org::gel::mauve::MauveConstants Interface Reference

Inheritance diagram for org::gel::mauve::MauveConstants:

Inheritance graph
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List of all members.

Static Public Attributes

final String ALL_MULTIPLICITY = "all_multiplicity_int"
final String ALL_SEQUENCES = "All Sequences"
 dummy string representing all genomes rather than one specific sequence

final String ANALYSIS_OUTPUT = "analysis"
 represents subfolder output from analysis package is written to

final HashSet ANNOTATION_KEYS = new HashSet ()
 contains default annotation keys to use for filters, etc.

final String ANY_FEATURE = "any"
 Represents a feature type corresponding to any feature; used for FeatureFilter.ByType or FeatureFilter.ByAnnotationType.

final String ASAP = "asap"
 String present in all ASAP generated db_xref values.

final String BACKBONE = "backbone_vector"
final String BACKBONE_MIN = "backbone_min"
final int BORDER = 10
 border between separate components in the navigation guis

final int BY_ALL_AND_BB = 3
final int BY_BB_LIST = 2
final int BY_GENOMES = 1
 Integer codes for how to cycle through segments for processing.

final int BY_ONE_AND_BB = 6
final int BY_ONE_GENOME = 4
final String CIRCULAR_CHAR = "*"
final String CONTIG_HANDLER = "contig_handler"
final String CONTIG_OUTPUT = "contigs"
 represents subfolder output from contig package is written to

final String DB_XREF = "db_xref"
 Strings representing annotation types.

final int DEFAULT_BACKBONE_MIN = 1
final String DEFAULT_CONTIG = "chromosome"
final int DEFAULT_ISLAND_MIN = 1
 default values for backbone processing for analysis package

final double DEFAULT_MAX_LENGTH_RATIO = .2
final double DEFAULT_MIN_PERCENT_CONTAINED = 99.8
final String DEFAULT_TITLES = "default_titles"
final String ERIC = "eric"
final int EXACT = 2
final int FEATURE_HEIGHT = 25
 height that should be added when a new type of feature is displayed

final int FIELD = 0
 ints representing indexes of data in data array used to represent constraints

final String FILE_STUB = "output_file_stub"
final String FIRSTS = "firsts"
final String GENOME_LENGTHS = "genome_lengths"
final String GO = "Go Features"
final String GO_FEATS
final String ID = "ID Number"
final String ID_NUMBER = "ec_number/db_xref/protein_id"
final String ISLAND_MIN = "island_min"
 Strings representing keys possibly present in a SegmentDataProcessor object.

final String LOC_NAME
final String LOCUS = "LOCUS"
 Fields biojava uses as constants that are protected for some reason.

final String MAX_LENGTH_RATIO = "max_length_ratio"
final String MINIMUM_PERCENT_CONTAINED = "minimum_percent_contained"
final String MODEL = "model"
final String NAME = "Name"
final OptimizableFilter NULL_AVOIDER
final String NUM_GENES_PER_MULT = "number_of_genes_per_multiplicity"
final String PRODUCT = "Product"
 Strings representing prebuilt groupings of search fields.

final String PRODUCT_NAME = "product/alternate_product_name"
 Strings representing choices for ways to navigate.

final Hashtable READ_TO_ACTUAL = new Hashtable ()
final String REFERENCE = "reference"
final String SEQUENCE_INDEX = "sequence index"
final String TOTAL_GENES = "total_genes"
final String TOTALS = "totals"
final int VALUE = 1

Member Data Documentation

final String org::gel::mauve::MauveConstants::ALL_MULTIPLICITY = "all_multiplicity_int" [static]
 

Definition at line 58 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::ALL_SEQUENCES = "All Sequences" [static]
 

dummy string representing all genomes rather than one specific sequence

Definition at line 109 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::ANALYSIS_OUTPUT = "analysis" [static]
 

represents subfolder output from analysis package is written to

Definition at line 142 of file MauveConstants.java.

final HashSet org::gel::mauve::MauveConstants::ANNOTATION_KEYS = new HashSet () [static]
 

contains default annotation keys to use for filters, etc.

Definition at line 122 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::ANY_FEATURE = "any" [static]
 

Represents a feature type corresponding to any feature; used for FeatureFilter.ByType or FeatureFilter.ByAnnotationType.

Definition at line 115 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::ASAP = "asap" [static]
 

String present in all ASAP generated db_xref values.

Definition at line 157 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::BACKBONE = "backbone_vector" [static]
 

Definition at line 56 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::BACKBONE_MIN = "backbone_min" [static]
 

Definition at line 42 of file MauveConstants.java.

final int org::gel::mauve::MauveConstants::BORDER = 10 [static]
 

border between separate components in the navigation guis

Definition at line 137 of file MauveConstants.java.

final int org::gel::mauve::MauveConstants::BY_ALL_AND_BB = 3 [static]
 

Definition at line 89 of file MauveConstants.java.

final int org::gel::mauve::MauveConstants::BY_BB_LIST = 2 [static]
 

Definition at line 87 of file MauveConstants.java.

final int org::gel::mauve::MauveConstants::BY_GENOMES = 1 [static]
 

Integer codes for how to cycle through segments for processing.

