edu.iastate.metnet.metaomgraph
Class MetaOmProject

java.lang.Object
  edu.iastate.metnet.metaomgraph.MetaOmProject

public class MetaOmProject
extends java.lang.Object

Class used for dealing with large data sets. A project can be created from either an InputStream or a File. When created from an InputStream, data access will be faster, but memory requirements will be much higher. The opposite is true when created from a File; slower data access, but much lower memory requirements. This is because

Author:

Nick Ransom

Field Summary

static java.lang.String	COMPLETE_LIST The name of the "complete list" list.
static java.lang.String	DELETE_INFO_COLUMN_CAUSE
static java.lang.String	KEEP_CORRELATION_CAUSE
static java.lang.String	LIST_CREATE_CAUSE
static java.lang.String	LIST_DELETE_CAUSE
static java.lang.String	LIST_RENAME_CAUSE
static java.lang.String	NEW_CORRELATION_CAUSE
static java.lang.String	ROW_NAME_CHANGE_CAUSE

Constructor Summary

MetaOmProject(java.io.File projectFile)
Constructs a MetaOmProject using the given MetaOmGraph project file.

MetaOmProject(java.io.File source, int infoColumns, char delimiter, boolean ignoreConsecutiveDelimiters, java.lang.Double blankValue)
Constructs a MetaOmProject with the given parameters.

MetaOmProject(java.io.InputStream instream, int infoColumns, char delimiter)
Constructs a MetaOmProject from the given InputStream.

MetaOmProject(java.io.InputStream instream, int infoColumns, char delimiter, boolean allowImport)
Constructs a MetaOmProject from the given InputStream.

