MZTabColumn.java
/*
* Copyright 2018 Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V..
*
* Licensed 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 uk.ac.ebi.pride.jmztab2.model;
import de.isas.mztab2.io.serialization.Serializers;
import de.isas.mztab2.model.IndexedElement;
/**
* Define a column header which used in {@link uk.ac.ebi.pride.jmztab2.model.Section#Protein_Header}, {@link uk.ac.ebi.pride.jmztab2.model.Section#Peptide_Header},
* {@link uk.ac.ebi.pride.jmztab2.model.Section#PSM_Header}, or {@link uk.ac.ebi.pride.jmztab2.model.Section#Small_Molecule_Header}. There are two kinds of columns: stable column
* and optional column. Stable column has stable position and header name, while optional column not.
* {@link uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory} used to create and maintain these column objects.
*
* @see MZTabColumnFactory
* @see SmallMoleculeColumn
* @see SmallMoleculeFeatureColumn
* @see SmallMoleculeEvidenceColumn
* @see OptionColumn
* @see ParameterOptionColumn
* @see AbundanceColumn
* @author qingwei
* @author nilshoffmann
* @since 23/05/13
*
*/
public class MZTabColumn implements IMZTabColumn {
private final String name;
private String order;
private Integer id;
private String header;
private String logicPosition;
private Class dataType;
private boolean optional;
private IndexedElement element;
/**
* Create a column header object. Default, the column header keep the same value with name, and logical position keep
* the same value with order.
*
* @param name define a stable name for column. For optional column, only set stable part for name.
* @param dataType define the data type for column.
* @param optional if false the column is stable type, otherwise is optional column.
* @param order internal order. Every non {@link uk.ac.ebi.pride.jmztab2.model.OptionColumn} has stable order. Column order is used to maintain the
* logical position in {@link uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory}
*/
public MZTabColumn(String name, Class dataType, boolean optional, String order) {
this(name, dataType, optional, order, null);
}
/**
* Create a column header object. Default, the column header keep the same value with name, and logical position keep
* the same value with order.
*
* @param name define a stable name for column. For optional column, only set stable part for name.
* @param dataType define the data type for column.
* @param optional if false the column is stable type, otherwise is optional column.
* @param order internal order. Every non {@link uk.ac.ebi.pride.jmztab2.model.OptionColumn} has stable order. Column order is used to maintain the
* logical position in {@link uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory}
* @param id incremental index used for some optional columns like best_search_engine_score[1], best_search_engine_score[2]
*/
public MZTabColumn(String name, Class dataType, boolean optional, String order, Integer id) {
if (MZTabStringUtils.isEmpty(name)) {
throw new IllegalArgumentException("Column name should not empty.");
}
this.name = name;
if (dataType == null) {
throw new NullPointerException("Column data type should not set null!");
}
this.dataType = dataType;
this.optional = optional;
this.order = order;
this.id = id;
this.header = generateHeader(name);
this.logicPosition = generateLogicalPosition();
}
private String generateHeader(String name) {
StringBuilder sb = new StringBuilder();
sb.append(name);
if (id != null) {
sb.append("[").append(id).append("]");
}
return sb.toString();
}
private String generateLogicalPosition() {
StringBuilder sb = new StringBuilder();
sb.append(order);
if (id != null) {
// generate id string which length is 2. Eg. 12, return 12; 1, return 01
sb.append(String.format("%02d", id));
} else {
sb.append("00");
}
if (element != null) {
sb.append(String.format("%02d", element.getId()));
} else {
sb.append("00");
}
return sb.toString();
}
/**
* {@inheritDoc}
*
* Get the column name. For stable column, name and header are same. But for optional column, name is part
* of its header. For example, optional column which header is search_engine_score_ms_run[1-n], and its name
* is search_engine_score. Besides this, ms_run[1-n] is kind of {@link #element}
*
* Notice: this design pattern not fit for {@link AbundanceColumn}, {@link OptionColumn} and {@link ParameterOptionColumn}.
