Constant Field Values


Contents
biggests.clustering.*

biggests.clustering.AbstractMetricClustering
public static final char CITYBLOCK_DISTANCE 98
public static final boolean CONDITIONS_DIMENSION true
public static final char EUCLIDEAN_DISTANCE 101
public static final boolean GENES_DIMENSION false
public static final char KENDALL_TAU_CORRELATION 107
public static final char NO_CLUSTERING 0
public static final char PEARSON_ABS_CORRELATION 97
public static final char PEARSON_CORRELATION 99
public static final char SPEARMAN_RANK_CORRELATION 115
public static final char UNCENTERED_ABS_CORRELATION 120
public static final char UNCENTERED_CORRELATION 117

biggests.clustering.HierarchicalClustering
public static final char AVERAGE_LINKAGE 97
public static final char CENTROID_LINKAGE 99
public static final char COMPLETE_LINKAGE 109
public static final char SINGLE_LINKAGE 115

biggests.gui.*

biggests.gui.BiggestsIO
public static final int BUF_SIZE 1024
public static final java.lang.String JPG ".jpg"
public static final int MAX_HEIGHT 50000
public static final int MAX_WIDTH 50000
public static final java.lang.String PNG ".png"
public static final java.lang.String SVG ".svg"

biggests.gui.PanelAnalyzingFunctionSignificanceGraph
public static final java.lang.String GIF "gif"
public static final java.lang.String PNG "png"
public static final java.lang.String SVG "svg"

biggests.gui.PanelAnalyzingMatrixDendrogram
public static final java.lang.String hierarchicalClusteringTempFilesDirectoryPath "hc-temp"

biggests.gui.PanelAnalyzingMatrixTables
public static final int COLORS 1
public static final int SYMBOLS 2
public static final int VALUES 0

biggests.gui.PanelBiclustering
public static final java.lang.String ALPHA "alpha"
public static final java.lang.String CC_TSB_BICLUSTERING "CC-TSB-Biclustering"
public static final java.lang.String CCC_BICLUSTERING "CCC-Biclustering"
public static final java.lang.String DELTA "delta"
public static final java.lang.String E_CCC_BICLUSTERING "e-CCC-Biclustering"
public static final java.lang.String MAX_ITERATIONS "maximum number of iterations"
public static final java.lang.String MAX_TIME_LAG "max time lag"
public static final java.lang.String NEIGHBORS "neighbors"
public static final java.lang.String NUMBER_OF_BICLUSTERS "number of biclusters"
public static final java.lang.String NUMBER_OF_ERRORS "number of errors"
public static final java.lang.String SHIFTS "shifts"

biggests.gui.PanelExpression
public static final int ALL_TIME_POINTS 1
public static final int BICLUSTER_TIME_POINTS 0
public static final int PATTERN 2

biggests.gui.PanelFunctionAnalysis
public static final java.lang.String OBO_FILE_NAME "gene_ontology.1_0.obo"

biggests.gui.PanelLoading
public static final int CDNA 0
public static final float DEFAULT_MISSING_VALUE -2.147483648E9f
public static final int OLIGO 1
public static final int SEMICOLON 2
public static final int SPACE 1
public static final int TAB 0

