Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DEFAULT_PARAM_FILE |
"default.param" |
public static final java.lang.String |
FIELD_SEPARATOR |
"\t" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
COLLAPSE_DEGEN_GEN_NEIGHBORS_RECON_METHOD |
"CDGR" |
public static final java.lang.String |
COLLAPSE_DEGEN_RECON_METHOD |
"CDR" |
public static final java.lang.String |
GEN_NEIGHBORS_RECON_METHOD |
"GR" |
public static final double |
MAX_AMB |
0.5 |
public static final java.lang.String |
MUTATION_METHOD |
"mutationMethod" |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final double |
MIN_SCORE |
5.0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
NUM_REPS |
1000 |
public static final int |
REPORT_TOP_N |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
AMBIGUIZER_NAME |
"PRISM" |
public static final java.lang.String |
BEAM_NAME |
"BEAM" |
private static final java.lang.String |
beamDriverScoreDataSuffix |
"BeamDriver subtracted bipartitePenalty from motif score: " |
public static final java.lang.String |
BIPARTITE_NAME |
"SPACER" |
public static final java.lang.String |
MERGED_NAME |
"SCOPE" |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final java.lang.String |
BEAM_PACKAGE |
"edu.dartmouth.bglab.beam." |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final java.lang.String |
GENES_WITH_MOTIF_WHICH_DO_NOT_IMPROVE_SCORE |
"genesWithMotifWhichDoNotImproveScore" |
private static final java.lang.String |
GENES_WITH_MOTIF_WHICH_IMPROVE_SCORE |
"genesWithMotifWhichImproveScore" |
private static final java.lang.String |
INTRON_MARKER |
"^intron" |
Modifier and Type | Constant Field | Value |
---|---|---|
private final boolean |
output |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final int |
DBRESULT_INVALIDFASTA |
5 |
private static final int |
DBRESULT_MISSINGGENES |
2 |
private static final int |
DBRESULT_SUCCESS |
1 |
private static final int |
DBRESULT_UNSPECIFIEDERROR |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
DISCARD_OVERLAPS |
false |
public static final int |
RAND_KNOWN_RATIO |
10 |
public static final boolean |
USE_REV_COMP |
true |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
MOTIF_LIST_SUFFIX |
"ml" |
public static final java.lang.String |
MOTIF_SUFFIX |
"m" |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final java.lang.String |
FONTNAME |
"Arial" |
private static final int |
FONTSIZE |
12 |
private static final int |
GENE_THICKNESS |
1 |
private static final int |
LEFT_PADDING |
20 |
private static final int |
MAX_NAME_WIDTH |
80 |
private static final int |
MIN_MOTIF_WIDTH |
3 |
private static final int |
MOTIF_THICKNESS |
11 |
private static final int |
NAME_OFFSET |
10 |
private static final int |
SCALE_THICKNESS |
2 |
private static final int |
TICK_HEIGHT |
8 |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final int |
ERROR_STRING_HEIGHT |
15 |
public static final java.lang.String |
FIELD_DELIMITER |
"___" |
protected static final java.lang.String |
FONTNAME |
"Arial" |
private static final int |
FONTSIZE |
12 |
private static final int |
GENE_THICKNESS |
1 |
public static final java.lang.String |
INSTANCE_DELIMITER |
";" |
private static final int |
LEFT_PADDING |
20 |
private static final int |
MAX_NAME_WIDTH |
80 |
private static final int |
MIN_MOTIF_WIDTH |
3 |
private static final int |
MOTIF_THICKNESS |
11 |
private static final int |
NAME_OFFSET |
10 |
public static final int |
PORTNUM |
6211 |
private static final int |
SCALE_THICKNESS |
2 |
public static final java.lang.String |
SERVER |
"genie.dartmouth.edu" |
public static final char |
SPACE |
126 |
private static final int |
TICK_HEIGHT |
8 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DARK_COLOR |
"\"#006600\"" |
public static final java.lang.String |
LIGHT_COLOR |
"\"#F7F5E6\"" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final char |
GENE_NAME_SEPARATOR |
59 |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final java.lang.String |
DELIMITER |
" \t\f\r\n" |
private static final int |
EOF |
-1 |
private static final int |
PUSHBACK_BUFFER_SIZE |
4096 |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final boolean |
DEBUGGING |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final java.lang.String |
AFFINITY_FILE_SUFFIX |
".tafy" |
private static final int |
AUTO_TRAINING_SIZE |
-1 |
private static final boolean |
BOOT_STRAP |
true |
public static final java.lang.String |
DIR |
"data/cre/bindingAffinityData/bindingSites/" |
private static final int |
FOLD |
50 |
private static final double |
MIN_AFFINITY |
0.5 |
private static final int |
NUM_RAND |
10000 |
private static final boolean |
PLOT_ROC |
false |
private static final boolean |
PRINT |
true |
private static final java.lang.String |
SITE_FILE_SUFFIX |
".sites" |
private static final boolean |
TEST_ON_ALL |
true |
private static final boolean |
TRUE_X_VAL |
true |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
DEFAULT_RC |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
BETA |
0.54 |
public static final double |
DEFAULT_STRINGENCY |
0.0 |
public static final double |
PSEUDO |
0.425 |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final int |
FN_AVE |
2 |
private static final int |
FP_AVE |
1 |
private static final boolean |
LOG_ODDS |
true |