Method Summary

void	addChangeListener(javax.swing.event.ChangeListener listener) Registers a ChangeListener to this project.
boolean	addGeneList(int[] entries) Adds a gene list to the project.
boolean	addGeneList(java.lang.String name, int[] entries) Adds a gene list to the project.
boolean	addGeneList(java.util.Vector entries) Adds a gene list to the project.
protected void	closeDataFile() Closes the RandomAccessFile used to read data.
void	deleteGeneList(java.lang.String name) Deletes a gene list from this project.
void	deleteInfoColumn(int col)
int	findDataColumnHeader(java.lang.String header) Locates the given data column header.
protected void	fireStateChanged(java.lang.String cause) Calls the stateChanged() method of all registered ChangeListeners.
java.lang.Double	getBlankValue()
java.awt.Color	getColor1() Retrieves the default color used for the bottom-left portion of new MetaOmChartPanels' background gradient.
java.awt.Color	getColor2() Retrieves the default color used for the top-right portion of new MetaOmChartPanels' background gradient.
java.lang.String[]	getColumnHeaders()
java.util.ArrayList<java.lang.Integer>	getCorrelationColumns()
double[]	getData(int row) Retrieves the numerical data from the given row.
int	getDataColumnCount()
java.lang.String	getDataColumnHeader(int index) Fetches the header of a given column of data, ignoring the infocolumns.
java.lang.String	getDataColumnHeader(int index, boolean shorten) Fetches the header of a given column of data, ignoring the infocolumns.
java.lang.String[]	getDataColumnHeaders()
double[]	getDataFromMemory(int row) Retrieves the numerical data from the given row for projects created from a stream.
int	getDefaultColumn() Retrieves the index of the "default" info column.
java.lang.String	getDefaultTitle() Retrieves the title used on all new MetaOmChartPanels.
java.lang.String	getDefaultXAxis() Retrieves the label used for the x-axis of all new MetaOmChartPanels.
java.lang.String	getDefaultYAxis() Retrieves the label used for the y-axis of all new MetaOmChartPanels.
char	getDelimiter()
ExtendedInfoTree	getExtendedInfo() Retrieves the root node of this project's extended info tree.
long	getFileIndex(int index) Fetches the file index that marks the start of a given entry.
java.lang.String[]	getGeneListNames() Fetches the names of all the gene lists in this project.
java.lang.Object[][]	getGeneListRowNames(java.lang.String name) Retrieves the row names of all the rows in the given list.
int[]	getGeneListRowNumbers(java.lang.String name) Retrieves the row numbers of all the rows in the given list.
int	getInfoColumnCount()
java.lang.String[]	getInfoColumnNames() Returns cleaned String representations of the names of the information columns.
int	getMaxNameLength() Retrieves the length of the longest data column header in this project.
int	getRowCount() Returns the number of rows in this project.
java.lang.Object[]	getRowName(int entry) Fetches the names of a given row.
java.lang.Object[][]	getRowNames() Fetches the names of the rows.
java.lang.Object[][]	getRowNames(int[] rows) Returns row names for a given list of entries.
java.util.Hashtable<java.lang.String,TreeSearchQueryConstructionPanel.QuerySet>	getSavedQueries() Fetches the saved metadata queries.
java.util.Hashtable<java.lang.String,CustomSortDialog.CustomSortObject>	getSavedSorts() Fetches the saved custom sorts.
java.io.File	getSourceFile() Fetches the delimited text file used to create this project.
boolean	hasLastCorrelation()
boolean	ignoreConsecutiveDelimiters()
boolean	isChanged() Determines if there are unsaved changes to this project.
boolean	isCreatedFromStream() Determines whether this project was created from a stream or a file.
boolean	isInitialized() Determines whether or not this project has been initialized successfully.
void	keepLastCorrelation()
boolean	loadExtendedInfo() Prompts the user to select an XML file, then attempts to initialize the extended info tree from the chosen file.
boolean	loadExtendedInfo(org.jdom.Element rootNode) Initializes this project's extended info tree from the given JDOM Element.
boolean	loadExtendedInfo(java.io.File source) Initializes this project's extended info tree from the given source file.
boolean	loadExtendedInfo(java.io.InputStream source) Initializes this project's extended info tree from the given InputStream.
boolean	mayContainBlankValues()
void	removeChangeListener(javax.swing.event.ChangeListener listener) Unregisters a ChangeListener from this project.
void	removeLastCorrelation()
void	renameColumnHeader(int col, java.lang.String name)
boolean	renameGeneList(java.lang.String oldName, java.lang.String newName) Renames a gene list.
boolean	saveProject(java.io.File destination) Saves this MetaOmProject to a given file.
void	saveQueries(TreeSearchQueryConstructionPanel.QuerySet queries, java.lang.String name) Stores the given metadata query
void	saveSort(CustomSortDialog.CustomSortObject sort, java.lang.String name) Stores the given custom sort.
void	setColor1(java.awt.Color color1) Sets the default color used for the bottom-left portion of new MetaOmChartPanels' background gradient.
void	setColor2(java.awt.Color color2) Sets the default color used for the bottom-left portion of new MetaOmChartPanels' background gradient.
void	setDataColumnHeaders(java.lang.Object[] headers) Sets the data column headers to the given values.
void	setDataColumnHeaders(java.lang.Object[][] headers) Sets the data column headers to the values in headers[x][0].
void	setDefaultColumn(int defaultColumn) Sets the index of the "default" info column.
void	setDefaultTitle(java.lang.String defaultTitle) Sets the title used on all new MetaOmChartPanels.
void	setDefaultXAxis(java.lang.String defaultXAxis) Sets the label used for the x-axis of all new MetaOmChartPanels.
void	setDefaultYAxis(java.lang.String defaultYAxis) Retrieves the label used for the y-axis of all new MetaOmChartPanels.
void	setLastCorrelation(CorrelationValue[] lastCorrelation, java.lang.String name)
void	setRowNames(java.lang.Object[][] rowNames) Sets the row names and info column headers to the given values.
void	setRowNames(java.lang.Object[][] rowNames, java.lang.String[] infoColumnNames) Sets the row names and info column headers to the given values.

Methods inherited from class java.lang.Object

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

Field Detail

COMPLETE_LIST

public static final java.lang.String COMPLETE_LIST

The name of the "complete list" list.