biggests.gui.PanelPostProcessing
public static final int FILTER_ACV 4
public static final int FILTER_ACV_ARV 6
public static final int FILTER_ARV 5
public static final int FILTER_CONDITIONS 2
public static final int FILTER_CONDITIONS_GENES_ARV_ACV 10
public static final int FILTER_CONDITIONS_GENES_ARV_ACV_MSR 11
public static final int FILTER_CONSTANT_PATTERN 14
public static final int FILTER_GENES 1
public static final int FILTER_GENES_CONDITIONS 3
public static final int FILTER_MSR 7
public static final int FILTER_OVERLAPPING_GENES 12
public static final int FILTER_OVERLAPPING_GENES_CONDITIONS 13
public static final int FILTER_PATTERN_COLUMNS_PVALUE_NOT_SIGNIFICANT 16
public static final int FILTER_PATTERN_PVALUE_NOT_SIGNIFICANT 15
public static final int FILTER_SIZE 8
public static final int FILTER_SIZE_ARV_ACV 9
public static final int FILTER_TRIVIAL 0
public static final java.lang.String PARAMETER_ACV "average column variance"
public static final java.lang.String PARAMETER_ARV "average row variance"
public static final java.lang.String PARAMETER_CONDITIONS "number of conditions"
public static final java.lang.String PARAMETER_GENES "number of genes"
public static final java.lang.String PARAMETER_MARKOV_FILTER "Markov chain order to filter"
public static final java.lang.String PARAMETER_MARKOV_SORT "Markov chain order to sort"
public static final java.lang.String PARAMETER_MSR "mean squared residue"
public static final java.lang.String PARAMETER_PVALUE "p-value threshold"
public static final java.lang.String PARAMETER_SIMILARITY "similarity"
public static final java.lang.String PARAMETER_SIZE "size"
public static final int SORT_ACV 0
public static final int SORT_ARV 1
public static final int SORT_ARV_ACV_DIFF 3
public static final int SORT_ARV_MSR_DIFF 4
public static final int SORT_BEST_GO_BONFERRONI_PVALUE 10
public static final int SORT_BEST_GO_PVALUE 9
public static final int SORT_CONDITIONS 6
public static final int SORT_GENES 5
public static final int SORT_MSR 2
public static final int SORT_PATTERN_COLUMNS_PVALUE 12
public static final int SORT_PATTERN_PVALUE 11
public static final int SORT_SIZE 7
public static final int SORT_VARIANCE 8

biggests.gui.PanelPreProcessing
public static final java.lang.String DISCRETIZE_ALPHA "alpha value"
public static final java.lang.String DISCRETIZE_PERCENT "percentage for discretization"
public static final java.lang.String DISCRETIZE_SYMBOLS "number of symbols"
public static final java.lang.String DISCRETIZE_THRESHOLD "threshold"
public static final java.lang.String FILL_NEIGHBORS "number of neighbors"
public static final java.lang.String FILL_VALUE "value to fill missings"
public static final java.lang.String FILTER_PERCENTAGE "percentage of genes to filter"
public static final java.lang.String NORMALIZE_MEAN "mean value to normalize expression data"
public static final java.lang.String NORMALIZE_STD "std value to normalize expression data"
public static final java.lang.String SMOOTH_WINDOW "smoothing window"

biggests.gui.SaveChartImageDialog
public static final java.lang.String PDF ".pdf"
public static final java.lang.String PNG ".png"
public static final java.lang.String SVG ".svg"

biggests.tables.*

biggests.tables.TableSorter
public static final int ASCENDING 1
public static final int DESCENDING -1
public static final int NOT_SORTED 0

biggests.tree.*

biggests.tree.Dataset
public static final long serialVersionUID -9150182590356849832L

biggests.tree.DatasetTree
public static final long serialVersionUID 3882987169020172801L

biggests.tree.NodeInfo
public static final int BICLUSTER_GROUP 3
public static final int BICLUSTER_SINGLE 5
public static final int DISCRETIZED 2
public static final int ORIGINAL 0
public static final int POSTPROCESSED_GROUP 4
public static final int POSTPROCESSED_SINGLE 6
public static final int PREPROCESSED 1
public static final long serialVersionUID 7553487355938947549L
public static final boolean SYMBOLS true
public static final boolean VALUES false

biggests.utils.*

biggests.utils.HeatmapColorScheme
public static final int RED_GREEN_SCHEME 0
public static final int YELLOW_BLUE_SCHEME 1

biggests.utils.VerticalTextIcon
public static final int DEFAULT_CJK 1
public static final int DEFAULT_MUST_ROTATE 2
public static final int DEFAULT_ROMAN 4
public static final int kBufferSpace 5
public static final int LEGAL_MUST_ROTATE 6
public static final int LEGAL_ROMAN 7
public static final int POSITION_FAR_TOP_RIGHT 2
public static final int POSITION_NORMAL 0
public static final int POSITION_TOP_RIGHT 1
public static final int ROTATE_DEFAULT 0
public static final int ROTATE_LEFT 2
public static final int ROTATE_NONE 1
public static final int ROTATE_RIGHT 4