A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

W

w - Variable in class statalign.model.subst.SubstitutionModel

The rate matrix must be diagonalized and represented in a v d w product, where d is a diagonal matrix

Wag - Class in statalign.model.subst.plugins

Implements the WAG (Whelan & Goldman model) substitution model, see also http://www.ncbi.nlm.nih.gov/pubmed/11319253

Wag() - Constructor for class statalign.model.subst.plugins.Wag

Constructor used when instantiation is necessary.

wasProposed - Variable in class statalign.postprocess.plugins.structalign.StructAlignTraceParameters.PlottableParameter

webPage - Variable in enum statalign.utils.Libraries

webPageURL - Static variable in class statalign.StatAlign

weightedChoose(int[]) - Static method in class statalign.base.Utils

This function returns a random index, weighted by the weights in the array `weights'

weightedChoose(List<Integer>) - Static method in class statalign.base.Utils

This function returns a random index, weighted by the weights in the array `weights'

weightedChoose(double[], MuDouble) - Static method in class statalign.base.Utils

Similar to weightedChoose(weights), but the log-probability of the selection will be subtracted from the mutable double object selectLogLike (reason: proposal is in the denominator of acceptance ratio) (MuDouble is used to allow for another return value, in C++ a double pointer/reference could be used instead)

weightedChoose(double[]) - Static method in class statalign.base.Utils

weightedChoose(List<Double>, MuDouble) - Static method in class statalign.base.Utils

weighting - Variable in class statalign.postprocess.plugins.contree.CNetworkEdge

WELCOME_MSG - Static variable in class statalign.ui.MainFrame

which - Variable in class statalign.model.score.SubstitutionScore

This array tells the mapping between characters and indices in the distance array.

width - Variable in class statalign.postprocess.gui.CNetworkView

width - Variable in class statalign.postprocess.gui.treeviews.NetworkTreeView

WINDOW_MULTIPLIER - Static variable in class statalign.base.Utils

Initial value for the alignment proposal window length multiplier.

writeMatrix(double[][], File) - Static method in class statalign.postprocess.utils.RNAFoldingTools

A helper method which writes double matrices to files.

writeMatrix(int[][], File) - Static method in class statalign.postprocess.utils.RNAFoldingTools

A helper method which writes integer matrices to files.

writePDB(double[][][], String[], String[], FileWriter) - Static method in class statalign.io.input.plugins.PDBReader

writeRotationFiles(Tree, double[][][], double[][], double[][], double[]) - Static method in class statalign.model.ext.plugins.structalign.Funcs

writeToFile(File, String, boolean) - Static method in class statalign.postprocess.utils.RNAFoldingTools