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Microplate library for parsing wet lab data.
The newest version!
/**
* 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.microflexbiginteger.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.microflexbiginteger.plate.Plate;
import com.github.jessemull.microflexbiginteger.plate.Stack;
import com.github.jessemull.microflexbiginteger.plate.Well;
import com.github.jessemull.microflexbiginteger.plate.WellSet;
/**
* 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" : "BigInteger",
* "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>BigInteger</type>
* <label>Example Result</label>
* <size>3</size>
* <wells>
* <well>
* <index>A2</index>
* <value>5587</value>
* </well>
* <well>
* <index>A3</index>
* <value>5389</value>
* </well>
* <well>
* <index>A4</index>
* <value>4937</value>
* </well>
* </wells>
* </result>
* </results>
*
*
*
*
*
* Example Well JSON:
*
* {
* "wells" : [ {
* "type" : "BigInteger",
* "index" : "F8",
* "size" : 24,
* "values" : [ 1511, 2882, 5254 ]
* } ]
* }
*
*
*
* Example Well Set JSON:
*
* {
* "wellsets" : [ {
* "type" : "BigInteger",
* "label" : "Example Well Set",
* "size" : 1,
* "wells" : [ {
* "index" : "A3",
* "values" : [ 4470, 9116, 5215 ]
* } ]
* } ]
* }
*
*
*
* Example Plate JSON:
*
* {
* "plates" : [ {
* "type" : "BigInteger",
* "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" : "BigInteger",
* "label" : "Example Stack",
* "rows" : 8,
* "columns" : 12,
* "size" : 1,
* "plates" : [ {
* "type" : "BigInteger",
* "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>BigInteger</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>BigInteger</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>BigInteger</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>BigInteger</type>
* <label>Example Stack</label>
* <rows>8</rows>
* <columns>12</columns>
* <size>1</size>
* <plates>
* <plate>
* <type>BigInteger</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
* @update Updated Oct 17, 2016
* @address http://www.jessemull.com
* @email [email protected]
*/
public class PlateWriter 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 PlateWriter(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 PlateWriter(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 PlateWriter(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 PlateWriter(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 PlateWriter(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 PlateWriter(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 PlateWriter(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 PlateWriter(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++) {
Well well = new Well(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++) {
Well well = new Well(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 ResultListPOJO(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 ResultListPOJO(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 ResultListPOJO(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 ResultListPOJO(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 ResultListPOJO(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 ResultListPOJO(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 ResultListPOJO(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 ResultListPOJO(data, labels));
}
/*--------------------- Methods for Well JSON Output ---------------------*/
/**
* Prints the well values in a JSON format.
* @param Well the well
* @throws IOException
*/
public void wellToJSON(Well well) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new WellListPOJO(well));
}
/**
* Returns a string containing the well values in a JSON format.
* @param Well the well
* @return String the JSON formatted well
* @throws JsonProcessingException
*/
public String wellToJSONAsString(Well well) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new WellListPOJO(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 WellListPOJO(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 WellListPOJO(collection));
}
/**
* Prints the wells values in the array in a JSON format.
* @param WellBigInteger[] array the array of wells
* @throws IOException
*/
public void wellToJSON(Well[] array) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new WellListPOJO(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(Well[] array) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new WellListPOJO(array));
}
/*------------------- Methods for Well Set JSON Output -------------------*/
/**
* Prints the well set values in a JSON format.
* @param WellSet set the well set
* @throws IOException
*/
public void setToJSON(WellSet set) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new WellSetListPOJO(set));
}
/**
* Returns a string containing the well set values in a JSON format.
* @param WellSet set the well set
* @return String the JSON formatted set
* @throws JsonProcessingException
*/
public String setToJSONAsString(WellSet set) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new WellSetListPOJO(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 WellSetListPOJO(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 WellSetListPOJO(collection));
}
/**
* Prints the well set values in a JSON format.
* @param WellSetBigInteger[] array the array of well sets
* @throws IOException
*/
public void setToJSON(WellSet[] array) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new WellSetListPOJO(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(WellSet[] array) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new WellSetListPOJO(array));
}
/*-------------------- Methods for Plate JSON Output ---------------------*/
/**
* Prints the plate values in a JSON format.
* @param Plate plate the plate
* @throws IOException
*/
public void plateToJSON(Plate plate) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new PlateListPOJO(plate));
}
/**
* Returns a string containing the plate values in a JSON format.
