org.biojava.nbio.survival.data

Class WorkSheet

java.lang.Object

org.biojava.nbio.survival.data.WorkSheet

public class WorkSheet
extends Object

Need to handle very large spreadsheets of expression data so keep memory footprint low

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor and Description
WorkSheet()
WorkSheet(Collection<String> rows, Collection<String> columns)
WorkSheet(CompactCharSequence[][] values)
WorkSheet(String[][] values)

Method Summary

Methods

Modifier and Type	Method and Description
void	addCell(String row, String col, String value) Add data to a cell
void	addColumn(String column, String defaultValue)
void	addColumns(ArrayList<String> columns, String defaultValue) Add columns to worksheet and set default value
void	addRow(String row, String defaultValue)
void	addRows(ArrayList<String> rows, String defaultValue) Add rows to the worksheet and fill in default value
void	appendWorkSheetColumns(WorkSheet worksheet) Add columns from a second worksheet to be joined by common row.
void	appendWorkSheetRows(WorkSheet worksheet) Add rows from a second worksheet to be joined by common column.
void	applyColumnFilter(String column, ChangeValue changeValue) Apply filter to a column to change values from say numberic to nominal based on some range
void	changeColumnHeader(ChangeValue changeValue)
void	changeColumnHeader(String col, String newCol)
void	changeColumnsHeaders(LinkedHashMap<String,String> newColumnValues) Change the columns in the HashMap Key to the name of the value
void	changeRowHeader(ChangeValue changeValue)
void	changeRowHeader(String row, String newRow)
void	clear() See if we can free up memory
ArrayList<String>	getAllColumns() Get the list of column names including those that may be hidden
ArrayList<String>	getAllRows() Get all rows including those that may be hidden
String	getCell(String row, String col) Get cell value
Double	getCellDouble(String row, String col)
Integer	getColumnIndex(String column)
LinkedHashMap<String,HeaderInfo>	getColumnLookup()
ArrayList<String>	getColumns() Get the list of column names.
static WorkSheet	getCopyWorkSheet(WorkSheet copyWorkSheet) Create a copy of a worksheet.
static WorkSheet	getCopyWorkSheetSelectedRows(WorkSheet copyWorkSheet, ArrayList<String> rows) Create a copy of a worksheet.
ArrayList<String>	getDataColumns()
ArrayList<String>	getDataRows() Get the list of row names
ArrayList<String>	getDiscreteColumnValues(String column) Get back a list of unique values in the column
ArrayList<String>	getDiscreteRowValues(String row) Get back a list of unique values in the row
String	getIndexColumnName()
WorkSheet	getLogScale(double base) Get the log scale of this worksheet where a zero value will be set to .1 as Log(0) is undefined
WorkSheet	getLogScale(double base, double zeroValue) Get the log scale of this worksheet
ArrayList<String>	getMetaDataColumns()
LinkedHashMap<String,String>	getMetaDataColumnsHashMap()
ArrayList<String>	getMetaDataRows()
LinkedHashMap<String,String>	getMetaDataRowsHashMap()
ArrayList<String>	getRandomDataColumns(int number)
ArrayList<String>	getRandomDataColumns(int number, ArrayList<String> columns)
String	getRowHeader()
Integer	getRowIndex(String row)
LinkedHashMap<String,HeaderInfo>	getRowLookup()
ArrayList<String>	getRows() Get the list of row names.
void	hideColumn(String column, boolean hide)
void	hideEmptyColumns()
void	hideEmptyRows()
void	hideMetaDataColumns(boolean value)
void	hideMetaDataRows(boolean value)
void	hideRow(String row, boolean hide)
boolean	isMetaDataColumn(String column)
boolean	isMetaDataRow(String row)
boolean	isValidColumn(String col)
boolean	isValidRow(String row)
void	markMetaDataColumn(String column)
void	markMetaDataColumns(ArrayList<String> metaDataColumns) marks columns as containing meta data
void	markMetaDataRow(String row)
void	randomlyDivideSave(double percentage, String fileName1, String fileName2) Split a worksheet randomly.
static WorkSheet	readCSV(File f, char delimiter)
static WorkSheet	readCSV(InputStream is, char delimiter) Read a CSV/Tab delimited file where you pass in the delimiter
static WorkSheet	readCSV(String fileName, char delimiter) Read a CSV/Tab delimitted file where you pass in the delimiter
void	replaceColumnValues(String column, HashMap<String,String> values) Change values in a column where 0 = something and 1 = something different
void	save(OutputStream outputStream, char delimitter, boolean quoteit)
void	saveCSV(String fileName) Save the worksheet as a csv file
void	saveTXT(String fileName)
void	setCacheDoubleValues(boolean value)
void	setIndexColumnName(String indexColumnName)
void	setMetaDataColumns(ArrayList<String> metaDataColumns) Clears existing meta data columns and sets new ones
void	setMetaDataColumnsAfterColumn()
void	setMetaDataColumnsAfterColumn(String column)
void	setMetaDataRows(ArrayList<String> metaDataRows)
void	setMetaDataRowsAfterRow()
void	setMetaDataRowsAfterRow(String row)
void	setRowHeader(String value)
void	shuffleColumnsAndThenRows(ArrayList<String> columns, ArrayList<String> rows) Randomly shuffle the columns and rows.
void	shuffleColumnValues(ArrayList<String> columns) Need to shuffle column values to allow for randomized testing.
void	shuffleRowValues(ArrayList<String> rows) Need to shuffle rows values to allow for randomized testing.
WorkSheet	swapRowAndColumns() Swap the row and columns returning a new worksheet
String	toString()
static WorkSheet	unionWorkSheetsRowJoin(String w1FileName, String w2FileName, char delimitter, boolean secondSheetMetaData) Combine two work sheets where you join based on rows.
static WorkSheet	unionWorkSheetsRowJoin(WorkSheet w1, WorkSheet w2, boolean secondSheetMetaData) * Combine two work sheets where you join based on rows.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