See Also:

Constant Field Values

LIST_CREATE_CAUSE

public static final java.lang.String LIST_CREATE_CAUSE

See Also:

Constant Field Values

LIST_DELETE_CAUSE

public static final java.lang.String LIST_DELETE_CAUSE

See Also:

Constant Field Values

LIST_RENAME_CAUSE

public static final java.lang.String LIST_RENAME_CAUSE

See Also:

Constant Field Values

NEW_CORRELATION_CAUSE

public static final java.lang.String NEW_CORRELATION_CAUSE

See Also:

Constant Field Values

KEEP_CORRELATION_CAUSE

public static final java.lang.String KEEP_CORRELATION_CAUSE

See Also:

Constant Field Values

ROW_NAME_CHANGE_CAUSE

public static final java.lang.String ROW_NAME_CHANGE_CAUSE

See Also:

Constant Field Values

DELETE_INFO_COLUMN_CAUSE

public static final java.lang.String DELETE_INFO_COLUMN_CAUSE

See Also:

Constant Field Values

Constructor Detail

MetaOmProject

public MetaOmProject(java.io.File source,
                     int infoColumns,
                     char delimiter,
                     boolean ignoreConsecutiveDelimiters,
                     java.lang.Double blankValue)

Constructs a MetaOmProject with the given parameters. The isInitialized() method can be used to determine if the construction was successful.

Parameters:

source - The data file used for the project.

infoColumns - The number of information columns in the data file.

delimiter - The character used as a delimiter in the data file.

MetaOmProject

public MetaOmProject(java.io.File projectFile)

Constructs a MetaOmProject using the given MetaOmGraph project file. MetaOmGraph project files have .mog extensions. The isInitialized() method can be used to determine if the project was opened successfully.

Parameters:

projectFile - the MetaOmGraph project file to open

MetaOmProject

public MetaOmProject(java.io.InputStream instream,
                     int infoColumns,
                     char delimiter)

Constructs a MetaOmProject from the given InputStream. If gene IDs appear in the information columns, the user will be prompted to import additional data from MetNetDB. Data from the stream must be delimited tabular data, just as if creating the project from a text file. The isInitialized() method can be used to determine if the construction was successful.

Parameters:

instream - the source InputStream

infoColumns - the number of information columns in the stream

delimiter - the delimiter used by the stream

MetaOmProject

public MetaOmProject(java.io.InputStream instream,
                     int infoColumns,
                     char delimiter,
                     boolean allowImport)

Constructs a MetaOmProject from the given InputStream. Data from the stream must be delimited tabular data, just as if creating the project from a text file. The isInitialized() method can be used to determine if the construction was successful.

Parameters:

instream - the source InputStream

infoColumns - the number of information columns in the stream

delimiter - the delimiter used by the stream

allowImport - if false, the user will not be prompted to import data from MetNetDB, even when gene IDs appear in the information columns

Method Detail

saveProject

public boolean saveProject(java.io.File destination)

Saves this MetaOmProject to a given file. Project files are compressed ZIP files containing at least an XML file called ProjectInfo.xml. If the project has metadata associated with it, an XML file called extended.xml will be created as well. Furthermore, if the project was created from a stream, a data file with the same name as the project file and a .data.txt extension will be output to the same directory (i.e. if saving to c:\myproject.mog, the data file c:\myproject.data.txt will be created as well).

Parameters:

destination - The file to save to.

Returns:

true if the project saved successfully, false otherwise.

isChanged

public boolean isChanged()

Determines if there are unsaved changes to this project.

Returns:

true if there are unsaved changes, false otherwise

getRowNames

public java.lang.Object[][] getRowNames()

Fetches the names of the rows. Dimension is (# of rows)x(# of information columns). Useful for initializing tables.

Returns:

The names of the data rows.

getRowName

public java.lang.Object[] getRowName(int entry)

Fetches the names of a given row.

Parameters:

entry - The row to name.

Returns:

The names of the indicated row in String[# of information columns]

getCorrelationColumns

public java.util.ArrayList<java.lang.Integer> getCorrelationColumns()

getSourceFile

public java.io.File getSourceFile()

Fetches the delimited text file used to create this project.

Returns:

The delimited text file used to create this project.

getFileIndex

public long getFileIndex(int index)

Fetches the file index that marks the start of a given entry.

Parameters:

index - The row number whose file index you want to fetch

Returns:

The index into the source file where the row begins.

getInfoColumnNames

public java.lang.String[] getInfoColumnNames()

Returns cleaned String representations of the names of the information columns. Useful for initializing tables.

Returns:

An array which contains the names of the information columns

getColumnHeaders

public java.lang.String[] getColumnHeaders()

Returns:

The headers of each column of the project, including the infocolumns.

addGeneList

public boolean addGeneList(java.lang.String name,
                           int[] entries)

Adds a gene list to the project.

