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biggests.clustering.* |
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biggests.clustering.AbstractMetricClustering | ||
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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 | ||
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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.* |
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biggests.gui.BiggestsIO | ||
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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 | ||
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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 | ||
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public static final java.lang.String |
hierarchicalClusteringTempFilesDirectoryPath |
"hc-temp" |
biggests.gui.PanelAnalyzingMatrixTables | ||
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public static final int |
COLORS |
1 |
public static final int |
SYMBOLS |
2 |
public static final int |
VALUES |
0 |
biggests.gui.PanelBiclustering | ||
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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 | ||
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public static final int |
ALL_TIME_POINTS |
1 |
public static final int |
BICLUSTER_TIME_POINTS |
0 |
public static final int |
PATTERN |
2 |
biggests.gui.PanelLoading | ||
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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 | ||
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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 | ||
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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 | ||
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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.* |
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biggests.tables.TableSorter | ||
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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.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 |
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