WorkSheet

public WorkSheet()

WorkSheet

public WorkSheet(Collection<String> rows,
         Collection<String> columns)
          throws Exception

Parameters:

rows -

columns -

Throws:

Exception

WorkSheet

public WorkSheet(String[][] values)

Parameters:

values -

WorkSheet

public WorkSheet(CompactCharSequence[][] values)

Parameters:

values -

Method Detail

clear

public void clear()

See if we can free up memory

toString

public String toString()

Overrides:

toString in class Object

randomlyDivideSave

public void randomlyDivideSave(double percentage,
                      String fileName1,
                      String fileName2)
                        throws Exception

Split a worksheet randomly. Used for creating a discovery/validation data set The first file name will matched the percentage and the second file the remainder

Parameters:

percentage -

fileName1 -

fileName2 -

Throws:

Exception

getCopyWorkSheetSelectedRows

public static WorkSheet getCopyWorkSheetSelectedRows(WorkSheet copyWorkSheet,
                                     ArrayList<String> rows)
                                              throws Exception

Create a copy of a worksheet. If shuffling of columns or row for testing a way to duplicate original worksheet

Parameters:

copyWorkSheet -

rows -

Returns:

Throws:

Exception

getCopyWorkSheet

public static WorkSheet getCopyWorkSheet(WorkSheet copyWorkSheet)
                                  throws Exception

Create a copy of a worksheet. If shuffling of columns or row for testing a way to duplicate original worksheet

Parameters:

copyWorkSheet -

Returns:

Throws:

Exception

getMetaDataColumns

public ArrayList<String> getMetaDataColumns()

Returns:

getMetaDataRows

public ArrayList<String> getMetaDataRows()

Returns:

getDataColumns

public ArrayList<String> getDataColumns()

Returns:

shuffleColumnsAndThenRows

public void shuffleColumnsAndThenRows(ArrayList<String> columns,
                             ArrayList<String> rows)
                               throws Exception

Randomly shuffle the columns and rows. Should be constrained to the same data type if not probably doesn't make any sense.

Parameters:

columns -

rows -

Throws:

Exception

shuffleColumnValues

public void shuffleColumnValues(ArrayList<String> columns)
                         throws Exception

Need to shuffle column values to allow for randomized testing. The columns in the list will be shuffled together

Parameters:

columns -

Throws:

Exception

shuffleRowValues

public void shuffleRowValues(ArrayList<String> rows)
                      throws Exception

Need to shuffle rows values to allow for randomized testing. The rows in the list will be shuffled together

Parameters:

rows -

Throws:

Exception

hideMetaDataColumns

public void hideMetaDataColumns(boolean value)

Parameters:

value -

hideMetaDataRows

public void hideMetaDataRows(boolean value)

Parameters:

value -

setMetaDataRowsAfterRow

public void setMetaDataRowsAfterRow()

setMetaDataColumnsAfterColumn

public void setMetaDataColumnsAfterColumn()

setMetaDataRowsAfterRow

public void setMetaDataRowsAfterRow(String row)

Parameters:

row -

setMetaDataColumnsAfterColumn

public void setMetaDataColumnsAfterColumn(String column)

Parameters:

column -

setMetaDataColumns

public void setMetaDataColumns(ArrayList<String> metaDataColumns)