* @param Plate plate the plate
* @return String the JSON formatted plate
* @throws JsonProcessingException
*/
public String plateToJSONAsString(Plate plate) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new PlateListPOJO(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 PlateListPOJO(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 PlateListPOJO(collection));
}
/**
* Prints the array of plates in a JSON format.
* @param PlateBigInteger[] array the array of plates
* @throws IOException
*/
public void plateToJSON(Plate[] array) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new PlateListPOJO(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(Plate[] array) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new PlateListPOJO(array));
}
/*-------------------- Methods for Stack JSON Output ---------------------*/
/**
* Prints the plate stack in a JSON format.
* @param Stack stack the plate stack
* @throws IOException
*/
public void stackToJSON(Stack stack) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new StackListPOJO(stack));
}
/**
* Returns a string containing the plate stack in a JSON format.
* @param Stack stack the plate stack
* @return String the JSON formatted stack
* @throws JsonProcessingException
*/
public String stackToJSONAsString(Stack stack) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new StackListPOJO(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 StackListPOJO(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 StackListPOJO(collection));
}
/**
* Prints the array of plate stacks in a JSON format.
* @param StackBigInteger[] array the array of plate stacks
* @throws IOException
*/
public void stackToJSON(Stack[] array) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.writerWithDefaultPrettyPrinter().writeValue(this, new StackListPOJO(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(Stack[] array) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(new StackListPOJO(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 {
ResultListXML resultList = new ResultListXML(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) {
ResultListXML resultList = new ResultListXML(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 {
ResultListXML resultList = new ResultListXML(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) {
ResultListXML resultList = new ResultListXML(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 {
ResultListXML resultList = new ResultListXML(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) {
ResultListXML resultList = new ResultListXML(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 {
ResultListXML resultList = new ResultListXML(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) {
ResultListXML resultList = new ResultListXML(collection, labels);
return this.printXMLResultAsString(resultList);
}
/**
* Prints the well set as an XML object.
* @param ResultListXML resultList the XML result list
* @throws IOException
*/
private void printXMLResult(ResultListXML resultList) throws IOException {
try {
JAXBContext context = JAXBContext.newInstance(ResultListXML.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 ResultListXML resultList the XML result list
* @return String the XML formatted result list
*/
private String printXMLResultAsString(ResultListXML resultList) {
try {
StringWriter writer = new StringWriter();
JAXBContext context = JAXBContext.newInstance(ResultListXML.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 Well set the set
* @throws IOException
* @throws ParserConfigurationException
* @throws TransformerException
*/
public void wellToXML(Well well) throws IOException,
ParserConfigurationException, TransformerException {
WellListXML wellList = new WellListXML(well);
this.printXMLWell(wellList);
}
/**
* Returns a string containing the well values in an XML format.
* @param Well set the set
* @return String the XML formatted well values
*/
public String wellToXMLAsString(Well well) {
WellListXML wellList = new WellListXML(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 {
WellListXML wellList = new WellListXML(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 {
WellListXML wellList = new WellListXML(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(Well[] array) throws IOException,
ParserConfigurationException, TransformerException {
WellListXML wellList = new WellListXML(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(Well[] array) throws IOException,
ParserConfigurationException, TransformerException {
WellListXML wellList = new WellListXML(array);
return this.printXMLWellAsString(wellList);
}
/**
* Prints the well list as an XML object.
* @param WellListXML wellList the well list
* @throws IOException
*/
private void printXMLWell(WellListXML wellList) throws IOException {
try {
JAXBContext context = JAXBContext.newInstance(WellListXML.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 WellListXML wellList the well list
* @return String the XML formatted well list
*/
private String printXMLWellAsString(WellListXML wellList) {
try {
StringWriter writer = new StringWriter();
JAXBContext context = JAXBContext.newInstance(WellListXML.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 WellSet set the well set
* @throws IOException
* @throws ParserConfigurationException
* @throws TransformerException
*/
public void setToXML(WellSet set) throws IOException,
ParserConfigurationException,
TransformerException {
WellSetListXML setList = new WellSetListXML(set);
this.printXMLSet(setList);
}
/**
* Returns a string containing the well set values in an XML format.
* @param WellSet set the well set
* @return String the XML formatted well sets
*/
public String setToXMLAsString(WellSet set) {
WellSetListXML setList = new WellSetListXML(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 {
WellSetListXML setList = new WellSetListXML(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) {
WellSetListXML setList = new WellSetListXML(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(WellSet[] array) throws IOException,
ParserConfigurationException,
TransformerException {
WellSetListXML setList = new WellSetListXML(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(WellSet[] array) {
WellSetListXML setList = new WellSetListXML(array);
return this.printXMLSetAsString(setList);
}
/**
* Prints the well set as an XML object.
