Constant Field Values

Contents

• de.unibi.*

de.unibi.*

de.unibi.techfak.jpredictor.jPREdictor

private static final int	FLAG_BS	2
private static final int	FLAG_DONTUSEPREDEFINED	512
private static final int	FLAG_FORCE	133169152
private static final int	FLAG_FORCE_CCC	8388608
private static final int	FLAG_FORCE_CLUSTERING	33554432
private static final int	FLAG_FORCE_EVOLUTION	67108864
private static final int	FLAG_FORCE_GUI	16777216
private static final int	FLAG_FORCE_SCORING	4194304
private static final int	FLAG_FORCE_SEARCHING	1048576
private static final int	FLAG_FORCE_WEIGHTING	2097152
private static final int	FLAG_MS	4
private static final int	FLAG_T	32
private static final int	FLAG_U	128
private static final int	FLAG_USEPREDEFINED	256
private static final java.lang.String	serialVersionDate	"2008/04/22"
private static final long	serialVersionUID	122L

de.unibi.techfak.jpredictor.clustering.Computable

public static final int	COMPUTATION_FAILED	3
public static final int	COMPUTATION_PENDING	2
public static final int	COMPUTATION_SUCCESS	0
public static final int	COMPUTATION_WAITING	1

de.unibi.techfak.jpredictor.gui.MainPanel

static final java.lang.String	ERROR	"Error"
static final java.lang.String	PASTED_SEQU	"[Pasted Sequence]"

de.unibi.techfak.jpredictor.gui.MotifMaker

static final int	MAX_TABLE_LENGTH	40
static final int	PANE_COUNT	5
static final int	PANE_MULTI	4
static final int	PANE_PSPM	2
static final int	PANE_PSSM	3
static final int	PANE_REGE	1
static final int	PANE_SEQU	0

de.unibi.techfak.jpredictor.gui.ScorePlotBrowser

public static final int	BARS	1
public static final int	DOTS	2
public static final int	LINES	4
public static final int	MAXIMUM	2
public static final int	MEAN	4
public static final int	MINIMUM	1

de.unibi.techfak.jpredictor.motifs.Motif

static final java.lang.String	DNA_DEGENERATED_CODE	"AaaabCGTcCccAdGTeeeeffffggGgAChTiiiijjjjkkGTllllACmmACGTooooppppqqqqArGrsCGstttTuuuuACGvAwwTxxxxyCyTzzzz"
public static final int	MARK_USABLE	256

de.unibi.techfak.jpredictor.motifs.MotifFilter

public static final java.lang.String	DNA_COMPLEMENT	"TVGH CD M KN YSAABW R "
public static final java.lang.String	DNA_FILTER	"A C G TT "
public static final java.lang.String	DNA_FILTER_DEGENERATED	"ABCD GH K MN RSTTVW Y "
public static final java.lang.String	DNA_FILTER_RESTRICTED	"A C G T "
public static final java.lang.String	DNA_RNA_FILTER	"A C G TU "
public static final java.lang.String	DNA_RNA_FILTER_DEGENERATED	"ABCD GH K MN RSTUVW Y "
public static final java.lang.String	RNA_COMPLEMENT	"UVGH CD M KN YSAABW R "
public static final java.lang.String	RNA_FILTER	"A C G UU "
public static final java.lang.String	RNA_FILTER_DEGENERATED	"ABCD GH K MN RSUUVW Y "
public static final java.lang.String	RNA_FILTER_RESTRICTED	"A C G U "

de.unibi.techfak.jpredictor.motifs.MotifSearcher

public static final int	SEARCH_ALL_ORIENTATIONS	3
public static final int	SEARCH_DIRECTION_MAX	4
public static final int	SEARCH_DIRECTION_MINUS	2
public static final int	SEARCH_DIRECTION_PLUS	1

de.unibi.techfak.jpredictor.motifs.PSPMotif

static final int	A	0
static final int	C	1
static final int	G	2
static final int	T	3

