map data the data set
* @param String label the data set label
* @throws IOException
*/
public void resultToJSON(Map data, String label) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new ResultListPOJOBigInteger(data, label));
}
/**
* Returns a string containing the well value pairs in a JSON format using the label.
* @param Map data the data set
* @param String label the data set label
* @return String the JSON formatted result
*/
public String resultToJSONAsString(Map data, String label) throws IOException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new ResultListPOJOBigInteger(data, label));
}
/**
* Prints the well value pairs in a JSON format for each data set using the
* specified labels.
* @param List> data the list of data sets
* @param List labels the list of data set labels
* @throws IOException
*/
public void resultToJSON(List> data, List labels) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new ResultListPOJOBigInteger(data, labels));
}
/**
* Returns a string containing the well value pairs in a JSON format for each data set using the
* specified labels.
* @param List> data the list of data sets
* @param List labels the list of data set labels
* @return String the JSON formatted results
* @throws JsonProcessingException
*/
public String resultToJSONAsString(List> data, List labels) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new ResultListPOJOBigInteger(data, labels));
}
/*--------------------- Methods for Well JSON Output ---------------------*/
/**
* Prints the well values in a JSON format.
* @param WellBigInteger the well
* @throws IOException
*/
public void wellToJSON(WellBigInteger well) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new WellListPOJOBigInteger(well));
}
/**
* Returns a string containing the well values in a JSON format.
* @param WellBigInteger the well
* @return String the JSON formatted well
* @throws JsonProcessingException
*/
public String wellToJSONAsString(WellBigInteger well) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new WellListPOJOBigInteger(well));
}
/**
* Prints the collection of wells in a JSON format.
* @param Collection collection the collection of wells
* @throws IOException
*/
public void wellToJSON(Collection collection) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new WellListPOJOBigInteger(collection));
}
/**
* Returns a string containing the collection of wells in a JSON format.
* @param Collection collection the collection of wells
* @return String the JSON formatted wells
* @throws JsonProcessingException
*/
public String wellToJSONAsString(Collection collection) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new WellListPOJOBigInteger(collection));
}
/**
* Prints the wells values in the array in a JSON format.
* @param WellBigInteger[] array the array of wells
* @throws IOException
*/
public void wellToJSON(WellBigInteger[] array) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new WellListPOJOBigInteger(array));
}
/**
* Returns a string containing the well values in the array in a JSON format.
* @param WellBigInteger[] array the array of wells
* @return String the JSON formatted wells
* @throws JsonProcessingException
*/
public String wellToJSONAsString(WellBigInteger[] array) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new WellListPOJOBigInteger(array));
}
/*------------------- Methods for Well Set JSON Output -------------------*/
/**
* Prints the well set values in a JSON format.
* @param WellSetBigInteger set the well set
* @throws IOException
*/
public void setToJSON(WellSetBigInteger set) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new WellSetListPOJOBigInteger(set));
}
/**
* Returns a string containing the well set values in a JSON format.
* @param WellSetBigInteger set the well set
* @return String the JSON formatted set
* @throws JsonProcessingException
*/
public String setToJSONAsString(WellSetBigInteger set) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new WellSetListPOJOBigInteger(set));
}
/**
* Prints the collection of well sets in a JSON format.
* @param Collection collection the collection of well sets
* @throws IOException
*/
public void setToJSON(Collection collection) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new WellSetListPOJOBigInteger(collection));
}
/**
* Returns a string containing the collection of well sets in a JSON format.
* @param Collection collection the collection of well sets
* @return String the JSON formatted set
* @throws JsonProcessingException
*/
public String setToJSONAsString(Collection collection) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new WellSetListPOJOBigInteger(collection));
}
/**
* Prints the well set values in a JSON format.
* @param WellSetBigInteger[] array the array of well sets
* @throws IOException
*/
public void setToJSON(WellSetBigInteger[] array) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new WellSetListPOJOBigInteger(array));
}
/**
* Returns a string containing the well set values in a JSON format.
