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

java/src/org/broadinstitute/sting/playground/utils/report/templates/TextTable.java

@@ -0,0 +1,180 @@
+package org.broadinstitute.sting.playground.utils.report.templates;
+
+import org.broadinstitute.sting.utils.StingException;
+
+import java.io.IOException;
+import java.io.Writer;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * this class handles generating text table output
+ */
+class TextTable {
+    // make a table of the number of rows
+    ArrayList<ArrayList<String>> rows = new ArrayList<ArrayList<String>>();
+
+    // keep a complementary array of the sizes of each column
+    ArrayList<Integer> minimumSizes = new ArrayList<Integer>();
+    List<String> header = new ArrayList<String>();
+
+    // our default width
+    private static final int defaultMinimumSize = 15;
+
+    // our seperator
+    private String seperator = "";
+
+    // our default cell entry
+    private static final String defaultCell = "";
+
+    private String name;
+    private String description;
+
+
+    /**
+     * create a text table, with the:
+     * @param name name of the table
+     * @param description what the table represents
+     * @param header the header fields
+     */
+    TextTable(String name, String description, List<String> header) {
+        this.name = name;
+        this.description = description;
+        for (int index = 0; index < header.size(); index++)
+            determineMinimumColumnWidth(header.get(index).length(),index);
+        this.header.addAll(header);
+    }
+
+    /**
+     * create a text table
+     */
+    TextTable() {
+    }
+
+    /**
+     * set a cell of the table
+     * @param row, zero based
+     * @param column zero based
+     * @param entry cell to set
+     */
+    public void setCell(int row, int column, String entry) {
+        if (rows.size() <= row)
+            createRow(row,column);
+        ArrayList<String> rowData = rows.get(row);
+        if (rowData.size() <= column)
+            for (int x = rowData.size(); x <= column; x++)
+                rowData.add("");
+        rows.get(row).set(column,entry);
+        determineMinimumColumnWidth(entry.length(),column);
+    }
+
+    private void createRow(int row, int column) {
+        for (int x = rows.size(); x <= row; x++) {
+            ArrayList<String> blank = new ArrayList<String>();
+            for (int col = 0; col <= column; col++)
+                blank.add(defaultCell);
+            rows.add(blank);
+
+        }
+    }
+
+    /**
+     * write the table to the writer
+     * @param writer the writer
+     */
+    public void toPrintWriter(Writer writer) {
+        int index = 0;
+        for (String col : header)
+            writeToDisk(writer, col, index++, (index == header.size() -1));
+        appendEndLine(writer,"\n");
+        index = 0;
+        for (String col : header)
+            writeToDisk(writer, col, index++, (index == header.size() -1));
+        appendEndLine(writer,"\n");
+        for (ArrayList<String> row : rows) {
+            if (row.size() > header.size())
+                throw new IllegalStateException("More row-cells in table " + name + " then header columns");
+            for (int y = 0; y < header.size(); y++)
+                if (row.size() >= y)
+                    writeToDisk(writer, "", y, (y == header.size() - 1));
+                else
+                    writeToDisk(writer, row.get(y), y, (y == header.size() - 1));
+        }
+        try {
+            writer.append("\n");
+        } catch (IOException e) {
+            throw new StingException("Unable to write to the Writer");
+        }
+    }
+
+    private void appendEndLine(Writer writer, String str) {
+        try {
+            writer.append(str);
+        } catch (IOException e) {
+            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
+        }
+    }
+
+    /**
+     * write to disk a single string
+     * @param writer the writer to use
+     * @param str the string to write
+     * @param y an index of the string, for column width look-up
+     * @param lastVal are we the last value
+     */
+    void writeToDisk(Writer writer, String str, int y, boolean lastVal) {
+        try {
+            writer.append(String.format("%1$-" + (getMinimumSizes(y) + 3) + "s", str));
+            if (y != rows.size() - 1)
+                writer.append(seperator);
+        } catch (IOException e) {
+            throw new StingException("Unable to write to the Writer");
+        }
+    }
+
+    /**
+     * get the minimum size for a column
+     * @param column the column index
+     * @return the width
+     */
+    public int getMinimumSizes(int column) {
+        if (column >= minimumSizes.size())
+            return defaultMinimumSize;
+        return minimumSizes.get(column);
+    }
+    /**
+     * determine the minimum column width
+     * @param size the size of this string
+     * @param position the position (column)
+     */
+    void determineMinimumColumnWidth(int size, int position) {
+        if (minimumSizes.size() <= position)
+            for (int x = minimumSizes.size(); x <= position; x++)
+                minimumSizes.add(x,0);
+        minimumSizes.set(position,(minimumSizes.get(position) > size) ? minimumSizes.get(position) : size);
+    }
+
+    public List<String> getHeader() {
+        return header;
+    }
+
+    public void setHeader(List<String> header) {
+        this.header = header;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public String getDescription() {
+        return description;
+    }
+
+    public void setDescription(String description) {
+        this.description = description;
+    }
+}

java/test/org/broadinstitute/sting/playground/utils/report/templates/TextTableUnitTest.java

@@ -0,0 +1,46 @@
+package org.broadinstitute.sting.playground.utils.report.templates;
+
+import org.broadinstitute.sting.playground.utils.report.templates.TextTable;
+import org.junit.Assert;
+import org.junit.Test;
+
+import java.util.ArrayList;
+
+/**
+ * test out the text table
+ */
+public class TextTableUnitTest {
+    @Test
+    public void testBasicSetCell() {
+        TextTable table = new TextTable("name","description",new ArrayList<String>());
+        table.setCell(1,5,"entry");
+        int entriesSeen = 0;
+        ArrayList<ArrayList<String>> rows = table.rows;
+        for (int x = 0; x <= 1; x++)
+            for (int y = 0; y <= 5; y++)
+                if (x == 1 && y == 5) {
+                    Assert.assertTrue(rows.get(x).get(y).equals("entry"));
+                    entriesSeen++;
+                } else
+                    Assert.assertTrue(rows.get(x).get(y).equals(""));
+        Assert.assertEquals("Incorrect number of entries seen",1,entriesSeen);
+    }
+
+    @Test
+    public void testBasicSetTwoCells() {
+        TextTable table = new TextTable("name","description",new ArrayList<String>());
+        table.setCell(1,5,"entry");
+        table.setCell(1,1,"entry");
+        int entriesSeen = 0;
+        ArrayList<ArrayList<String>> rows = table.rows;
+        for (int x = 0; x <= 1; x++)
+            for (int y = 0; y <= 5; y++)
+                if ((x == 1 && y == 5) || (x == 1 && y == 1)) {
+                    Assert.assertTrue(rows.get(x).get(y).equals("entry"));
+                    entriesSeen++;
+                }
+                else
+                    Assert.assertTrue(rows.get(x).get(y).equals(""));
+        Assert.assertEquals("Incorrect number of entries seen",2,entriesSeen);
+    }
+}