Clears existing meta data columns and sets new ones

Parameters:

metaDataColumns -

markMetaDataColumns

public void markMetaDataColumns(ArrayList<String> metaDataColumns)

marks columns as containing meta data

Parameters:

metaDataColumns -

markMetaDataColumn

public void markMetaDataColumn(String column)

Parameters:

column -

isMetaDataColumn

public boolean isMetaDataColumn(String column)

Parameters:

column -

Returns:

isMetaDataRow

public boolean isMetaDataRow(String row)

Parameters:

row -

Returns:

markMetaDataRow

public void markMetaDataRow(String row)

Parameters:

row -

setMetaDataRows

public void setMetaDataRows(ArrayList<String> metaDataRows)

Parameters:

metaDataRows -

hideEmptyRows

public void hideEmptyRows()
                   throws Exception

Throws:

Exception

hideEmptyColumns

public void hideEmptyColumns()
                      throws Exception

Throws:

Exception

hideRow

public void hideRow(String row,
           boolean hide)

Parameters:

row -

hide -

hideColumn

public void hideColumn(String column,
              boolean hide)

Parameters:

column -

hide -

replaceColumnValues

public void replaceColumnValues(String column,
                       HashMap<String,String> values)
                         throws Exception

Change values in a column where 0 = something and 1 = something different

Parameters:

column -

values -

Throws:

Exception

applyColumnFilter

public void applyColumnFilter(String column,
                     ChangeValue changeValue)
                       throws Exception

Apply filter to a column to change values from say numberic to nominal based on some range

Parameters:

column -

changeValue -

Throws:

Exception

addColumn

public void addColumn(String column,
             String defaultValue)

Parameters:

column -

defaultValue -

addColumns

public void addColumns(ArrayList<String> columns,
              String defaultValue)

Add columns to worksheet and set default value

Parameters:

columns -

defaultValue -

addRow

public void addRow(String row,
          String defaultValue)

Parameters:

row -

defaultValue -

addRows

public void addRows(ArrayList<String> rows,
           String defaultValue)

Add rows to the worksheet and fill in default value

Parameters:

rows -

defaultValue -

addCell

public void addCell(String row,
           String col,
           String value)
             throws Exception

Add data to a cell

Parameters:

row -

col -

value -

Throws:

Exception

isValidRow

public boolean isValidRow(String row)

Parameters:

row -

Returns:

isValidColumn

public boolean isValidColumn(String col)

Parameters:

col -

Returns:

setCacheDoubleValues

public void setCacheDoubleValues(boolean value)

Parameters:

value -

getCellDouble

public Double getCellDouble(String row,
                   String col)
                     throws Exception

Parameters:

row -

col -

Returns:

Throws:

Exception

getCell

public String getCell(String row,
             String col)
               throws Exception

Get cell value

Parameters:

row -

col -

Returns:

Throws:

Exception

changeRowHeader

public void changeRowHeader(ChangeValue changeValue)

Parameters:

changeValue -

changeColumnHeader

public void changeColumnHeader(ChangeValue changeValue)

Parameters:

changeValue -

changeRowHeader

public void changeRowHeader(String row,
                   String newRow)
                     throws Exception

Parameters:

row -

newRow -

Throws:

Exception

changeColumnsHeaders

public void changeColumnsHeaders(LinkedHashMap<String,String> newColumnValues)
                          throws Exception

Change the columns in the HashMap Key to the name of the value

Parameters:

newColumnValues -

Throws:

Exception

changeColumnHeader

public void changeColumnHeader(String col,
                      String newCol)
                        throws Exception

Parameters:

col -

newCol -

Throws:

Exception

getColumnIndex

public Integer getColumnIndex(String column)
                       throws Exception

Parameters:

column -

Returns:

Throws:

Exception

getRowIndex

public Integer getRowIndex(String row)
                    throws Exception

Parameters:

row -

Returns:

Throws:

Exception

getRandomDataColumns

public ArrayList<String> getRandomDataColumns(int number)

Parameters:

number -

Returns:

getRandomDataColumns

public ArrayList<String> getRandomDataColumns(int number,
                                     ArrayList<String> columns)

Parameters:

number -

columns -

Returns:

getAllColumns

public ArrayList<String> getAllColumns()

Get the list of column names including those that may be hidden

Returns:

getColumns

public ArrayList<String> getColumns()

Get the list of column names. Does not include hidden columns

Returns:

getDiscreteColumnValues

public ArrayList<String> getDiscreteColumnValues(String column)
                                          throws Exception

Get back a list of unique values in the column

Parameters:

column -

Returns:

Throws:

Exception

getDiscreteRowValues

public ArrayList<String> getDiscreteRowValues(String row)
                                       throws Exception