* @param WellSetBigInteger[] array the array of well sets
* @return String the JSON formatted set
* @throws JsonProcessingException
*/
public String setToJSONAsString(WellSetBigInteger[] array) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new WellSetListPOJOBigInteger(array));
}
/*-------------------- Methods for Plate JSON Output ---------------------*/
/**
* Prints the plate values in a JSON format.
* @param PlateBigInteger plate the plate
* @throws IOException
*/
public void plateToJSON(PlateBigInteger plate) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new PlateListPOJOBigInteger(plate));
}
/**
* Returns a string containing the plate values in a JSON format.
* @param PlateBigInteger plate the plate
* @return String the JSON formatted plate
* @throws JsonProcessingException
*/
public String plateToJSONAsString(PlateBigInteger plate) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new PlateListPOJOBigInteger(plate));
}
/**
* Prints the collection of plates in a JSON format.
* @param Collection collection the collection of plates
* @throws IOException
*/
public void plateToJSON(Collection collection) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new PlateListPOJOBigInteger(collection));
}
/**
* Returns a string containing the collection of plates in a JSON format.
* @param Collection collection the collection of plates
* @return String the JSON formatted plates
* @throws JsonProcessingException
*/
public String plateToJSONAsString(Collection collection) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new PlateListPOJOBigInteger(collection));
}
/**
* Prints the array of plates in a JSON format.
* @param PlateBigInteger[] array the array of plates
* @throws IOException
*/
public void plateToJSON(PlateBigInteger[] array) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new PlateListPOJOBigInteger(array));
}
/**
* Returns a string containing the array of plates in a JSON format.
* @param PlateBigInteger[] array the array of plates
* @throws JsonProcessingException
*/
public String plateToJSONAsString(PlateBigInteger[] array) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new PlateListPOJOBigInteger(array));
}
/*-------------------- Methods for Stack JSON Output ---------------------*/
/**
* Prints the plate stack in a JSON format.
* @param StackBigInteger stack the plate stack
* @throws IOException
*/
public void stackToJSON(StackBigInteger stack) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new StackListPOJOBigInteger(stack));
}
/**
* Returns a string containing the plate stack in a JSON format.
* @param StackBigInteger stack the plate stack
* @return String the JSON formatted stack
* @throws JsonProcessingException
*/
public String stackToJSONAsString(StackBigInteger stack) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new StackListPOJOBigInteger(stack));
}
/**
* Prints the collection of plate stacks in a JSON format.
* @param Collection collection the collection of plate stacks
* @throws IOException
*/
public void stackToJSON(Collection collection) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new StackListPOJOBigInteger(collection));
}
/**
* Returns a string containing the collection of plate stacks in a JSON format.
* @param Collection collection the collection of plate stacks
* @return String the JSON formatted stacks
* @throws JsonProcessingException
*/
public String stackToJSONAsString(Collection collection) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new StackListPOJOBigInteger(collection));
}
/**
* Prints the array of plate stacks in a JSON format.
* @param StackBigInteger[] array the array of plate stacks
* @throws IOException
*/
public void stackToJSON(StackBigInteger[] array) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new StackListPOJOBigInteger(array));
}
/**
* Prints the array of plate stacks in a JSON format.
* @param StackBigInteger[] array the array of plate stacks
* @return String the JSON formatted stacks
* @throws JsonProcessingException
*/
public String stackToJSONAsString(StackBigInteger[] array) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new StackListPOJOBigInteger(array));
}
/*-------------------- Methods for Result XML Output --------------------*/
/**
* Prints the well result values in an XML format.
* @param Map map the result map
* @throws IOException
* @throws ParserConfigurationException
* @throws TransformerException
*/
public void resultToXML(Map map) throws IOException,
ParserConfigurationException, TransformerException {
ResultListXMLBigInteger resultList = new ResultListXMLBigInteger(map);
this.printXMLResult(resultList);
}
/**
* Returns a string containing the result values in an XML format.