Parameters:

name - The name of the list.

entries - The numbers of the rows to include in the list.

renameGeneList

public boolean renameGeneList(java.lang.String oldName,
                              java.lang.String newName)

Renames a gene list. If newName is null, the user will be prompted to enter a new name. This method only checks for duplicate names when newName is null, so if you're specifying the new name, make sure a list with the new name doesn't already exist.

Parameters:

oldName - the gene list's current name

newName - the gene list's new name

Returns:

true if the list was renamed successfully

getGeneListNames

public java.lang.String[] getGeneListNames()

Fetches the names of all the gene lists in this project. The complete list will always be at index 0.

Returns:

the names of all gene lists

getGeneListRowNumbers

public int[] getGeneListRowNumbers(java.lang.String name)

Retrieves the row numbers of all the rows in the given list.

Parameters:

name - the name of a gene list

Returns:

the rows included in the list. Returns null if the list does not exist.

getGeneListRowNames

public java.lang.Object[][] getGeneListRowNames(java.lang.String name)

Retrieves the row names of all the rows in the given list.

Parameters:

name - The name of a gene list.

Returns:

The names of the rows included in the list.

addGeneList

public boolean addGeneList(int[] entries)

Adds a gene list to the project. Prompts the user to name the list before adding.

Parameters:

entries - The indices of the rows to include in the list.

Returns:

False if the user cancelled the name entry dialog, true otherwise.

addGeneList

public boolean addGeneList(java.util.Vector entries)

Adds a gene list to the project. Prompts the user to name the list before adding.

Parameters:

entries - A Vector that contains the indices of the rows to include in the list as Integers.

Returns:

False if the user cancelled the name entry dialog or if the Vector contains something other than Integers, true otherwise.

deleteGeneList

public void deleteGeneList(java.lang.String name)

Deletes a gene list from this project.

Parameters:

name - The name of the list to delete.

getInfoColumnCount

public int getInfoColumnCount()

Returns:

The number of info columns.

getDataColumnCount

public int getDataColumnCount()

Returns:

The number of data columns.

getRowNames

public java.lang.Object[][] getRowNames(int[] rows)

Returns row names for a given list of entries.

Parameters:

rows - The entries to name.

Returns:

String[inactiveEntries.length][infoColumns] containing the names of the given entries.

getDataColumnHeader

public java.lang.String getDataColumnHeader(int index)

Fetches the header of a given column of data, ignoring the infocolumns. Thus, getDataColumnHeader(0) will fetch the header of the first column of data, rather than the first info column.

Parameters:

index - The column of data.

Returns:

The full name of the given column.

getDataColumnHeader

public java.lang.String getDataColumnHeader(int index,
                                            boolean shorten)

Fetches the header of a given column of data, ignoring the infocolumns. Thus, getDataColumnHeader(0) will fetch the header of the first column of data, rather than the first info column.

Parameters:

index - The column of data.

shorten - If true, the returned name will be shortened. If false, the result is the same as getDataColumnHeader(index)

Returns:

The name of the given column.

getDataColumnHeaders

public java.lang.String[] getDataColumnHeaders()

Returns:

An array of the data column headers (info columns are excluded)

getDelimiter

public char getDelimiter()

Returns:

The character used as a delimiter in the source file.

setRowNames

public void setRowNames(java.lang.Object[][] rowNames,
                        java.lang.String[] infoColumnNames)

Sets the row names and info column headers to the given values.

Parameters:

rowNames - the names of the rows of this project (non-null)

infoColumnNames - the names of the info columns (non-null)

setRowNames

public void setRowNames(java.lang.Object[][] rowNames)

Sets the row names and info column headers to the given values. The first row of rowNames (rowNames[0]) will be used as the info column headers. The rest will be used as row names.

Parameters:

rowNames - an array in which index 0 contains the info column headers, and the rest contain the row names (non-null)

setDataColumnHeaders

public void setDataColumnHeaders(java.lang.Object[][] headers)

Sets the data column headers to the values in headers[x][0]. A two-dimensional array is used so that data can be taken from a TableModel. If there are more data columns than headers, the number of the data column is used for the extra columns.