de.unibi.techfak.jpredictor.operator.ICommunicator

public static final java.lang.String	DISTANCE_ADJACENT	"Adjacent"
public static final java.lang.String	DISTANCE_ADJACENT73	"Adjacent_73"
public static final java.lang.String	DISTANCE_ANYSPACE	"Any_Space"
public static final java.lang.String	DISTANCE_BELOW220	"Below_220"
public static final java.lang.String	DISTANCE_ONETURN	"One_Turn"
public static final java.lang.String	DISTANCE_SINGLE	"Single"
public static final java.lang.String	DISTANCE_TWOTURNS	"Two_Turns"
public static final int	FLAG_B	1
public static final int	FLAG_F	16
public static final int	FLAG_M	4
public static final int	OBJECT_FASTA_MODIFIER	1
public static final int	OBJECT_FILENAME	256
public static final int	OBJECT_FILENAME_FASTA	257
public static final int	OBJECT_NOTYPE	0
public static final int	OBJECT_READER	1024
public static final int	OBJECT_READER_FASTA	1025
public static final int	OBJECT_SEQUENCE	2048
public static final int	OBJECT_STRING	512
public static final int	OBJECT_STRING_FASTA	513

de.unibi.techfak.jpredictor.operator.Operator

private static final int	METHOD_CALC	2
private static final int	METHOD_COUNT	1
private static final int	METHOD_SCORE	3
private static final int	METHOD_SEARCH	0

de.unibi.techfak.jpredictor.operator.OptionFile

static final int	SECTION_COUNT	4
static final int	SECTION_MMLIST	2
static final int	SECTION_MOTIF	0
static final int	SECTION_MULTIMOTIF	1
static final int	SECTION_NONE	-1
static final int	SECTION_SEQUENCE	3

de.unibi.techfak.jpredictor.operator.ScoringFactory

public static final int	TASK_COMPRISE_SCORES	2
public static final int	TASK_CUTOFF_CALC	1

de.unibi.techfak.jpredictor.operator.de.unibi.techfak.jpredictor.operator.States

public static final double	fixedCutoffDefault	0d/0d
public static final boolean	sequenceLengthNormalizationDefault	true
protected static final int	STORE_NEGATIVE_TRAINING_SET	2
protected static final int	STORE_POSITIVE_TRAINING_SET	1
protected static final int	STORE_SEQUENCE	0
public static final int	windowShiftDefault	10
public static final int	windowWidthDefault	500

de.unibi.techfak.jpredictor.sequences.FastaReader

public static final int

MAX_NAME_LENGTH

32000

de.unibi.techfak.jpredictor.sequences.SequenceFilter

public static final java.lang.String	DNA_COMPLEMENT	"TVGH CD M KN YSAABW R "
public static final java.lang.String	DNA_FILTER	"A-C---G------------TT-----"
public static final java.lang.String	DNA_FILTER_DEGENERATED	"ABCD--GH--K-M----RSTTVW-Y-"
public static final java.lang.String	DNA_FILTER_RESTRICTED	"A-C---G------------T------"
public static final java.lang.String	DNA_RNA_FILTER	"A-C---G------------TU-----"
public static final java.lang.String	DNA_RNA_FILTER_DEGENERATED	"ABCD--GH--K-M----RSTUVW-Y-"
public static final java.lang.String	RNA_COMPLEMENT	"UVGH CD M KN YSAABW R "
public static final java.lang.String	RNA_FILTER	"A-C---G------------UU-----"
public static final java.lang.String	RNA_FILTER_DEGENERATED	"ABCD--GH--K-M----RSUUVW-Y-"
public static final java.lang.String	RNA_FILTER_RESTRICTED	"A-C---G-------------U-----"

de.unibi.techfak.misc.IOTools

private static final long

serialVersionUID

1000L

de.unibi.techfak.misc.Markable

public static final int	MARK_BASIC	1
public static final int	MARK_DELETED	8
public static final int	MARK_EXP	8
public static final int	MARK_MOVED	128
public static final int	MARK_REPLACED	32
public static final int	MARK_SELECTED	2
public static final int	MARK_TOBEDELETED	4
public static final int	MARK_TOBEMOVED	64
public static final int	MARK_TOBEREPLACED	16

de.unibi.techfak.misc.MathTools

private static final long

serialVersionUID

1000L