* @param Map map the result map
* @return String the XML formatted result
*/
public String resultToXMLAsString(Map map) {
ResultListXMLBigInteger resultList = new ResultListXMLBigInteger(map);
return this.printXMLResultAsString(resultList);
}
/**
* Prints the well result values in an XML format.
* @param Map map the result map
* @param String label the label
* @throws IOException
* @throws ParserConfigurationException
* @throws TransformerException
*/
public void resultToXML(Map map, String label)
throws IOException, ParserConfigurationException, TransformerException {
ResultListXMLBigInteger resultList = new ResultListXMLBigInteger(map, label);
this.printXMLResult(resultList);
}
/**
* Returns a string containing the result values in an XML format.
* @param Map map the result map
* @param String label the label
* @return String the XML formatted result values
*/
public String resultToXMLAsString(Map map, String label) {
ResultListXMLBigInteger resultList = new ResultListXMLBigInteger(map, label);
return this.printXMLResultAsString(resultList);
}
/**
* Prints the collection of result values in an XML format.
* @param Collection collection the collection of well sets
* @throws IOException
* @throws TransformerException
* @throws ParserConfigurationException
*/
public void resultToXML(Collection> collection)
throws IOException, TransformerException, ParserConfigurationException {
ResultListXMLBigInteger resultList = new ResultListXMLBigInteger(collection);
this.printXMLResult(resultList);
}
/**
* Returns a string containing the collection of result values in an XML format.
* @param Collection collection the collection of well sets
* @return String the XML formatted result values
*/
public String resultToXMLAsString(Collection> collection) {
ResultListXMLBigInteger resultList = new ResultListXMLBigInteger(collection);
return this.printXMLResultAsString(resultList);
}
/**
* Prints the collection of result values in an XML format.
* @param Collection collection the collection of well sets
* @param List labels result labels
* @throws IOException
* @throws TransformerException
* @throws ParserConfigurationException
*/
public void resultToXML(Collection> collection, List labels)
throws IOException, TransformerException, ParserConfigurationException {
ResultListXMLBigInteger resultList = new ResultListXMLBigInteger(collection, labels);
this.printXMLResult(resultList);
}
/**
* Returns a string containing the collection of result values in an XML format.
* @param Collection collection the collection of well sets
* @param List labels result labels
* @return String the XML formatted result values
*/
public String resultToXMLAsString(Collection> collection, List labels) {
ResultListXMLBigInteger resultList = new ResultListXMLBigInteger(collection, labels);
return this.printXMLResultAsString(resultList);
}
/**
* Prints the well set as an XML object.
* @param ResultListXMLBigInteger resultList the XML result list
* @throws IOException
*/
private void printXMLResult(ResultListXMLBigInteger resultList) throws IOException {
try {
JAXBContext context = JAXBContext.newInstance(ResultListXMLBigInteger.class);
Marshaller marshaller = context.createMarshaller();
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
marshaller.marshal(resultList, this);
} catch (JAXBException e) {
e.printStackTrace();
}
}
/**
* Returns a string containing the result as an XML object.
* @param ResultListXMLBigInteger resultList the XML result list
* @return String the XML formatted result list
*/
private String printXMLResultAsString(ResultListXMLBigInteger resultList) {
try {
StringWriter writer = new StringWriter();
JAXBContext context = JAXBContext.newInstance(ResultListXMLBigInteger.class);
Marshaller marshaller = context.createMarshaller();
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
marshaller.marshal(resultList, writer);
return writer.toString();
} catch (JAXBException e) {
e.printStackTrace();
return null;
}
}
/*--------------------- Methods for Well XML Output ----------------------*/
/**
* Prints the well values in an XML format.
* @param WellBigInteger set the set
* @throws IOException
* @throws ParserConfigurationException
* @throws TransformerException
*/
public void wellToXML(WellBigInteger well) throws IOException,
ParserConfigurationException, TransformerException {
WellListXMLBigInteger wellList = new WellListXMLBigInteger(well);
this.printXMLWell(wellList);
}
/**
* Returns a string containing the well values in an XML format.
