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contextFold.common.* |
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contextFold.common.CmdArgumentsHandler | ||
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public static final java.lang.String |
noValue |
"$$$NO_VALUE!$$$" |
contextFold.common.Env | ||
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public static final int |
MAX_SERVER_SEQUENCE_LENGTH |
1000 |
contextFold.features.* |
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contextFold.features.WordFeatureCalculator | ||
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public static final int |
FULL |
0 |
public static final int |
REDUCED |
1 |
public static final int |
TRIVIAL |
2 |
contextFold.models.* |
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contextFold.models.FeatureSetter | ||
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protected static final int |
LONG |
1 |
protected static final int |
SHORT |
0 |
contextFold.rna.* |
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contextFold.rna.AnnotationFilter | ||
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public static final java.lang.String |
SPACE_RPLACE |
"@@@" |
contextFold.rna.OneLineReader | ||
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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 | ||
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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.* |
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contextFold.rnaFolding.StructureRecognizer | ||
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public static final int |
UNPAIRED_BASE |
-1 |
contextFold.rnaFolding.Traceback | ||
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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 |
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