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/** |
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$Id$ |
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Copyright (C) 2009 Nicklas Nordborg |
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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BASE is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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as published by the Free Software Foundation; either version 3 |
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of the License, or (at your option) any later version. |
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|
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BASE is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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You should have received a copy of the GNU General Public License |
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along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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*/ |
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package net.sf.basedb.util.bfs; |
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import java.util.ArrayList; |
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import java.util.HashMap; |
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import java.util.List; |
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import java.util.Map; |
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import net.sf.basedb.util.Values; |
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/** |
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A model container for BFS annotation files. This class is primarily |
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intended to be used when parsing small annotation files. It is not |
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recommended to use this class with large files since it may use too |
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much memory. |
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<p> |
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Data may be retreived by either column name or index and by row id |
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or index. Lookup by index is a lot faster than by name or id. |
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|
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@author Nicklas |
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@version 2.15 |
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@base.modified $Date$ |
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*/ |
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public class AnnotationModel |
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implements EventHandler |
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{ |
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|
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private String[] headers; |
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private List<String[]> data; |
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|
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private Map<String, Integer> columnIndex; |
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private Map<Integer, Integer> rowIndex; |
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|
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/** |
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Create a new annotation model. |
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*/ |
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public AnnotationModel() |
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{ |
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this.data = new ArrayList<String[]>(); |
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this.rowIndex = new HashMap<Integer, Integer>(); |
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} |
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|
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/* |
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From the EventHandler interface |
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-------------------------------- |
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*/ |
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@Override |
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public <T> void handleEvent(EventType<T> eventType, T eventData, BfsParser parser) |
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{ |
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if (eventType == AnnotationParser.HEADER_EVENT) |
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{ |
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setHeaders((String[])eventData); |
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} |
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else if (eventType == AnnotationParser.DATA_EVENT) |
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{ |
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addRow((String[])eventData); |
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} |
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} |
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// ------------------------------------ |
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|
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/** |
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Set the column headers. It is expected that each |
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array element is unique. |
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@param headers An array with the column headers |
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*/ |
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public void setHeaders(String... headers) |
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{ |
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this.headers = headers; |
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this.columnIndex = new HashMap<String, Integer>(headers.length); |
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for (int i = 0; i < headers.length; ++i) |
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{ |
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columnIndex.put(headers[i], i); |
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} |
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} |
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|
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/** |
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Get all column headers. |
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*/ |
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public String[] getHeaders() |
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{ |
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return headers; |
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} |
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|
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/** |
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Add a row of data to the model. The number of array elements |
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in the array should be the same as the number of columns. The |
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first array element must be the ID of the row. This must be |
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a unique positive integer. |
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*/ |
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public void addRow(String... row) |
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{ |
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int id = Values.getInt(row[0]); |
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data.add(row); |
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rowIndex.put(id, data.size()-1); |
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} |
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|
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/** |
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Get the number of column. |
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*/ |
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public int getColumnCount() |
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{ |
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return headers.length; |
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} |
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|
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/** |
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Get the number of rows. |
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*/ |
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public int getRowCount() |
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{ |
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return data.size(); |
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} |
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|
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/** |
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Get the column index for a given header. |
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@param header The column header |
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@return The column index, or -1 if no column is found |
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*/ |
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public int getColumnIndex(String header) |
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{ |
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Integer index = columnIndex.get(header); |
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return index == null ? -1 : index; |
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} |
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|
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/** |
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Get the column header for a given column index. |
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@param colIndex The index of the column, a value between |
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0 and {@link #getColumnCount()}-1 |
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@return The column header |
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*/ |
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public String getHeader(int colIndex) |
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{ |
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return headers[colIndex]; |
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} |
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|
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/** |
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Get the row index for a given row id. |
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@param rowId The row id |
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@return The row index, or -1 if no row with the given id exists |
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*/ |
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public int getRowIndex(int rowId) |
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{ |
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Integer index = rowIndex.get(rowId); |
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return index == null ? -1 : index; |
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} |
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|
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/** |
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Get the row id for a given row. |
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@param rowIndex The index of the row, a value between 0 and |
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{@link #getRowCount()}-1 |
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@return The row id |
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*/ |
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public int getRowId(int rowIndex) |
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{ |
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String[] row = getRowByIndex(rowIndex); |
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return Values.getInt(row[0]); |
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} |
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|
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/** |
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Get the data element at a given row and column index. |
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@param rowIndex The row index, a value between 0 and |
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{@link #getRowCount()}-1 |
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@param colIndex The column index, a value between |
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0 and {@link #getColumnCount()}-1 |
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@return The data at the given location |
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*/ |
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public String getData(int rowIndex, int colIndex) |
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{ |
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String[] row = getRowByIndex(rowIndex); |
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return row[colIndex]; |
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} |
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|
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/** |
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Get the data element at a given row and column. |
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Do not use this method repeatedly with the same |
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row id or column header. It is faster to use {@link |
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#getData(int, int)}. |
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@param rowId The row id |
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@param header The column header |
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@return The data at the given location, or null if the |
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location doesn't exists |
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*/ |
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public String getData(int rowId, String header) |
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{ |
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String[] row = getRowById(rowId); |
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return row[getColumnIndex(header)]; |
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} |
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|
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public String[] getRowById(int rowId) |
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{ |
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int rowIndex = getRowIndex(rowId); |
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return getRowByIndex(rowIndex); |
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} |
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|
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public String[] getRowByIndex(int rowIndex) |
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{ |
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return data.get(rowIndex); |
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} |
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|
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|
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} |