Parameters:

headers - array in which index [x][0] contains the values to be used for the data column headers.

setDataColumnHeaders

public void setDataColumnHeaders(java.lang.Object[] headers)

Sets the data column headers to the given values. If there are more data columns than headers, the number of the data column is used for the extra columns.

Parameters:

headers - the new data column headers

getColor1

public java.awt.Color getColor1()

Retrieves the default color used for the bottom-left portion of new MetaOmChartPanels' background gradient.

Returns:

the bottom-left color of the chart panel background gradient

setColor1

public void setColor1(java.awt.Color color1)

Sets the default color used for the bottom-left portion of new MetaOmChartPanels' background gradient.

Parameters:

color1 - the new bottom-left color of the chart panel background gradient

getColor2

public java.awt.Color getColor2()

Retrieves the default color used for the top-right portion of new MetaOmChartPanels' background gradient.

Returns:

the top-right color of the chart panel background gradient

setColor2

public void setColor2(java.awt.Color color2)

Sets the default color used for the bottom-left portion of new MetaOmChartPanels' background gradient.

Parameters:

color2 - the top-right color of the chart panel background gradient

getDefaultColumn

public int getDefaultColumn()

Retrieves the index of the "default" info column. The default column is the one that should be used when there are multiple info columns, but only one of them can be displayed. The default column should contain as few blank and repeat entries as possible.

Returns:

the index of the info column that contains the default row name

setDefaultColumn

public void setDefaultColumn(int defaultColumn)

Sets the index of the "default" info column. The default column is the one that should be used when there are multiple info columns, but only one of them can be displayed. The default column should contain as few blank and repeat entries as possible.

Parameters:

defaultColumn - The index of the info column that contains the default row name.

getDefaultTitle

public java.lang.String getDefaultTitle()

Retrieves the title used on all new MetaOmChartPanels.

Returns:

The default chart title.

setDefaultTitle

public void setDefaultTitle(java.lang.String defaultTitle)

Sets the title used on all new MetaOmChartPanels.

Parameters:

defaultTitle - the new default chart title

getDefaultXAxis

public java.lang.String getDefaultXAxis()

Retrieves the label used for the x-axis of all new MetaOmChartPanels.

Returns:

the default x-axis label

setDefaultXAxis

public void setDefaultXAxis(java.lang.String defaultXAxis)

Sets the label used for the x-axis of all new MetaOmChartPanels.

Parameters:

defaultXAxis - the new default x-axis label

getDefaultYAxis

public java.lang.String getDefaultYAxis()

Retrieves the label used for the y-axis of all new MetaOmChartPanels.

Returns:

the default y-axis label

setDefaultYAxis

public void setDefaultYAxis(java.lang.String defaultYAxis)

Retrieves the label used for the y-axis of all new MetaOmChartPanels.

Parameters:

defaultYAxis - the new default y-axis label

getMaxNameLength

public int getMaxNameLength()

Retrieves the length of the longest data column header in this project.

Returns:

the length of the longest data column header in this project

getExtendedInfo

public ExtendedInfoTree getExtendedInfo()

Retrieves the root node of this project's extended info tree. Returns null if there is no extended info associated with this project.

Returns:

the root node of this project's extended info tree

loadExtendedInfo

public boolean loadExtendedInfo()

Prompts the user to select an XML file, then attempts to initialize the extended info tree from the chosen file.

Returns:

true if the extended info tree was initialized successfully, false otherwise.

loadExtendedInfo

public boolean loadExtendedInfo(java.io.File source)

Initializes this project's extended info tree from the given source file.

Parameters:

source - an XML file

Returns:

true if the extended info tree was successfully initialized, false otherwise.

loadExtendedInfo

public boolean loadExtendedInfo(java.io.InputStream source)

Initializes this project's extended info tree from the given InputStream.

Parameters:

source - an InputStream with an XML source

Returns:

true if the extended info tree was successfully initialized, false otherwise.

loadExtendedInfo

public boolean loadExtendedInfo(org.jdom.Element rootNode)

Initializes this project's extended info tree from the given JDOM Element.

Parameters:

rootNode - the root of the JDOM XML tree from which the extended info will be loaded

Returns:

true if the extended info tree was successfully initialized, false otherwise

findDataColumnHeader

public int findDataColumnHeader(java.lang.String header)

Locates the given data column header. Info columns are not counted, so if the passed header is the first data column header, 0 will be returned. If the given header isn't a data column header, -1 will be returned.

