Constant Field Values


Contents
contextFold.common.*

contextFold.common.CmdArgumentsHandler
public static final java.lang.String noValue "$$$NO_VALUE!$$$"

contextFold.common.Env
public static final int MAX_SERVER_SEQUENCE_LENGTH 1000

contextFold.features.*

contextFold.features.WordFeatureCalculator
public static final int FULL 0
public static final int REDUCED 1
public static final int TRIVIAL 2

contextFold.models.*

contextFold.models.FeatureSetter
protected static final int LONG 1
protected static final int SHORT 0

contextFold.rna.*

contextFold.rna.AnnotationFilter
public static final java.lang.String SPACE_RPLACE "@@@"

contextFold.rna.OneLineReader
public static final int ANNOTATION_GROUP 1
public static final java.lang.String extendedRNARegexp "([a-zA-Z]*[acgutACGUT]+[a-zA-Z]*)+"
public static final java.lang.String FoldingLineRegexp "[ \\t]*([a-zA-Z\\[\\]\\{\\}<>]*[()\\.]+[a-zA-Z\\[\\]\\{\\}<>]*)+[ \\t]*[\\n\\r]"
public static final java.lang.String FoldingRegexp "([a-zA-Z\\[\\]\\{\\}<>]*[()\\.]+[a-zA-Z\\[\\]\\{\\}<>]*)+"
public static final int ITEM_GROUP 0
public static final java.lang.String RNAItemRegexp "(([>#][^\\n\\r]*[\\n\\r])*)[\\n\\r]*([ \\t]*(([a-zA-Z]*[acgutACGUT]+[a-zA-Z]*)+)[ \\t]*[\\n\\r])(([ \\t]*([a-zA-Z\\[\\]\\{\\}<>]*[()\\.]+[a-zA-Z\\[\\]\\{\\}<>]*)+[ \\t]*[\\n\\r])*)"
public static final java.lang.String RNALine_Regexp "[ \\t]*(([a-zA-Z]*[acgutACGUT]+[a-zA-Z]*)+)[ \\t]*[\\n\\r]"
public static final int SEQUENCE_GROUP 3
public static final int STRUCTURE_GROUP 6

contextFold.rna.RNA
public static final byte A 0
public static final java.lang.String annotationRegexp "[>#][^\\n\\r]*[\\n\\r]"
public static final byte C 1
public static final int CLOSE 1
public static final byte G 2
public static final int OPEN 0
public static final int PS_CLOSE 4
public static final int PS_OPEN 3
public static final java.lang.String pseudoClose ")>}\\]a-z"
public static final java.lang.String pseudoOpen "(<{\\[A-Z"
public static final int ROUND 0
public static final int SHARP 1
public static final java.lang.String STANDARD_RNA_CHARS "acgutACGUT"
public static final java.lang.String standardClose ")"
public static final java.lang.String standardOpen "("
public static final byte T 3
public static final byte U 3
public static final int UN_PAIRED 2

contextFold.rnaFolding.*

contextFold.rnaFolding.StructureRecognizer
public static final int UNPAIRED_BASE -1

contextFold.rnaFolding.Traceback
public static final int BEST 2
public static final int JUST_ONE_BRANCH 0
public static final int MORE_THAN_ONE_BRANCH 1
public static final int PAIRED 0
public static final int UNPAIRED 1