uk.ac.ebi.arrayexpress2.magetab.datamodel.layout

Class IDFLayout

java.lang.Object

uk.ac.ebi.arrayexpress2.magetab.datamodel.layout.IDFLayout

All Implemented Interfaces:

Layout<IDF>

public class IDFLayout
extends Object
implements Layout<IDF>

An object that describes the relationship between an IDF datamodel object and the serialized version of it. This is useful for tracking the Location of data items from their "original" location in a parsed text file

As the IDF datamodel object is more or less equivalent to the spreadsheet view, this layout object simply gives the line numbers of each field in the IDF. For a given value, it's index in a list (if cardinality > 1) is the column number. So, for example, if I have an IDF:

Protocol Name P-ABC-123 P-XYZ-456

Then I can determine the location of the field named protocolName as '1' (line one, not zero indexed). idf.protocolName.indexOf("P-XYZ-456") will return 1 (because this list is zero indexed) - from this I can evaluate that the location of this field is line 1, column 3 (assuming one considers the header to be column "1").

Author:

Tony Burdett

Constructor Summary

Constructors

Constructor and Description
IDFLayout()

Method Summary

Methods

Modifier and Type	Method and Description
void	addCommentLocation(String commentType, int lineNumber) Add a location of an IDF comment type.
void	addLocation(Field field, int lineNumber) Add a location of a field from IDF.
void	calculateLocations(IDF idf) A factory method for fully calculates the layout of the given datamodel object, using Limpopo's own MAGE-TAB printing algorithms.
void	calculateUnassignedLocations(IDF idf) A factory method for calculating the locations of any data items not already assigned.
boolean	containsUnassignedElements(IDF idf) Returns true if the supplied datamodel has elements with no assigned location in this layout.
String	getCommentType(int lineNumber) Get the comment type on a given line, or null if none exists
Field	getField(int lineNumber) Get the field on the given line, or null if none exists.
int	getLineCount() Get the number of lines in the serialized IDF.
int	getLineNumberForComment(String commentType) Get the line number assigned to the supplied comment type.
int	getLineNumberForField(Field field) Get the line number assigned to the supplied field.
int	getLineNumberForHeader(String header)
protected org.slf4j.Logger	getLog()
boolean	isCompletelyUnassigned() Returns true if there is no layout information contained within this layout

Methods inherited from class java.lang.Object

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

Constructor Detail

IDFLayout

public IDFLayout()

Method Detail

getLog

protected org.slf4j.Logger getLog()

addLocation

public void addLocation(Field field,
               int lineNumber)

Add a location of a field from IDF. The field should be a reflected field from a specific IDF instance and the lineNumber should be this field was either parsed from, or is being assigned to by a layout calculation.

Parameters:

field - the field of the IDF to assign a location to

lineNumber - the linenumber this field was read from or is being assigned to

addCommentLocation

public void addCommentLocation(String commentType,
                      int lineNumber)

Add a location of an IDF comment type. The passed string should be the type of comment from a specific IDF instance and the lineNumber should be this comment was either parsed from, or is being assigned to by a layout calculation.

Parameters:

commentType - the type of comment in the IDF to assign a location to

lineNumber - the linenumber this field was read from or is being assigned to

getField

public Field getField(int lineNumber)

Get the field on the given line, or null if none exists.

Parameters:

lineNumber - the line number a field should be found on

Returns:

the field on this line

getCommentType

public String getCommentType(int lineNumber)

Get the comment type on a given line, or null if none exists

Parameters:

lineNumber - the line number a field should be found on

Returns:

the comment type on this line

getLineNumberForField

public int getLineNumberForField(Field field)

Get the line number assigned to the supplied field. Sometimes IDF files can contain duplicate fields - in this case, the parser should warn and an error raised when duplicates are read in. Both will be recorded in the layout, but this method will only return the first location found. If no location was found, -1 is returned.

Parameters:

field - the field to find the line number for

Returns:

the line number on which the field is written

getLineNumberForComment

public int getLineNumberForComment(String commentType)

Get the line number assigned to the supplied comment type. Sometimes IDF files can contain duplicate comment types - in this case, the parser should warn and an error raised when the duplicate is read in. Both will be recorded in the layout, but this method will only return the first location found. If no location was found, -1 is returned.

Parameters:

commentType - the comment type to find the line number for

Returns:

the line number on which this comment type is written

getLineNumberForHeader

public int getLineNumberForHeader(String header)

getLineCount

public int getLineCount()

Get the number of lines in the serialized IDF.

Returns:

the serialized IDF line count

containsUnassignedElements

public boolean containsUnassignedElements(IDF idf)

Description copied from interface: Layout

Returns true if the supplied datamodel has elements with no assigned location in this layout.

Specified by:

containsUnassignedElements in interface Layout<IDF>

Returns:

true if there are unassigned elements, false otherwise

isCompletelyUnassigned

public boolean isCompletelyUnassigned()

Description copied from interface: Layout

Returns true if there is no layout information contained within this layout

Specified by:

isCompletelyUnassigned in interface Layout<IDF>

Returns:

true if there is no layout information for this datamodel at all

calculateUnassignedLocations

public void calculateUnassignedLocations(IDF idf)

Description copied from interface: Layout

A factory method for calculating the locations of any data items not already assigned. Locations can be assigned during parsing or during any calculation step. If data is subsequently added after calculating locations, it will have an unassigned location. To ensure the layout is changed minimally after adding data, use this method.

Specified by:

calculateUnassignedLocations in interface Layout<IDF>

Parameters:

idf - the datamodel for which to assign layout data for anything that hasn't been laid out previously

calculateLocations

public void calculateLocations(IDF idf)

Description copied from interface: Layout

A factory method for fully calculates the layout of the given datamodel object, using Limpopo's own MAGE-TAB printing algorithms. Any previous location information may become invalid. So, if you use this method to calculate locations on a parsed document, the location information will not be the same as that in the original file.

Specified by:

calculateLocations in interface Layout<IDF>

Parameters:

idf - the datamodel to layout