Parameters:

header - the data column header to find

Returns:

the data column index of the header, or -1 if the header isn't found

closeDataFile

protected void closeDataFile()
                      throws java.io.IOException

Closes the RandomAccessFile used to read data. Since there's no way to reopen it without reinitializing the project, this method should only be called when this project is no longer needed.

Throws:

java.io.IOException - if dataIn.close() throws an IOException

isInitialized

public boolean isInitialized()

Determines whether or not this project has been initialized successfully. If this method returns false, most other methods will either cause errors, or return bad/unreliable data. This value will only be set after a constructor call and will never change afterwards, so it should generally be checked right after creating a new instance of this class.

Returns:

true if the project has been initialized successfully, false otherwise.

getData

public double[] getData(int row)
                 throws java.io.IOException

Retrieves the numerical data from the given row. The returned array will have length getDataColumnCount(). Any "blank" values will have the value Double.NaN. Since (Double.NaN==Double.NaN) returns false, to test if a given value from the result is blank, use Double.isNaN(result[x]).

Parameters:

row - the row to retrieve

Returns:

an array of the numbers on the given row

Throws:

java.io.IOException - if there is an error reading from the source file (for non-stream projects)

getDataFromMemory

public double[] getDataFromMemory(int row)

Retrieves the numerical data from the given row for projects created from a stream. The returned array will have length getDataColumnCount().

Parameters:

row - the row to retrieve

Returns:

an array of the numbers on the given row

getRowCount

public int getRowCount()

Returns the number of rows in this project.

Returns:

the number of rows in this project

saveQueries

public void saveQueries(TreeSearchQueryConstructionPanel.QuerySet queries,
                        java.lang.String name)

Stores the given metadata query

Parameters:

queries - the QuerySet to save

name - a name for the metadata query

getSavedQueries

public java.util.Hashtable<java.lang.String,TreeSearchQueryConstructionPanel.QuerySet> getSavedQueries()

Fetches the saved metadata queries.

Returns:

a Hashtable of all saved metadata queries, or null if no metadata queries have been saved.

saveSort

public void saveSort(CustomSortDialog.CustomSortObject sort,
                     java.lang.String name)

Stores the given custom sort.

Parameters:

sort - the CustomSortObject to save

name - a name for the custom sort

getSavedSorts

public java.util.Hashtable<java.lang.String,CustomSortDialog.CustomSortObject> getSavedSorts()

Fetches the saved custom sorts.

Returns:

a Hashtable of all saved custom sorts, or null if no custom sorts have been saved.

isCreatedFromStream

public boolean isCreatedFromStream()

Determines whether this project was created from a stream or a file.

Returns:

true if the project was created from a stream, false if it was created from a file

addChangeListener

public void addChangeListener(javax.swing.event.ChangeListener listener)

Registers a ChangeListener to this project. Currently, ChangeListeners will be notified when a gene list is added/removed/renamed, or when the row names change. More events will be added in the future.

Parameters:

listener - the ChangeListener to register

removeChangeListener

public void removeChangeListener(javax.swing.event.ChangeListener listener)

Unregisters a ChangeListener from this project. The ChangeListener will no longer be notified when this project changes.

Parameters:

listener - the ChangeListener to remove

fireStateChanged

protected void fireStateChanged(java.lang.String cause)

Calls the stateChanged() method of all registered ChangeListeners. Currently, this method is called when gene lists are added/removed/renamed, and when row names change.

ignoreConsecutiveDelimiters

public boolean ignoreConsecutiveDelimiters()

mayContainBlankValues

public boolean mayContainBlankValues()

setLastCorrelation

public void setLastCorrelation(CorrelationValue[] lastCorrelation,
                               java.lang.String name)

renameColumnHeader

public void renameColumnHeader(int col,
                               java.lang.String name)

hasLastCorrelation

public boolean hasLastCorrelation()

keepLastCorrelation

public void keepLastCorrelation()

removeLastCorrelation

public void removeLastCorrelation()

deleteInfoColumn

public void deleteInfoColumn(int col)

getBlankValue

public java.lang.Double getBlankValue()