* @param WellBigInteger set the set
* @return String the XML formatted well values
*/
public String wellToXMLAsString(WellBigInteger well) {
WellListXMLBigInteger wellList = new WellListXMLBigInteger(well);
return this.printXMLWellAsString(wellList);
}
/**
* Prints the collection of well values in an XML format.
* @param Collection collection the collection of wells
* @throws IOException
* @throws TransformerException
* @throws ParserConfigurationException
*/
public void wellToXML(Collection collection) throws IOException,
TransformerException, ParserConfigurationException {
WellListXMLBigInteger wellList = new WellListXMLBigInteger(collection);
this.printXMLWell(wellList);
}
/**
* Returns a string containing the collection of well values in an XML format.
* @param Collection collection the collection of wells
* @return String the XML formatted wells
*/
public String wellToXMLAsString(Collection collection) throws IOException,
TransformerException, ParserConfigurationException {
WellListXMLBigInteger wellList = new WellListXMLBigInteger(collection);
return this.printXMLWellAsString(wellList);
}
/**
* Prints the well values in the array in an XML format.
* @param WellBigInteger[] array the array of wells
* @throws IOException
* @throws ParserConfigurationException
* @throws TransformerException
*/
public void wellToXML(WellBigInteger[] array) throws IOException,
ParserConfigurationException, TransformerException {
WellListXMLBigInteger wellList = new WellListXMLBigInteger(array);
this.printXMLWell(wellList);
}
/**
* Prints the well values in the array in an XML format.
* @param WellBigInteger[] array the array of wells
* @return String the XML formatted wells
*/
public String wellToXMLAsString(WellBigInteger[] array) throws IOException,
ParserConfigurationException, TransformerException {
WellListXMLBigInteger wellList = new WellListXMLBigInteger(array);
return this.printXMLWellAsString(wellList);
}
/**
* Prints the well list as an XML object.
* @param WellListXMLBigInteger wellList the well list
* @throws IOException
*/
private void printXMLWell(WellListXMLBigInteger wellList) throws IOException {
try {
JAXBContext context = JAXBContext.newInstance(WellListXMLBigInteger.class);
Marshaller marshaller = context.createMarshaller();
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
marshaller.marshal(wellList, this);
} catch (JAXBException e) {
e.printStackTrace();
}
}
/**
* Returns a string containing the well list as an XML object.
* @param WellListXMLBigInteger wellList the well list
* @return String the XML formatted well list
*/
private String printXMLWellAsString(WellListXMLBigInteger wellList) {
try {
StringWriter writer = new StringWriter();
JAXBContext context = JAXBContext.newInstance(WellListXMLBigInteger.class);
Marshaller marshaller = context.createMarshaller();
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
marshaller.marshal(wellList, writer);
return writer.toString();
} catch (JAXBException e) {
e.printStackTrace();
return null;
}
}
/*-------------------- Methods for Well Set XML Output --------------------*/
/**
* Prints the well set values in an XML format.
* @param WellSetBigInteger set the well set
* @throws IOException
* @throws ParserConfigurationException
* @throws TransformerException
*/
public void setToXML(WellSetBigInteger set) throws IOException,
ParserConfigurationException,
TransformerException {
WellSetListXMLBigInteger setList = new WellSetListXMLBigInteger(set);
this.printXMLSet(setList);
}
/**
* Returns a string containing the well set values in an XML format.
* @param WellSetBigInteger set the well set
* @return String the XML formatted well sets
*/
public String setToXMLAsString(WellSetBigInteger set) {
WellSetListXMLBigInteger setList = new WellSetListXMLBigInteger(set);
return this.printXMLSetAsString(setList);
}
/**
* Prints the collection of well sets in an XML format.