private static final int |
MAX_K |
10 |
public static final int |
MAX_KMM_EXPANSION_SIZE |
100000 |
private static final int |
PHI_AVE |
0 |
private static final boolean |
RUN_LISTS |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
DEFAULT_STRINGENCY |
0.0 |
public static final int |
LAPLACE |
1 |
public static final int |
MAX_EXPANSION |
100000 |
public static final double |
PSEUDO |
0.425 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MAX_KMM_EXPANSION_SIZE |
10000 |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final int |
_N |
15 |
private static final int |
A |
1 |
private static final int |
ACGTRY_ID |
2 |
private static final int |
B |
14 |
private static final int |
C |
2 |
private static final int |
D |
13 |
public static final char |
FILLER |
95 |
private static final int |
FULL_ID |
0 |
private static final int |
G |
4 |
private static final int |
H |
11 |
private static final int |
K |
12 |
private static final int |
M |
3 |
public static final java.lang.String |
MOTIF_SEPARATOR |
"\\?" |
public static final char |
N |
110 |
public static final char |
NO_VALID_BASE |
90 |
private static final int |
PRIMARY_ID |
1 |
private static final int |
R |
5 |
private static final int |
S |
6 |
public static final char |
SEQUENCE_BREAK |
36 |
private static final int |
T |
8 |
private static final int |
V |
7 |
private static final int |
W |
9 |
private static final int |
Y |
10 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
LEFT |
false |
public static final double |
MIN_COVERAGE |
0.5 |
public static final int |
MIN_RANDOM_LENGTH |
5 |
public static final double |
PRIMARY_BASE_PROBABILITY |
0.8 |
public static final boolean |
PRINT_REV_COMP_ALPH_LAST |
true |
public static final boolean |
RIGHT |
true |
public static final java.lang.String |
SEPARATOR |
"," |
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
NEGATIVE_STRAND |
"-" |
public static final java.lang.String |
POSITIVE_STRAND |
"+" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
MOTIF_DELIMITER |
"|" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MAX_PERIODICITY |
2 |
public static final int |
MIN_REPETITIVE_STRETCH_LENGTH |
6 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
MIN_OVERLAP |
0.5 |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_HD |
1 |
public static final int |
WOC |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
WOC |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
WOC |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
WOC |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
LAPLACE |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final int |
INIT_SIZE |
100 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
HD |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
WOC |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
LAPLACE |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
WOC |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
SCORER_PACKAGE |
"edu.dartmouth.bglab.score." |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
-1L |
Modifier and Type | Constant Field | Value |
---|---|---|
private final transient int |
cacheRetrievalCountForCount |
0 |
private final transient int |
cacheRetrievalCountForFind |
0 |
private final transient int |
cacheStorageCountForCount |
0 |
private final transient int |
cacheStorageCountForFind |
0 |
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BIPARTITE_INIT_CACHE_SIZE |
20000 |
public static final int |
BIPARTITE_INIT_LEN |
6 |
public static final int |
BIPARTITE_INIT_N_COUNT_MAX |
11 |
public static final int |
BIPARTITE_INIT_N_COUNT_MIN |
6 |
protected static final int |
DEFAULT_MAX_HASH_LENGTH |
17 |
public static final java.lang.String |
ExtraGeneMotifFinderIdentifier |
"_extraGeneMotifFinder" |
public static final int |
NO_WILDCARD_OPTIMIZATION |
0 |
private static final long |
regexSearchCounterReportInterval |
250L |
static final long |
serialVersionUID |
-1L |
public static final java.lang.String |
TemporaryMotifFinderIdentifier |
"_temporaryMotifFinder" |
public static final int |
UNEQUAL_GENE_LENGTHS |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
-1L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
-1L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
MF_PACKAGE_NAME |
"edu.dartmouth.bglab.search." |
public static final java.lang.String |
OBJ_FILE_EXT |
".obj" |
public static final java.lang.String |
SEQ_FILE_EXT |
".raw" |
Modifier and Type | Constant Field | Value |
---|---|---|
static final long |
serialVersionUID |
-1L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
-1L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final int |
MAX_N |
1000 |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final int |
INIT_CAPACITY |
10 |
public static final int |
MAX_HEAP |
1 |
public static final int |
MIN_HEAP |
-1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
MIN_SUM_DELTA |
1.0E-8 |
public static final double |
MIN_TERM_DELTA |
0.001 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
NUM_DECIMALS |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final int |
MIN_COUNT |
10 |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
SLEEP_TIME |
10 |
Modifier and Type | Constant Field | Value |
---|---|---|
private static final long |
serialVersionUID |
1L |