Definition at line 85 of file MauveConstants.java.

final int org::gel::mauve::MauveConstants::BY_ONE_AND_BB = 6 [static]
 

Definition at line 93 of file MauveConstants.java.

final int org::gel::mauve::MauveConstants::BY_ONE_GENOME = 4 [static]
 

Definition at line 91 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::CIRCULAR_CHAR = "*" [static]
 

Definition at line 75 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::CONTIG_HANDLER = "contig_handler" [static]
 

Definition at line 66 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::CONTIG_OUTPUT = "contigs" [static]
 

represents subfolder output from contig package is written to

Definition at line 147 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::DB_XREF = "db_xref" [static]
 

Strings representing annotation types.

Definition at line 80 of file MauveConstants.java.

final int org::gel::mauve::MauveConstants::DEFAULT_BACKBONE_MIN = 1 [static]
 

Definition at line 100 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::DEFAULT_CONTIG = "chromosome" [static]
 

Definition at line 181 of file MauveConstants.java.

final int org::gel::mauve::MauveConstants::DEFAULT_ISLAND_MIN = 1 [static]
 

default values for backbone processing for analysis package

Definition at line 98 of file MauveConstants.java.

final double org::gel::mauve::MauveConstants::DEFAULT_MAX_LENGTH_RATIO = .2 [static]
 

Definition at line 102 of file MauveConstants.java.

final double org::gel::mauve::MauveConstants::DEFAULT_MIN_PERCENT_CONTAINED = 99.8 [static]
 

Definition at line 104 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::DEFAULT_TITLES = "default_titles" [static]
 

Definition at line 50 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::ERIC = "eric" [static]
 

Definition at line 159 of file MauveConstants.java.

final int org::gel::mauve::MauveConstants::EXACT = 2 [static]
 

Definition at line 132 of file MauveConstants.java.

final int org::gel::mauve::MauveConstants::FEATURE_HEIGHT = 25 [static]
 

height that should be added when a new type of feature is displayed

Definition at line 152 of file MauveConstants.java.

final int org::gel::mauve::MauveConstants::FIELD = 0 [static]
 

ints representing indexes of data in data array used to represent constraints

Definition at line 128 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::FILE_STUB = "output_file_stub" [static]
 

Definition at line 48 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::FIRSTS = "firsts" [static]
 

Definition at line 54 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::GENOME_LENGTHS = "genome_lengths" [static]
 

Definition at line 64 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::GO = "Go Features" [static]
 

Definition at line 32 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::GO_FEATS [static]
 

Initial value:

 "go_biological_process/"
                        + "go_cellular_component/go_molecular_function"

Definition at line 20 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::ID = "ID Number" [static]
 

Definition at line 34 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::ID_NUMBER = "ec_number/db_xref/protein_id" [static]
 

Definition at line 23 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::ISLAND_MIN = "island_min" [static]
 

Strings representing keys possibly present in a SegmentDataProcessor object.

Definition at line 40 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::LOC_NAME [static]
 

Initial value:

 "gene/synonym/standard_name/name/"
                        + "locus_tag/label/old_locus_tag"

Definition at line 17 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::LOCUS = "LOCUS" [static]
 

Fields biojava uses as constants that are protected for some reason.

Definition at line 164 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::MAX_LENGTH_RATIO = "max_length_ratio" [static]
 

Definition at line 44 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::MINIMUM_PERCENT_CONTAINED = "minimum_percent_contained" [static]
 

Definition at line 46 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::MODEL = "model" [static]
 

Definition at line 62 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::NAME = "Name" [static]
 

Definition at line 30 of file MauveConstants.java.

final OptimizableFilter org::gel::mauve::MauveConstants::NULL_AVOIDER [static]
 

Initial value:

 new OptimizableFilter () {
                public boolean accept (Feature f) {
                        return f.getAnnotation () != null;
                }

                public boolean isDisjoint (FeatureFilter filt) {
                        return false;
                }

                public boolean isProperSubset (FeatureFilter sup) {
                        return this.equals (sup);
                }

        }

Definition at line 166 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::NUM_GENES_PER_MULT = "number_of_genes_per_multiplicity" [static]
 

Definition at line 68 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::PRODUCT = "Product" [static]
 

Strings representing prebuilt groupings of search fields.

Definition at line 28 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::PRODUCT_NAME = "product/alternate_product_name" [static]
 

Strings representing choices for ways to navigate.

Definition at line 15 of file MauveConstants.java.

final Hashtable org::gel::mauve::MauveConstants::READ_TO_ACTUAL = new Hashtable () [static]
 

Definition at line 117 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::REFERENCE = "reference" [static]
 

Definition at line 52 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::SEQUENCE_INDEX = "sequence index" [static]
 

Definition at line 60 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::TOTAL_GENES = "total_genes" [static]
 

Definition at line 70 of file MauveConstants.java.

final String org::gel::mauve::MauveConstants::TOTALS = "totals" [static]
 

Definition at line 72 of file MauveConstants.java.

final int org::gel::mauve::MauveConstants::VALUE = 1 [static]
 

Definition at line 130 of file MauveConstants.java.


The documentation for this interface was generated from the following file:
Generated on Mon Aug 19 06:03:47 2013 for Mauve by doxygen 1.3.6