* @param Collection collection the collection of well sets
* @throws IOException
* @throws TransformerException
* @throws ParserConfigurationException
*/
public void setToXML(Collection collection) throws IOException,
TransformerException,
ParserConfigurationException {
WellSetListXMLBigInteger setList = new WellSetListXMLBigInteger(collection);
this.printXMLSet(setList);
}
/**
* Returns a string containing the collection of well sets in an XML format.
* @param Collection collection the collection of well sets
* @return String the XML formatted well sets
*/
public String setToXMLAsString(Collection collection) {
WellSetListXMLBigInteger setList = new WellSetListXMLBigInteger(collection);
return this.printXMLSetAsString(setList);
}
/**
* Prints the well set values in an XML format.
* @param WellSetBigInteger[] array the array of well sets
* @throws IOException
* @throws ParserConfigurationException
* @throws TransformerException
*/
public void setToXML(WellSetBigInteger[] array) throws IOException,
ParserConfigurationException,
TransformerException {
WellSetListXMLBigInteger setList = new WellSetListXMLBigInteger(array);
this.printXMLSet(setList);
}
/**
* Returns a string containing the well set values in an XML format.
* @param WellSetBigInteger[] array the array of well sets
* @return String the XML formatted well sets
*/
public String setToXMLAsString(WellSetBigInteger[] array) {
WellSetListXMLBigInteger setList = new WellSetListXMLBigInteger(array);
return this.printXMLSetAsString(setList);
}
/**
* Prints the well set as an XML object.
* @param WellSetListXMLBigInteger setList the well set list
* @throws IOException
*/
private void printXMLSet(WellSetListXMLBigInteger setList) throws IOException {
try {
JAXBContext context = JAXBContext.newInstance(WellSetListXMLBigInteger.class);
Marshaller marshaller = context.createMarshaller();
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
marshaller.marshal(setList, this);
} catch (JAXBException e) {
e.printStackTrace();
}
}
/**
* Returns a string containing the well set as an XML object.
* @param WellSetListXMLBigInteger setList the well set list
* @return String the XML formatted set list
*/
private String printXMLSetAsString(WellSetListXMLBigInteger setList) {
try {
StringWriter writer = new StringWriter();
JAXBContext context = JAXBContext.newInstance(WellSetListXMLBigInteger.class);
Marshaller marshaller = context.createMarshaller();
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
marshaller.marshal(setList, writer);
return writer.toString();
} catch (JAXBException e) {
e.printStackTrace();
return null;
}
}
/*-------------------- Methods for Plate XML Output ---------------------*/
/**
* Prints the plate values in an XML format.
* @param PlateBigInteger plate the plate
* @throws IOException
* @throws TransformerException
* @throws ParserConfigurationException
*/
public void plateToXML(PlateBigInteger plate) throws IOException,
TransformerException, ParserConfigurationException {
PlateListXMLBigInteger plateList = new PlateListXMLBigInteger(plate);
this.printXMLPlate(plateList);
}
/**
* Returns a string containing the plate values in an XML format.
* @param PlateBigInteger plate the plate
* @return String the XML formatted plates
*/
public String plateToXMLAsString(PlateBigInteger plate) {
PlateListXMLBigInteger plateList = new PlateListXMLBigInteger(plate);
return this.printXMLPlateAsString(plateList);
}
/**
* Prints the collection of plates in an XML format.
* @param Collection collection the collection of plates
* @throws IOException
* @throws TransformerException
* @throws ParserConfigurationException
*/
public void plateToXML(Collection collection) throws IOException,
TransformerException, ParserConfigurationException {
PlateListXMLBigInteger plateList = new PlateListXMLBigInteger(collection);
this.printXMLPlate(plateList);
}
/**
* Returns a string containing the collection of plates in an XML format.
* @param Collection collection the collection of plates
* @return String the XML formatted plates
*/
public String plateToXMLAsString(Collection collection) {
PlateListXMLBigInteger plateList = new PlateListXMLBigInteger(collection);
return this.printXMLPlateAsString(plateList);
}
/**
* Prints the array of plates in an XML format.