* These optional columns need be generated by calling {@link MZTabColumnFactory} 's methods.
* @see #getHeader()
* @see #setElement(IndexedElement)
* @see #getHeader()
* @see #setElement(IndexedElement)
*/
@Override
public String getName() {
return name;
}
/**
* {@inheritDoc}
*
* Get the column internal order. For stable column, order and logical position are same. But for optional column,
* the logical position need to be calculated by concatenating order and index element id. For example, optional column
* search_engine_score_ms_run[2] in Protein section, its order is 09, and the logical position is 092. Because the
* element ms_run[2] 's index is 2.
*
* Notice: this design pattern not fit for {@link AbundanceColumn}, {@link OptionColumn} and {@link ParameterOptionColumn}.
* These optional columns need be generated by calling {@link MZTabColumnFactory} 's methods.
* @see #getLogicPosition()
*/
@Override
public String getOrder() {
return order;
}
/*
* Allows to reassign the order in case the file doesn't follow the recommended order
*/
/** {@inheritDoc} */
@Override
public void setOrder(String order) {
//As the order change, the logic position need to be regenerated.
this.order = order;
this.logicPosition = generateLogicalPosition();
}
/**
* {@inheritDoc}
*
* Get the column name. For stable column, name and header are same. While for optional column, name is part
* of its header. For example, optional column which header is search_engine_score_ms_run[1-n], and its name
* is search_engine_score. Besides this, ms_run[1-n] is kind of {@link #element}
*
* Notice: this design pattern not fit for {@link AbundanceColumn}, {@link OptionColumn} and {@link ParameterOptionColumn}.
* These optional columns need be generated by calling {@link MZTabColumnFactory} 's methods.
* @see #getName()
* @see #setElement(IndexedElement)
* @see #getName()
* @see #setElement(IndexedElement)
*/
@Override
public String getHeader() {
return header;
}
/** {@inheritDoc} */
@Override
public void setHeader(String header) {
this.header = header;
}
/**
* {@inheritDoc}
*
* Get the column logical position. For stable column, order and logical position are same. But for optional column,
* the logical position need to calculate by concatenate order and index element id. For example, optional column
* search_engine_score_ms_run[2] in Protein section, its order is 09, and the logical position is 092. Because the
* element ms_run[2] 's index is 2.
*
*<p>Notice: this design pattern not fit for {@link AbundanceColumn}, {@link OptionColumn} and {@link ParameterOptionColumn}.
* These optional columns need be generated by calling {@link MZTabColumnFactory} 's methods.</p>
*
*<p>Notice: in {@link MZTabColumnFactory}, we use logical position to maintain the logical consistence within the {@link de.isas.mztab2.model.MzTab} file.
* During the process of parsing mzTab file, we create a mapping between physical position and internal logical position.</p>
* @see #getOrder()
*/
@Override
public String getLogicPosition() {
generateLogicalPosition();
return logicPosition;
}
/** {@inheritDoc} */
@Override
public void setLogicPosition(String logicPosition) {
this.logicPosition = logicPosition;
}
/**
* {@inheritDoc}
*
* Get the column data type Class.
*/
@Override
public Class getDataType() {
return dataType;
}
/**
* {@inheritDoc}
*
* Judge this column belong to stable column or optional column.
*/
@Override
public boolean isOptional() {
return optional;
}
/**
* {@inheritDoc}
*
* Indexed element used in optional column header and logical position definition.
* In stable column, the return is null.
*
* Notice: this design pattern not fit for {@link AbundanceColumn}, {@link OptionColumn} and {@link ParameterOptionColumn}.
* These optional columns need be generated by calling {@link MZTabColumnFactory} 's methods.
* @see #getHeader()
* @see #getLogicPosition()
* @see #getHeader()
* @see #getLogicPosition()
*/
@Override
public IndexedElement getElement() {
return element;
}
/**
* {@inheritDoc}
*
* Indexed element used in optional column header and logical position definition.
