A convenience class for maintaining a dynamically growing table of values with access to the elements by named row and column identifiers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1988 348d0f76-0448-11de-a6fe-93d51630548a
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kiran
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package org.broadinstitute.sting.playground.utils;
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import java.util.*;
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/**
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* NamedTable is a utility class for maintaining a table and accessing rows and columns
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* with named identifiers, rather than indicies that must be remembered. It also grows
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* dynamically; you needn't specify the rows and columns before accessing them, so you can
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* continuously expand the table in situations where you don't necessarily know how many
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* rows or columns you'll have in the end.
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*/
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public class NamedTable {
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// If in the future, this class gets templatized, the counter variable should really become a CountedObject<T>.
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private HashMap<String, HashMap<String, Double>> table;
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private HashSet<String> rowNames;
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private HashSet<String> colNames;
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public NamedTable() {
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table = new HashMap<String, HashMap<String, Double>>();
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rowNames = new HashSet<String>();
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colNames = new HashSet<String>();
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}
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/**
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* Copy another table into this new table
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* @param ct the table to copy
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*/
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public NamedTable(NamedTable ct) {
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table = new HashMap<String, HashMap<String, Double>>();
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rowNames = new HashSet<String>();
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colNames = new HashSet<String>();
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for (String rowName : ct.getRowNames()) {
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for (String colName : ct.getColumnNames()) {
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this.set(rowName, colName, ct.get(rowName, colName));
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}
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}
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}
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/**
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* If the entry we're trying to access doesn't exist, create it.
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*
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* @param rowName the name of the row
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* @param colName the name of the column
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*/
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private void verifyEntry(String rowName, String colName) {
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rowNames.add(rowName);
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colNames.add(colName);
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if (!table.containsKey(rowName)) {
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table.put(rowName, new HashMap<String, Double>());
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}
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if (!table.get(rowName).containsKey(colName)) {
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table.get(rowName).put(colName, 0.0);
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}
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}
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/**
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* Set an entry in the table
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*
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* @param rowName the name of the row
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* @param colName the name of the column
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* @param value the value to set for the (row,column)-th entry
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*/
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public void set(String rowName, String colName, double value) {
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verifyEntry(rowName, colName);
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table.get(rowName).put(colName, value);
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}
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/**
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* Get an entry in the table
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*
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* @param rowName the name of the row
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* @param colName the name of the column
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* @return the value of the (row,column)-th entry
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*/
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public double get(String rowName, String colName) {
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verifyEntry(rowName, colName);
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return table.get(rowName).get(colName);
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}
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/**
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* For convenience, increment the (row,column)-th entry in the table so that the
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* user doesn't need to extract, increment, and then reassign the value. One day,
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* this should probably be rewritten to use Andrey's CountedObject class.
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*
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* @param rowName the name of the row
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* @param colName the name of the column
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*/
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public void increment(String rowName, String colName) {
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double value = get(rowName, colName);
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table.get(rowName).put(colName, value + 1.0);
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}
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/**
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* For convenience, decrement the (row,column)-th entry in the table so that the
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* user doesn't need to extract, increment, and then reassign the value. One day,
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* this should probably be rewritten to use Andrey's CountedObject class.