* @param PlateBigInteger[] array the array of plates
* @throws IOException
* @throws ParserConfigurationException
* @throws TransformerException
*/
public void plateToXML(PlateBigInteger[] array) throws IOException,
ParserConfigurationException, TransformerException {
PlateListXMLBigInteger plateList = new PlateListXMLBigInteger(array);
this.printXMLPlate(plateList);
}
/**
* Returns a string containing the array of plates in an XML format.
* @param PlateBigInteger[] array the array of plates
* @return String the XML formatted plates
*/
public String plateToXMLAsString(PlateBigInteger[] array) {
PlateListXMLBigInteger plateList = new PlateListXMLBigInteger(array);
return this.printXMLPlateAsString(plateList);
}
/**
* Prints the plate as an XML object.
* @param PlateListXMLBigInteger plateList the plate list
* @throws IOException
*/
private void printXMLPlate(PlateListXMLBigInteger plateList) throws IOException {
try {
JAXBContext context = JAXBContext.newInstance(PlateListXMLBigInteger.class);
Marshaller marshaller = context.createMarshaller();
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
marshaller.marshal(plateList, this);
} catch (JAXBException e) {
e.printStackTrace();
}
}
/**
* Prints the plate as an XML object.
* @param PlateListXMLBigInteger plateList the plate list
* @return String the XML formatted plate list
*/
private String printXMLPlateAsString(PlateListXMLBigInteger plateList) {
try {
StringWriter writer = new StringWriter();
JAXBContext context = JAXBContext.newInstance(PlateListXMLBigInteger.class);
Marshaller marshaller = context.createMarshaller();
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
marshaller.marshal(plateList, writer);
return writer.toString();
} catch (JAXBException e) {
e.printStackTrace();
return null;
}
}
/*-------------------- Methods for Stack XML Output ---------------------*/
/**
* Prints the plate stack in an XML format.
* @param StackBigInteger stack the plate stack
* @throws IOException
* @throws TransformerException
* @throws ParserConfigurationException
*/
public void stackToXML(StackBigInteger stack) throws IOException,
TransformerException, ParserConfigurationException {
StackListXMLBigInteger stackList = new StackListXMLBigInteger(stack);
this.printXMLStack(stackList);
}
/**
* Returns a string containing the plate stack in an XML format.
* @param StackBigInteger stack the plate stack
* @return String the XML formatted stacks
*/
public String stackToXMLAsString(StackBigInteger stack) {
StackListXMLBigInteger stackList = new StackListXMLBigInteger(stack);
return this.printXMLStackAsString(stackList);
}
/**
* Prints the collection of plate stacks in an XML format.
* @param Collection collection the collection of plate stacks
* @throws IOException
* @throws ParserConfigurationException
* @throws TransformerException
*/
public void stackToXML(Collection collection) throws IOException,
ParserConfigurationException, TransformerException {
StackListXMLBigInteger stackList = new StackListXMLBigInteger(collection);
this.printXMLStack(stackList);
}
/**
* Returns a string containing the collection of plate stacks in an XML format.
* @param Collection collection the collection of plate stacks
* @return String the XML formatted stacks
*/
public String stackToXMLAsString(Collection collection) {
StackListXMLBigInteger stackList = new StackListXMLBigInteger(collection);
return this.printXMLStackAsString(stackList);
}
/**
* Prints the array of plate stacks in an XML format.
* @param StackBigInteger[] array the array of plate stacks
* @throws IOException
* @throws ParserConfigurationException
* @throws TransformerException
*/
public void stackToXML(StackBigInteger[] array) throws IOException,
ParserConfigurationException, TransformerException {
StackListXMLBigInteger stackList = new StackListXMLBigInteger(array);
this.printXMLStack(stackList);
}
/**
* Returns a string containing the array of plate stacks in an XML format.
