some refactoring for the variant eval output system
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3576 348d0f76-0448-11de-a6fe-93d51630548a
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aaron
parent
db1383d0b2
commit
3d049204ed
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package org.broadinstitute.sting.playground.utils.report.templates;
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import org.broadinstitute.sting.utils.StingException;
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import java.io.IOException;
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import java.io.Writer;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* this class handles generating text table output
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*/
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class TextTable {
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// make a table of the number of rows
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ArrayList<ArrayList<String>> rows = new ArrayList<ArrayList<String>>();
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// keep a complementary array of the sizes of each column
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ArrayList<Integer> minimumSizes = new ArrayList<Integer>();
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List<String> header = new ArrayList<String>();
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// our default width
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private static final int defaultMinimumSize = 15;
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// our seperator
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private String seperator = "";
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// our default cell entry
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private static final String defaultCell = "";
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private String name;
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private String description;
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/**
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* create a text table, with the:
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* @param name name of the table
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* @param description what the table represents
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* @param header the header fields
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*/
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TextTable(String name, String description, List<String> header) {
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this.name = name;
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this.description = description;
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for (int index = 0; index < header.size(); index++)
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determineMinimumColumnWidth(header.get(index).length(),index);
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this.header.addAll(header);
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}
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/**
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* create a text table
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*/
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TextTable() {
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}
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/**
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* set a cell of the table
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* @param row, zero based
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* @param column zero based
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* @param entry cell to set
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*/
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public void setCell(int row, int column, String entry) {
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if (rows.size() <= row)
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createRow(row,column);
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ArrayList<String> rowData = rows.get(row);
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if (rowData.size() <= column)
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for (int x = rowData.size(); x <= column; x++)
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rowData.add("");
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rows.get(row).set(column,entry);
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determineMinimumColumnWidth(entry.length(),column);
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}
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private void createRow(int row, int column) {
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for (int x = rows.size(); x <= row; x++) {
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ArrayList<String> blank = new ArrayList<String>();
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for (int col = 0; col <= column; col++)
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blank.add(defaultCell);
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rows.add(blank);
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}
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}
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/**
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* write the table to the writer
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* @param writer the writer
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*/
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public void toPrintWriter(Writer writer) {
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int index = 0;
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for (String col : header)
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writeToDisk(writer, col, index++, (index == header.size() -1));
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appendEndLine(writer,"\n");
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index = 0;
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for (String col : header)
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writeToDisk(writer, col, index++, (index == header.size() -1));
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appendEndLine(writer,"\n");
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for (ArrayList<String> row : rows) {
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if (row.size() > header.size())
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throw new IllegalStateException("More row-cells in table " + name + " then header columns");
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for (int y = 0; y < header.size(); y++)
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if (row.size() >= y)
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writeToDisk(writer, "", y, (y == header.size() - 1));
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else
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writeToDisk(writer, row.get(y), y, (y == header.size() - 1));
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}
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try {
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writer.append("\n");
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} catch (IOException e) {
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throw new StingException("Unable to write to the Writer");
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}
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}
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private void appendEndLine(Writer writer, String str) {
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try {
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writer.append(str);
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} catch (IOException e) {
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e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
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}
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}
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/**
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* write to disk a single string
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* @param writer the writer to use
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* @param str the string to write
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* @param y an index of the string, for column width look-up
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* @param lastVal are we the last value
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*/
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void writeToDisk(Writer writer, String str, int y, boolean lastVal) {
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try {
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writer.append(String.format("%1$-" + (getMinimumSizes(y) + 3) + "s", str));
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if (y != rows.size() - 1)
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writer.append(seperator);
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} catch (IOException e) {
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throw new StingException("Unable to write to the Writer");
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}
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}
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/**
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* get the minimum size for a column
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* @param column the column index
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* @return the width
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*/
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public int getMinimumSizes(int column) {
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if (column >= minimumSizes.size())
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return defaultMinimumSize;
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return minimumSizes.get(column);
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}
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/**
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* determine the minimum column width
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* @param size the size of this string
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* @param position the position (column)
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*/
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void determineMinimumColumnWidth(int size, int position) {
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if (minimumSizes.size() <= position)
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for (int x = minimumSizes.size(); x <= position; x++)
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minimumSizes.add(x,0);
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minimumSizes.set(position,(minimumSizes.get(position) > size) ? minimumSizes.get(position) : size);
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}
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public List<String> getHeader() {
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return header;
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}
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public void setHeader(List<String> header) {
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this.header = header;
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}
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public String getName() {
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return name;
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}
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public void setName(String name) {
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this.name = name;
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}
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public String getDescription() {
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return description;
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}
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public void setDescription(String description) {
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this.description = description;
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}
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}
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@ -0,0 +1,46 @@
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package org.broadinstitute.sting.playground.utils.report.templates;
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import org.broadinstitute.sting.playground.utils.report.templates.TextTable;
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import org.junit.Assert;
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import org.junit.Test;
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import java.util.ArrayList;
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/**
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* test out the text table
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*/
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public class TextTableUnitTest {
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@Test
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public void testBasicSetCell() {
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TextTable table = new TextTable("name","description",new ArrayList<String>());
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table.setCell(1,5,"entry");
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int entriesSeen = 0;
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ArrayList<ArrayList<String>> rows = table.rows;
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for (int x = 0; x <= 1; x++)
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for (int y = 0; y <= 5; y++)
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if (x == 1 && y == 5) {
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Assert.assertTrue(rows.get(x).get(y).equals("entry"));
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entriesSeen++;
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} else
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Assert.assertTrue(rows.get(x).get(y).equals(""));
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Assert.assertEquals("Incorrect number of entries seen",1,entriesSeen);
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}
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@Test
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public void testBasicSetTwoCells() {
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TextTable table = new TextTable("name","description",new ArrayList<String>());
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table.setCell(1,5,"entry");
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table.setCell(1,1,"entry");
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int entriesSeen = 0;
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ArrayList<ArrayList<String>> rows = table.rows;
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for (int x = 0; x <= 1; x++)
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for (int y = 0; y <= 5; y++)
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if ((x == 1 && y == 5) || (x == 1 && y == 1)) {
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Assert.assertTrue(rows.get(x).get(y).equals("entry"));
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entriesSeen++;
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}
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else
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Assert.assertTrue(rows.get(x).get(y).equals(""));
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Assert.assertEquals("Incorrect number of entries seen",2,entriesSeen);
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}
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}
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