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*
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* @param rowName the name of the row
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* @param colName the name of the column
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*/
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public void decrement(String rowName, String colName) {
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double value = get(rowName, colName);
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table.get(rowName).put(colName, value - 1.0);
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}
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/**
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* Get a sorted list of all the rows in the table
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*
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* @return a sorted list of all the rows in the table
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*/
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public ArrayList<String> getRowNames() {
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ArrayList<String> rows = new ArrayList<String>();
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Iterator<String> rowit = rowNames.iterator();
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while (rowit.hasNext()) {
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rows.add(rowit.next());
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}
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Collections.sort(rows);
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return rows;
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}
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/**
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* Get a sorted list of all the columns in the table
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*
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* @return a sorted list of all the columns in the table
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*/
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public ArrayList<String> getColumnNames() {
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ArrayList<String> cols = new ArrayList<String>();
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Iterator<String> colit = colNames.iterator();
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while (colit.hasNext()) {
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cols.add(colit.next());
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}
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Collections.sort(cols);
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return cols;
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}
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/**
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* Get a new table representing a subset of the current table
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* @param rowNames a list of rows to extract
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* @param colNames a list of columns to extract
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* @return the subsetted table
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*/
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public NamedTable getSubset(ArrayList<String> rowNames, ArrayList<String> colNames) {
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NamedTable ct = new NamedTable();
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for (String rowName : rowNames) {
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for (String colName : colNames) {
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ct.set(rowName, colName, get(rowName, colName));
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}
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}
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return ct;
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}
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/* This stuff doesn't belong in this class, but I don't want
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to delete the code until it's moved somewhere appropriate */
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/*
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public boolean twoTailedFisherExactTest(double pValueLimit) {
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return (twoTailedFisherExactTest() < pValueLimit);
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}
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public double oneTailedFisherExactTestRight() {
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NamedTable ct = new NamedTable(this);
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double pCutoff = pValue();
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double pValue = pCutoff;
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while (ct.rotateRight()) {
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double pValuePiece = ct.pValue();
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if (pValuePiece <= pCutoff) {
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pValue += pValuePiece;
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}
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}
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return pValue;
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}
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public double oneTailedFisherExactTestLeft() {
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NamedTable ct = new NamedTable(this);
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double pCutoff = pValue();
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double pValue = pCutoff;
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while (ct.rotateLeft()) {
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double pValuePiece = ct.pValue();
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if (pValuePiece <= pCutoff) {
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pValue += pValuePiece;
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}
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}
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return pValue;
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}
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public double twoTailedFisherExactTest() {
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return oneTailedFisherExactTestLeft() + oneTailedFisherExactTestRight();
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}
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public double pValue() {
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double p = 0.0;
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if (rowNames.size() == 2 && colNames.size() == 2) {
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String[] rows = rowNames.toArray(new String[1]);
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String[] columns = colNames.toArray(new String[1]);
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double a = get(rows[0], columns[0]);
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double b = get(rows[0], columns[1]);
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double c = get(rows[1], columns[0]);
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double d = get(rows[1], columns[1]);
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double n = a + b + c + d;
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double p1 = Arithmetic.binomial(a + b, (long) a);
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double p2 = Arithmetic.binomial(c + d, (long) c);
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double pn = Arithmetic.binomial(n, (long) (a + c));
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p = p1*p2/pn;
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}
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return p;
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}
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public boolean rotateRight() {
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String[] rows = rowNames.toArray(new String[1]);
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String[] columns = colNames.toArray(new String[1]);
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decrement(rows[0], columns[0]);
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increment(rows[1], columns[0]);
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increment(rows[0], columns[1]);
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decrement(rows[1], columns[1]);
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return (get(rows[0], columns[0]) >= 0 && get(rows[1], columns[1]) >= 0);
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}
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public boolean rotateLeft() {
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String[] rows = rowNames.toArray(new String[1]);
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String[] columns = colNames.toArray(new String[1]);
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increment(rows[0], columns[0]);
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decrement(rows[1], columns[0]);
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decrement(rows[0], columns[1]);
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increment(rows[1], columns[1]);
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return (get(rows[0], columns[1]) >= 0 && get(rows[1], columns[0]) >= 0);
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}
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*/
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/**
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* Get a nicely-formatted version of the contents of the table.
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*
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* @return a String representing the contents of the table
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*/
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public String toString() {
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String tableString = "";
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boolean headerPrinted = false;
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ArrayList<String> rows = getRowNames();
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ArrayList<String> cols = getColumnNames();
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for (String rowName : rows) {
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if (!headerPrinted) {
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tableString += "rowName ";
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for (String colName : cols) {
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tableString += "\t" + colName;
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}
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tableString += "\n";
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headerPrinted = true;
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}
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tableString += rowName;
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for (String colName : cols) {
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tableString += String.format("\t%7.7f", get(rowName, colName));
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}
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tableString += "\n";
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}
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return tableString;
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}
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}
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