* @param StackBigInteger[] array the array of plate stacks
* @return String the XML formatted stacks
*/
public String stackToXMLAsString(StackBigInteger[] array) {
StackListXMLBigInteger stackList = new StackListXMLBigInteger(array);
return this.printXMLStackAsString(stackList);
}
/**
* Prints the stack as an XML object.
* @param StackListXMLBigInteger stackList the stack list
* @throws IOException
* @throws TransformerException
*/
public void printXMLStack(StackListXMLBigInteger stackList) throws IOException,
TransformerException {
try {
JAXBContext context = JAXBContext.newInstance(StackListXMLBigInteger.class);
Marshaller marshaller = context.createMarshaller();
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
marshaller.marshal(stackList, this);
} catch (JAXBException e) {
e.printStackTrace();
}
}
/**
* Returns a string containing the stack list as an XML object.
* @param StackListXMLBigInteger stackList the stack list
* @return String the XML formatted stack list
*/
public String printXMLStackAsString(StackListXMLBigInteger stackList) {
try {
StringWriter writer = new StringWriter();
JAXBContext context = JAXBContext.newInstance(StackListXMLBigInteger.class);
Marshaller marshaller = context.createMarshaller();
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
marshaller.marshal(stackList, writer);
return writer.toString();
} catch (JAXBException e) {
e.printStackTrace();
return null;
}
}
/*-------------------- Methods for Setting Delimiter ---------------------*/
/**
* Sets the delimiter for the plate writer.
* @param String delimiter the delimiter
*/
public void setDelimiter(String delimiter) {
this.delimiter = delimiter;
}
/**
* Returns the delimiter.
* @return String the delimiter
*/
public String getDelimiter() {
return this.delimiter;
}
/*----------------------- Helper Methods for Output ----------------------*/
/**
* Returns the row ID.
* @return String row ID
*/
private String rowString(int row) {
String rowString = "";
while (row >= 0) {
rowString = (char) (row % ALPHA_BASE + 65) + rowString;
row = (row / ALPHA_BASE) - 1;
}
return rowString;
}
/**
* Returns the row number for the plate type.
* @param int type the plate type
* @return int the number of plate rows
*/
private int parseRows(int type) {
switch(type) {
case PlateBigInteger.PLATE_6WELL: return PlateBigInteger.ROWS_6WELL;
case PlateBigInteger.PLATE_12WELL: return PlateBigInteger.ROWS_12WELL;
case PlateBigInteger.PLATE_24WELL: return PlateBigInteger.ROWS_24WELL;
case PlateBigInteger.PLATE_48WELL: return PlateBigInteger.ROWS_48WELL;
case PlateBigInteger.PLATE_96WELL: return PlateBigInteger.ROWS_96WELL;
case PlateBigInteger.PLATE_384WELL: return PlateBigInteger.ROWS_384WELL;
case PlateBigInteger.PLATE_1536WELL: return PlateBigInteger.ROWS_1536WELL;
default: throw new IllegalArgumentException("Invalid plate type.");
}
}
/**
* Returns the column number for the plate type.
* @param int type the plate type
* @return int the number of plate columns
*/
private int parseColumns(int type) {
switch(type) {
case PlateBigInteger.PLATE_6WELL: return PlateBigInteger.COLUMNS_6WELL;
case PlateBigInteger.PLATE_12WELL: return PlateBigInteger.COLUMNS_12WELL;
case PlateBigInteger.PLATE_24WELL: return PlateBigInteger.COLUMNS_24WELL;
case PlateBigInteger.PLATE_48WELL: return PlateBigInteger.COLUMNS_48WELL;
case PlateBigInteger.PLATE_96WELL: return PlateBigInteger.COLUMNS_96WELL;
case PlateBigInteger.PLATE_384WELL: return PlateBigInteger.COLUMNS_384WELL;
case PlateBigInteger.PLATE_1536WELL: return PlateBigInteger.COLUMNS_1536WELL;
default: throw new IllegalArgumentException("Invalid plate type.");
}
}
}
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