* In stable column, the return is null.
*
* Notice: this design pattern not fit for {@link AbundanceColumn}, {@link OptionColumn} and {@link ParameterOptionColumn}.
* These optional columns need be generated by calling {@link MZTabColumnFactory} 's methods.
* @see #getHeader()
* @see #getLogicPosition()
* @see #getHeader()
* @see #getLogicPosition()
*/
public void setElement(IndexedElement element) {
if (element == null) {
throw new NullPointerException("Can not set null indexed element for optional column!");
}
this.element = element;
this.logicPosition = generateLogicalPosition();
StringBuilder sb = new StringBuilder();
if(this instanceof AbundanceColumn) {
sb.append(this.header).append("[").
append(element.getId()).
append("]");
} else {
sb.append(this.header).append("_").append(Serializers.getReference(element, element.getId()));
}
this.header = sb.toString();
}
/**
* Create a optional column for {@link Section#Protein_Header}, {@link Section#Peptide_Header},
* {@link Section#PSM_Header}, {@link Section#Small_Molecule_Header}, {@link Section#Small_Molecule_Feature_Header},
* or {@link Section#Small_Molecule_Evidence_Header}.
*
* Notice: this function only used to create stable order optional column, such as num_psms_ms_run[1-n] and so on.
* Not used to create {@link AbundanceColumn}, {@link OptionColumn} and {@link ParameterOptionColumn}.
* These optional columns need be generated by calling {@link MZTabColumnFactory} 's methods.
*
* @see MZTabColumnFactory#addOptionalColumn(MZTabColumn, MsRun)
*/
static IMZTabColumn createOptionalColumn(Section section, IMZTabColumn column, Integer id, IndexedElement element) {
if (! column.isOptional()) {
throw new IllegalArgumentException(column + " is not optional column!");
}
IMZTabColumn optionColumn = null;
switch (section) {
// case Protein_Header:
// optionColumn = new ProteinColumn(column.getName(), column.getDataType(), column.isOptional(), column.getOrder(), id);
// break;
// case Peptide_Header:
// optionColumn = new PeptideColumn(column.getName(), column.getDataType(), column.isOptional(), column.getOrder(), id);
// break;
// case PSM_Header:
// optionColumn = new PSMColumn(column.getName(), column.getDataType(), column.isOptional(), column.getOrder(), id);
// break;
case Small_Molecule_Header:
optionColumn = new SmallMoleculeColumn(column.getName(), column.getDataType(), column.isOptional(), column.getOrder(), id);
break;
case Small_Molecule_Feature_Header:
optionColumn = new SmallMoleculeFeatureColumn(column.getName(), column.getDataType(), column.isOptional(), column.getOrder(), id);
break;
case Small_Molecule_Evidence_Header:
optionColumn = new SmallMoleculeEvidenceColumn(column.getName(), column.getDataType(), column.isOptional(), column.getOrder(), id);
break;
}
if (optionColumn != null && element != null) {
optionColumn.setElement(element);
}
return optionColumn;
}
/** {@inheritDoc} */
@Override
public String toString() {
return "MZTabColumn{" +
"header='" + header + '\'' +
", logicPosition='" + logicPosition + '\'' +
", dataType=" + dataType +
", optional=" + optional +
'}';
}
/** {@inheritDoc} */
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
MZTabColumn column = (MZTabColumn) o;
if (optional != column.optional) return false;
if (dataType != null ? !dataType.equals(column.dataType) : column.dataType != null) return false;
return (header != null ? header.equals(column.header) : column.header == null) && (logicPosition != null ? logicPosition.equals(column.logicPosition) : column.logicPosition == null);
}
/** {@inheritDoc} */
@Override
public int hashCode() {
int result = header != null ? header.hashCode() : 0;
result = 31 * result + (logicPosition != null ? logicPosition.hashCode() : 0);
result = 31 * result + (dataType != null ? dataType.hashCode() : 0);
result = 31 * result + (optional ? 1 : 0);
return result;
}
}