* @param WellSetListXML setList the well set list
* @throws IOException
*/
private void printXMLSet(WellSetListXML setList) throws IOException {
try {
JAXBContext context = JAXBContext.newInstance(WellSetListXML.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 WellSetListXML setList the well set list
* @return String the XML formatted set list
*/
private String printXMLSetAsString(WellSetListXML setList) {
try {
StringWriter writer = new StringWriter();
JAXBContext context = JAXBContext.newInstance(WellSetListXML.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 Plate plate the plate
* @throws IOException
* @throws TransformerException
* @throws ParserConfigurationException
*/
public void plateToXML(Plate plate) throws IOException,
TransformerException, ParserConfigurationException {
PlateListXML plateList = new PlateListXML(plate);
this.printXMLPlate(plateList);
}
/**
* Returns a string containing the plate values in an XML format.
* @param Plate plate the plate
* @return String the XML formatted plates
*/
public String plateToXMLAsString(Plate plate) {
PlateListXML plateList = new PlateListXML(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 {
PlateListXML plateList = new PlateListXML(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) {
PlateListXML plateList = new PlateListXML(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(Plate[] array) throws IOException,
ParserConfigurationException, TransformerException {
PlateListXML plateList = new PlateListXML(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(Plate[] array) {
PlateListXML plateList = new PlateListXML(array);
return this.printXMLPlateAsString(plateList);
}
/**
* Prints the plate as an XML object.
* @param PlateListXML plateList the plate list
* @throws IOException
*/
private void printXMLPlate(PlateListXML plateList) throws IOException {
try {
JAXBContext context = JAXBContext.newInstance(PlateListXML.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 PlateListXML plateList the plate list
* @return String the XML formatted plate list
*/
private String printXMLPlateAsString(PlateListXML plateList) {
try {
StringWriter writer = new StringWriter();
JAXBContext context = JAXBContext.newInstance(PlateListXML.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 Stack stack the plate stack
* @throws IOException
* @throws TransformerException
* @throws ParserConfigurationException
*/
public void stackToXML(Stack stack) throws IOException,
TransformerException, ParserConfigurationException {
StackListXML stackList = new StackListXML(stack);
this.printXMLStack(stackList);
}
/**
* Returns a string containing the plate stack in an XML format.
* @param Stack stack the plate stack
* @return String the XML formatted stacks
*/
public String stackToXMLAsString(Stack stack) {
StackListXML stackList = new StackListXML(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 {
StackListXML stackList = new StackListXML(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) {
StackListXML stackList = new StackListXML(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(Stack[] array) throws IOException,
ParserConfigurationException, TransformerException {
StackListXML stackList = new StackListXML(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(Stack[] array) {
StackListXML stackList = new StackListXML(array);
return this.printXMLStackAsString(stackList);
}
/**
* Prints the stack as an XML object.
* @param StackListXML stackList the stack list
* @throws IOException
* @throws TransformerException
*/
public void printXMLStack(StackListXML stackList) throws IOException,
TransformerException {
try {
JAXBContext context = JAXBContext.newInstance(StackListXML.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 StackListXML stackList the stack list
* @return String the XML formatted stack list
*/
public String printXMLStackAsString(StackListXML stackList) {
try {
StringWriter writer = new StringWriter();
JAXBContext context = JAXBContext.newInstance(StackListXML.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 Plate.PLATE_6WELL: return Plate.ROWS_6WELL;
case Plate.PLATE_12WELL: return Plate.ROWS_12WELL;
case Plate.PLATE_24WELL: return Plate.ROWS_24WELL;
case Plate.PLATE_48WELL: return Plate.ROWS_48WELL;
case Plate.PLATE_96WELL: return Plate.ROWS_96WELL;
case Plate.PLATE_384WELL: return Plate.ROWS_384WELL;
case Plate.PLATE_1536WELL: return Plate.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 Plate.PLATE_6WELL: return Plate.COLUMNS_6WELL;
case Plate.PLATE_12WELL: return Plate.COLUMNS_12WELL;
case Plate.PLATE_24WELL: return Plate.COLUMNS_24WELL;
case Plate.PLATE_48WELL: return Plate.COLUMNS_48WELL;
case Plate.PLATE_96WELL: return Plate.COLUMNS_96WELL;
case Plate.PLATE_384WELL: return Plate.COLUMNS_384WELL;
case Plate.PLATE_1536WELL: return Plate.COLUMNS_1536WELL;
default: throw new IllegalArgumentException("Invalid plate type.");
}
}
}
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