Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
NO FRAMES
All Classes
A
B
C
D
E
F
G
H
I
J
L
M
N
O
P
R
S
T
U
V
W
X
P
Pair
<
T1
,
T2
> - Class in
contextFold.common
Pair(T1, T2)
- Constructor for class contextFold.common.
Pair
PAIRED
- Static variable in class contextFold.rnaFolding.
Traceback
possibleReplacements
- Static variable in class contextFold.rna.
RNA
PPV()
- Method in class contextFold.scoring.
PredictionQuality
Predict
- Class in
contextFold.app
Produces secondary structure predictions for RNA sequences.
Predict()
- Constructor for class contextFold.app.
Predict
predictAll(FeatureManager, String, List<RNA>)
- Static method in class contextFold.app.
Predict
predictAll(FeatureManager, String, List<RNA>, String)
- Static method in class contextFold.app.
Predict
predicted
- Variable in class contextFold.rna.
RNA
predictFolding(String)
- Method in class contextFold.rnaFolding.
Folder
PredictionQuality
- Class in
contextFold.scoring
PredictionQuality(int[], int[])
- Constructor for class contextFold.scoring.
PredictionQuality
PredictionQuality(int[], int[], float)
- Constructor for class contextFold.scoring.
PredictionQuality
predictionStatistics(String)
- Static method in class contextFold.scoring.
PredictionQuality
predictionStatistics(String, int)
- Static method in class contextFold.scoring.
PredictionQuality
predictionStatistics(String, int, boolean)
- Static method in class contextFold.scoring.
PredictionQuality
predictionStatistics(List<RNA>, int)
- Static method in class contextFold.scoring.
PredictionQuality
predictionStatistics(List<RNA>, int, boolean)
- Static method in class contextFold.scoring.
PredictionQuality
preprocess(byte[])
- Method in class contextFold.features.
BinnedLengthFeatureExtractor
preprocess(byte[])
- Method in class contextFold.features.
DoublePosContext
preprocess(byte[])
- Method in class contextFold.features.
FeatureExtractor
preprocess(byte[])
- Method in class contextFold.features.
SinglePosContext
PrintModelFeatures
- Class in
contextFold.app
Prints feature names and their weights for a given scoring model.
PrintModelFeatures()
- Constructor for class contextFold.app.
PrintModelFeatures
printStructure(int[], int[])
- Static method in class contextFold.rnaFolding.
Folder
processArgs(String[])
- Method in class contextFold.common.
CmdArgumentsHandler
PS_CLOSE
- Static variable in class contextFold.rna.
RNA
PS_OPEN
- Static variable in class contextFold.rna.
RNA
pseudoClose
- Static variable in class contextFold.rna.
RNA
pseudoClosePattern
- Static variable in class contextFold.rna.
RNA
pseudoFoldPattern
- Static variable in class contextFold.rna.
RNA
pseudoOpen
- Static variable in class contextFold.rna.
RNA
pseudoOpenPattern
- Static variable in class contextFold.rna.
RNA
Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
NO FRAMES
All Classes
A
B
C
D
E
F
G
H
I
J
L
M
N
O
P
R
S
T
U
V
W
X