Get back a list of unique values in the row

Parameters:

row -

Returns:

Throws:

Exception

getAllRows

public ArrayList<String> getAllRows()

Get all rows including those that may be hidden

Returns:

getRows

public ArrayList<String> getRows()

Get the list of row names. Will exclude hidden values

Returns:

getDataRows

public ArrayList<String> getDataRows()

Get the list of row names

Returns:

getLogScale

public WorkSheet getLogScale(double base)
                      throws Exception

Get the log scale of this worksheet where a zero value will be set to .1 as Log(0) is undefined

Parameters:

base -

Returns:

Throws:

Exception

getLogScale

public WorkSheet getLogScale(double base,
                    double zeroValue)
                      throws Exception

Get the log scale of this worksheet

Parameters:

base -

Returns:

Throws:

Exception

swapRowAndColumns

public WorkSheet swapRowAndColumns()
                            throws Exception

Swap the row and columns returning a new worksheet

Returns:

Throws:

Exception

unionWorkSheetsRowJoin

public static WorkSheet unionWorkSheetsRowJoin(String w1FileName,
                               String w2FileName,
                               char delimitter,
                               boolean secondSheetMetaData)
                                        throws Exception

Combine two work sheets where you join based on rows. Rows that are found in one but not the other are removed. If the second sheet is meta data then a meta data column will be added between the two joined columns

Parameters:

w1FileName -

w2FileName -

delimitter -

secondSheetMetaData -

Returns:

Throws:

Exception

unionWorkSheetsRowJoin

public static WorkSheet unionWorkSheetsRowJoin(WorkSheet w1,
                               WorkSheet w2,
                               boolean secondSheetMetaData)
                                        throws Exception

* Combine two work sheets where you join based on rows. Rows that are found in one but not the other are removed. If the second sheet is meta data then a meta data column will be added between the two joined columns

Parameters:

w1 -

w2 -

secondSheetMetaData -

Returns:

Throws:

Exception

readCSV

public static WorkSheet readCSV(String fileName,
                char delimiter)
                         throws Exception

Read a CSV/Tab delimitted file where you pass in the delimiter

Parameters:

fileName -

delimiter -

Returns:

Throws:

Exception

readCSV

public static WorkSheet readCSV(File f,
                char delimiter)
                         throws Exception

Throws:

Exception

readCSV

public static WorkSheet readCSV(InputStream is,
                char delimiter)
                         throws Exception

Read a CSV/Tab delimited file where you pass in the delimiter

Parameters:

f -

delimiter -

Returns:

Throws:

Exception

saveCSV

public void saveCSV(String fileName)
             throws Exception

Save the worksheet as a csv file

Parameters:

fileName -

Throws:

Exception

saveTXT

public void saveTXT(String fileName)
             throws Exception

Parameters:

fileName -

Throws:

Exception

setRowHeader

public void setRowHeader(String value)

Parameters:

value -

appendWorkSheetColumns

public void appendWorkSheetColumns(WorkSheet worksheet)
                            throws Exception

Add columns from a second worksheet to be joined by common row. If the appended worksheet doesn't contain a row in the master worksheet then default value of "" is used. Rows in the appended worksheet not found in the master worksheet are not added.

Parameters:

worksheet -

Throws:

Exception

appendWorkSheetRows

public void appendWorkSheetRows(WorkSheet worksheet)
                         throws Exception

Add rows from a second worksheet to be joined by common column. If the appended worksheet doesn't contain a column in the master worksheet then default value of "" is used. Columns in the appended worksheet not found in the master worksheet are not added.

Parameters:

worksheet -

Throws:

Exception

save

public void save(OutputStream outputStream,
        char delimitter,
        boolean quoteit)
          throws Exception

Parameters:

outputStream -

delimitter -

quoteit -

Throws:

Exception

getIndexColumnName

public String getIndexColumnName()

Returns:

the indexColumnName

setIndexColumnName

public void setIndexColumnName(String indexColumnName)

Parameters:

indexColumnName - the indexColumnName to set

getColumnLookup

public LinkedHashMap<String,HeaderInfo> getColumnLookup()

Returns:

the columnLookup

getRowLookup

public LinkedHashMap<String,HeaderInfo> getRowLookup()

Returns:

the rowLookup

getMetaDataColumnsHashMap

public LinkedHashMap<String,String> getMetaDataColumnsHashMap()

Returns:

the metaDataColumnsHashMap

getMetaDataRowsHashMap

public LinkedHashMap<String,String> getMetaDataRowsHashMap()

Returns:

the metaDataRowsHashMap

getRowHeader

public String getRowHeader()

Returns:

the rowHeader