org::gel::mauve::SeqFeatureData Class Reference

Utility class for data specific to sequence navigator involving genomes and their features. More...

Inheritance diagram for org::gel::mauve::SeqFeatureData:

[legend]Collaboration diagram for org::gel::mauve::SeqFeatureData:

[legend]List of all members.

Static Public Member Functions
long	centerOfFeature (Feature feature)
	finds the center sequence coordinate of a feature
Genome[]	convertIndexToSequence (Vector choices, int index)
	returns an array representing the user selected genomes.
LinkedList[]	findFeatures (Genome[] nomes, String[][] data)
	Finds all features associated with specified genomes matching the specified key value pairs.
FeatureFilter	getFilter (String[][] data)
	Returns a filter that will accept annotations matching the desired keys and values.
String	getTypeFromFilter (FeatureFilter filter)
	Parses a FeatureFilter to see if it contains a filter that is associated with a particular type of Feature.
String	getTypeFromFilterSpec (FilterCacheSpec spec)
	Parses a FilterCacheSpec to see if it contains a filter that is associated with a particular type of Feature.
String	readToActual (String field)
	converts spaces in string to underscores
void	removeLocationDuplicates (LinkedList feats)
	Removes multiple features with the same location, so only one is displayed in the tree.
StringTokenizer	separateFields (String fields)
	returns a tokenizer with string separated at '/'
Vector	userSelectableGenomes (BaseViewerModel model, boolean all_ok, boolean needs_annotations)
	constructs an array of all possible genomes a user should be able to pick from.
Genome[]	userSelectedGenomes (Component parent, BaseViewerModel model, boolean all_ok, boolean needs_annotations)
	Pops up a dialog box that allows a user to choose a specific (or all) genome/s.
Static Public Attributes
FeatureComparator	feature_comp = new FeatureComparator ()
Private Member Functions
	SeqFeatureData ()
	private constructor prevents instantiation; all static

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Detailed Description

Utility class for data specific to sequence navigator involving genomes and their features.

Author:

rissman

Definition at line 27 of file SeqFeatureData.java.

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Constructor & Destructor Documentation

org::gel::mauve::SeqFeatureData::SeqFeatureData (   )  [inline, private]

private constructor prevents instantiation; all static Definition at line 35 of file SeqFeatureData.java.

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Member Function Documentation

long org::gel::mauve::SeqFeatureData::centerOfFeature (  Feature  feature  )  [inline, static]

finds the center sequence coordinate of a feature Parameters: feature  The feature whose center should be found Returns: A long representing the sequence position of the center of the feature Definition at line 185 of file SeqFeatureData.java.

Genome [] org::gel::mauve::SeqFeatureData::convertIndexToSequence (  Vector  choices, int  index )  [inline, static]

returns an array representing the user selected genomes. If the first choices in the Parameters: choices  The vector of possible genomes index  The index selected from the vector of choices Returns: An array of 1 containing the selected sequence unless the user chose all sequences, in which case the array will return all of them Definition at line 300 of file SeqFeatureData.java.

LinkedList [] org::gel::mauve::SeqFeatureData::findFeatures (  Genome[]  nomes, Stringdata  [][] )  [inline, static]

Finds all features associated with specified genomes matching the specified key value pairs. Parameters: nomes  An array of which genomes whose features should be searched. data  An array of arrays containing desired key-value pairs, indeces specified in MauveConstants Returns: An array of LinkedLists. The first value in each list is the genome the list corresponds to; all other values are features associated with that genome Definition at line 89 of file SeqFeatureData.java. References org::gel::mauve::Genome::getAnnotationSequence(), getFilter(), and org::gel::mauve::Genome::length.

FeatureFilter org::gel::mauve::SeqFeatureData::getFilter (  Stringdata  [][]  )  [inline, static]

Returns a filter that will accept annotations matching the desired keys and values. Parameters: data  An array of length 3 arrays, each corresponding to a key, value, and whether the value is exact (array indeces specified in MauveConstants) Returns: A filter that can be used to accept matching features Definition at line 48 of file SeqFeatureData.java. References readToActual(). Referenced by findFeatures().

String org::gel::mauve::SeqFeatureData::getTypeFromFilter (  FeatureFilter  filter  )  [inline, static]

Parses a FeatureFilter to see if it contains a filter that is associated with a particular type of Feature. Will only return one type; so will not work for some or filters. Parameters: filter  The filter to search Returns: A string corresponding to the type associated with the filter, or MauveConstants.ANY_FEATURE Definition at line 217 of file SeqFeatureData.java. Referenced by getTypeFromFilterSpec().

String org::gel::mauve::SeqFeatureData::getTypeFromFilterSpec (  FilterCacheSpec  spec  )  [inline, static]

Parses a FilterCacheSpec to see if it contains a filter that is associated with a particular type of Feature. Will only return one type; so will not work for some or filters. Parameters: spec  The spec to search Returns: A string corresponding to the type associated with the spec, or MauveConstants.ANY_FEATURE Definition at line 200 of file SeqFeatureData.java. References org::gel::mauve::FilterCacheSpec::getFilter(), and getTypeFromFilter().

String org::gel::mauve::SeqFeatureData::readToActual (  String  field  )  [inline, static]

converts spaces in string to underscores Parameters: field  The human readible version of the field Returns: The qualifier name as it appears in data Definition at line 168 of file SeqFeatureData.java. Referenced by getFilter().

void org::gel::mauve::SeqFeatureData::removeLocationDuplicates (  LinkedList  feats  )  [inline, static]

Removes multiple features with the same location, so only one is displayed in the tree. Parameters: feats  The list of features that might contain duplicates Definition at line 112 of file SeqFeatureData.java. References org::gel::mauve::SeqFeatureData::FeatureComparator::compare(), and feature_comp.

StringTokenizer org::gel::mauve::SeqFeatureData::separateFields (  String  fields  )  [inline, static]

returns a tokenizer with string separated at '/' Parameters: fields  Returns: Definition at line 157 of file SeqFeatureData.java.

Vector org::gel::mauve::SeqFeatureData::userSelectableGenomes (  BaseViewerModel  model, boolean  all_ok, boolean  needs_annotations )  [inline, static]

constructs an array of all possible genomes a user should be able to pick from. Will have an "All" option depending on parameters Parameters: model  The model whose genomes are possible user selections all_ok  True if user should have the option to choose "All Genomes". needs_annotations  True if a genome should only be selectable if it has annotations loaded Returns: An vector of genomes a user can choose between Definition at line 271 of file SeqFeatureData.java. References org::gel::mauve::Genome::getAnnotationSequence(), and org::gel::mauve::BaseViewerModel::getGenomes(). Referenced by userSelectedGenomes().

Genome [] org::gel::mauve::SeqFeatureData::userSelectedGenomes (  Component  parent, BaseViewerModel  model, boolean  all_ok, boolean  needs_annotations )  [inline, static]

Pops up a dialog box that allows a user to choose a specific (or all) genome/s. Parameters: parent  The frame the JDialogs for user input should block model  The BaseViewerModel containing all possible genome choices all_ok  True if user should have the option to choose "All Genomes". needs_annotations  True if a genome should only be selectable if it has annotations loaded Returns: An array of genomes that contains all genomes the user picked. Definition at line 245 of file SeqFeatureData.java. References userSelectableGenomes().

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Member Data Documentation

FeatureComparator org::gel::mauve::SeqFeatureData::feature_comp = new FeatureComparator () [static]

Definition at line 29 of file SeqFeatureData.java. Referenced by removeLocationDuplicates().

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The documentation for this class was generated from the following file:

• src/org/gel/mauve/SeqFeatureData.java

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