/*
* #%L
* org.gitools.utils
* %%
* Copyright (C) 2013 - 2014 Universitat Pompeu Fabra - Biomedical Genomics group
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
package org.gitools.utils.readers.profile;
import org.gitools.utils.readers.FileHeader;
import java.util.List;
public abstract class ReaderProfile {
public static String TABLE = "Table";
public static String MATRIX = "Matrix";
public static String[] FILE_LAYOUTS = new String[]{MATRIX, TABLE};
protected String name;
protected Separator separator;
protected String layout;
protected int skipLines;
protected char commentChar;
protected String metaDataChar = "#?";
/**
* columns where the heatmap data will be found
*/
protected int[] valueColumns;
/**
* columns that will be ignored upon reading
*/
protected int[] ignoredColumns;
protected int[] rowAnnotationColumns;
protected int[] columnAnnotationColumns;
public abstract void validate(List<FileHeader> inFileHeaders) throws ReaderProfileValidationException;
public abstract int getValueColumnsNumber();
protected ReaderProfile() {
this.name = "default";
this.separator = Separator.TAB;
this.skipLines = 0;
this.commentChar = '#';
this.ignoredColumns = new int[0];
this.valueColumns = new int[0];
this.rowAnnotationColumns = new int[0];
this.columnAnnotationColumns = new int[0];
}
public static ReaderProfile fromProfile(ReaderProfile profile) {
return profile;
}
public char getCommentChar() {
return commentChar;
}
public void setCommentChar(char commentChar) {
this.commentChar = commentChar;
}
public Separator getSeparator() {
return separator;
}
public void setSeparator(Separator separator) {
this.separator = separator;
}
public String getLayout() {
return layout;
}
public void setLayout(String layout) {
this.layout = layout;
}
public int getSkipLines() {
return skipLines;
}
public void setSkipLines(int skipLines) {
this.skipLines = skipLines;
}
public String getMetaDataChar() {
return metaDataChar;
}
public int[] getIgnoredColumns() {
return ignoredColumns;
}
public void setIgnoredColumns(int[] ignoredColumns) {
this.ignoredColumns = ignoredColumns;
}
public int[] getColumnAnnotationColumns() {
return columnAnnotationColumns;
}
public void setColumnAnnotationColumns(int[] columnAnnotationColumns) {
this.columnAnnotationColumns = columnAnnotationColumns;
}
public int[] getRowAnnotationColumns() {
return rowAnnotationColumns;
}
public void setRowAnnotationColumns(int[] rowAnnotationColumns) {
this.rowAnnotationColumns = rowAnnotationColumns;
}
public int[] getValueColumns() {
return valueColumns;
}
public void setValueColumns(int[] valueColumns) {
this.valueColumns = valueColumns;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
}