src/org/gel/mauve/MauveConstants.java

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00001 package org.gel.mauve;
00002 
00003 import java.util.HashSet;
00004 import java.util.Hashtable;
00005 
00006 import org.biojava.bio.seq.Feature;
00007 import org.biojava.bio.seq.FeatureFilter;
00008 import org.biojava.bio.seq.OptimizableFilter;
00009 
00010 public interface MauveConstants {
00011 
00015         public static final String PRODUCT_NAME = "product/alternate_product_name";
00016 
00017         public static final String LOC_NAME = "gene/synonym/standard_name/name/"
00018                         + "locus_tag/label/old_locus_tag";
00019 
00020         public static final String GO_FEATS = "go_biological_process/"
00021                         + "go_cellular_component/go_molecular_function";
00022 
00023         public static final String ID_NUMBER = "ec_number/db_xref/protein_id";
00024 
00028         public static final String PRODUCT = "Product";
00029 
00030         public static final String NAME = "Name";
00031 
00032         public static final String GO = "Go Features";
00033 
00034         public static final String ID = "ID Number";
00035 
00040         public static final String ISLAND_MIN = "island_min";
00041 
00042         public static final String BACKBONE_MIN = "backbone_min";
00043 
00044         public static final String MAX_LENGTH_RATIO = "max_length_ratio";
00045 
00046         public static final String MINIMUM_PERCENT_CONTAINED = "minimum_percent_contained";
00047         
00048         public static final String FILE_STUB = "output_file_stub";
00049 
00050         public static final String DEFAULT_TITLES = "default_titles";
00051 
00052         public static final String REFERENCE = "reference";
00053 
00054         public static final String FIRSTS = "firsts";
00055 
00056         public static final String BACKBONE = "backbone_vector";
00057 
00058         public static final String ALL_MULTIPLICITY = "all_multiplicity_int";
00059 
00060         public static final String SEQUENCE_INDEX = "sequence index";
00061         
00062         public static final String MODEL = "model";
00063         
00064         public static final String GENOME_LENGTHS = "genome_lengths";
00065         
00066         public static final String CONTIG_HANDLER = "contig_handler";
00067         
00068         public static final String NUM_GENES_PER_MULT = "number_of_genes_per_multiplicity";
00069         
00070         public static final String TOTAL_GENES = "total_genes";
00071         
00072         public static final String TOTALS = "totals";
00073         
00075         public static final String CIRCULAR_CHAR = "*";
00076         
00080         public static final String DB_XREF = "db_xref";
00081         
00085         public static final int BY_GENOMES = 1;
00086 
00087         public static final int BY_BB_LIST = 2;
00088 
00089         public static final int BY_ALL_AND_BB = 3;
00090 
00091         public static final int BY_ONE_GENOME = 4;
00092 
00093         public static final int BY_ONE_AND_BB = 6;
00094 
00098         public static final int DEFAULT_ISLAND_MIN = 1;
00099 
00100         public static final int DEFAULT_BACKBONE_MIN = 1;
00101 
00102         public static final double DEFAULT_MAX_LENGTH_RATIO = .2;
00103         
00104         public static final double DEFAULT_MIN_PERCENT_CONTAINED = 99.8;
00105 
00109         public static final String ALL_SEQUENCES = "All Sequences";
00110 
00115         public static final String ANY_FEATURE = "any";
00116 
00117         public static final Hashtable READ_TO_ACTUAL = new Hashtable ();
00118 
00122         public static final HashSet ANNOTATION_KEYS = new HashSet ();
00123 
00128         public static final int FIELD = 0;
00129 
00130         public static final int VALUE = 1;
00131 
00132         public static final int EXACT = 2;
00133 
00137         public static final int BORDER = 10;
00138         
00142         public static final String ANALYSIS_OUTPUT = "analysis";
00143         
00147         public static final String CONTIG_OUTPUT = "contigs";
00148         
00152         public static final int FEATURE_HEIGHT = 25;
00153         
00157         public static final String ASAP = "asap";
00158         
00159         public static final String ERIC = "eric";
00160         
00164         public static final String LOCUS = "LOCUS";
00165         
00166         public static final OptimizableFilter NULL_AVOIDER = new OptimizableFilter () {
00167                 public boolean accept (Feature f) {
00168                         return f.getAnnotation () != null;
00169                 }
00170 
00171                 public boolean isDisjoint (FeatureFilter filt) {
00172                         return false;
00173                 }
00174 
00175                 public boolean isProperSubset (FeatureFilter sup) {
00176                         return this.equals (sup);
00177                 }
00178 
00179         };
00180 
00181         public final static String DEFAULT_CONTIG = "chromosome";
00182 }

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