apollo.gui
Class DetailInfo

java.lang.Object
  apollo.gui.DetailInfo

public class DetailInfo
extends java.lang.Object

This class is mainly for EvidencePanel and its SetDetailPanel, but there is handy methods that could be widely used. Perhaps it belongs in util? I think it does belong in util

Field Summary

static int	BIOTYPE
static int	CODING_PROPERTIES
static int	END
static int	END_PHASE
static int	EVIDENCE
static int	GENOMIC_LENGTH
static int	GENOMIC_RANGE
static int	GENOMIC_SEQUENCE
static int	HIGH
static int	ID
protected static org.apache.log4j.Logger	logger
static int	LOW
static int	MATCH_LENGTH
static int	MATCH_RANGE
static int	MATCH_SEQUENCE
static int	NAME
static int	PHASE
static int	Range
static int	SCORE
static int	START
static int	STRAND
static int	TIER
static int	Type
static int	TYPE

Constructor Summary

DetailInfo()

Method Summary

static java.util.Enumeration	getAllProperties()
static java.util.Enumeration	getAllPropertyStrings()
static java.lang.String	getBioType(SeqFeatureI feature)
static java.lang.Object	getCodingProperties(SeqFeatureI feature)
static java.lang.Object	getEnd(SeqFeatureI feature)
static java.lang.Object	getEndPhase(SeqFeatureI feature)
static java.lang.Object	getEvidence(SeqFeatureI feature)
static java.lang.Object	getGenomicLength(SeqFeatureI feature)
static java.lang.Object	getGenomicRange(SeqFeatureI feature)
static java.lang.String	getGenomicSequence(SeqFeatureI feature)
static java.lang.Object	getHigh(SeqFeatureI feature)
protected static SeqFeatureI	getHitFeature(SeqFeatureI feature)
static java.lang.String	getID(SeqFeatureI feature)
static java.lang.Object	getLow(SeqFeatureI feature)
static java.lang.Object	getMatchLength(SeqFeatureI feature)
static java.lang.Object	getMatchRange(SeqFeatureI feature)
static java.lang.String	getMatchSequence(SeqFeatureI feature)
static java.lang.String	getName(SeqFeatureI feature) The whole logic of this section has been put into the individual getDisplayName() methods of the various classes
static java.lang.Object	getPhase(SeqFeatureI feature)
static java.lang.String	getPrettyNameForProperty(java.lang.Integer key)
static java.lang.String	getPrettyNameForString(java.lang.String key)
static java.util.Vector	getPrettyNamesFromStrings(java.util.Vector values)
static java.lang.Object	getPropertyForFeature(java.lang.String prop, SeqFeatureI feature)
static java.lang.Integer	getPropertyForString(java.lang.String name)
static java.lang.String	getPropertyType(SeqFeatureI feature) Changed return from Object to String since FeatureProperty.getDisplayType is a String - rename this getVisualType?
static java.util.Vector	getRow(java.util.Vector def, SeqFeatureI feature)
static java.lang.Object	getScore(SeqFeatureI feature)
static java.lang.Object	getStart(SeqFeatureI feature)
static java.lang.Object	getStrand(SeqFeatureI feature)
static java.lang.Object	getTier(SeqFeatureI feature)
static java.lang.String	getTranslation(SeqFeatureI feature)
static java.lang.Object	getTranslationLength(SeqFeatureI feature)
static java.lang.Object	getType(SeqFeatureI feature)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logger

protected static final org.apache.log4j.Logger logger

GENOMIC_LENGTH

public static final int GENOMIC_LENGTH

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Constant Field Values

MATCH_LENGTH

public static final int MATCH_LENGTH

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Constant Field Values

GENOMIC_RANGE

public static final int GENOMIC_RANGE

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Constant Field Values

MATCH_RANGE

public static final int MATCH_RANGE

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Constant Field Values

SCORE

public static final int SCORE

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Constant Field Values

ID

public static final int ID

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Constant Field Values

TYPE

public static final int TYPE

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Constant Field Values

TIER

public static final int TIER

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Constant Field Values

NAME

public static final int NAME

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Constant Field Values

EVIDENCE

public static final int EVIDENCE

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Constant Field Values

GENOMIC_SEQUENCE

public static final int GENOMIC_SEQUENCE

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Constant Field Values

MATCH_SEQUENCE

public static final int MATCH_SEQUENCE

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Constant Field Values

START

public static final int START

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Constant Field Values

END

public static final int END

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Constant Field Values

LOW

public static final int LOW

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Constant Field Values

HIGH

public static final int HIGH

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Constant Field Values

STRAND

public static final int STRAND

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Constant Field Values

Type

public static final int Type

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Constant Field Values

Range

public static final int Range

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Constant Field Values

PHASE

public static final int PHASE

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Constant Field Values

BIOTYPE

public static final int BIOTYPE

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Constant Field Values

END_PHASE

public static final int END_PHASE

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Constant Field Values

CODING_PROPERTIES

public static final int CODING_PROPERTIES

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Constant Field Values

Constructor Detail

DetailInfo

public DetailInfo()

Method Detail

getPropertyForString

public static java.lang.Integer getPropertyForString(java.lang.String name)

getAllProperties

public static java.util.Enumeration getAllProperties()

getAllPropertyStrings

public static java.util.Enumeration getAllPropertyStrings()

getPrettyNameForString

public static java.lang.String getPrettyNameForString(java.lang.String key)

getPrettyNameForProperty

public static java.lang.String getPrettyNameForProperty(java.lang.Integer key)

getPrettyNamesFromStrings

public static java.util.Vector getPrettyNamesFromStrings(java.util.Vector values)

getRow

public static java.util.Vector getRow(java.util.Vector def,
                                      SeqFeatureI feature)

getPropertyForFeature

public static java.lang.Object getPropertyForFeature(java.lang.String prop,
                                                     SeqFeatureI feature)

getStrand

public static java.lang.Object getStrand(SeqFeatureI feature)

getLow

public static java.lang.Object getLow(SeqFeatureI feature)

getHigh

public static java.lang.Object getHigh(SeqFeatureI feature)

getStart

public static java.lang.Object getStart(SeqFeatureI feature)

getEnd

public static java.lang.Object getEnd(SeqFeatureI feature)

getPhase

public static java.lang.Object getPhase(SeqFeatureI feature)

getEndPhase

public static java.lang.Object getEndPhase(SeqFeatureI feature)

getCodingProperties

public static java.lang.Object getCodingProperties(SeqFeatureI feature)

getEvidence

public static java.lang.Object getEvidence(SeqFeatureI feature)

getTranslationLength

public static java.lang.Object getTranslationLength(SeqFeatureI feature)

getTranslation

public static java.lang.String getTranslation(SeqFeatureI feature)

getMatchSequence

public static java.lang.String getMatchSequence(SeqFeatureI feature)

getGenomicSequence

public static java.lang.String getGenomicSequence(SeqFeatureI feature)

getID

public static java.lang.String getID(SeqFeatureI feature)

getName

public static java.lang.String getName(SeqFeatureI feature)

The whole logic of this section has been put into the individual getDisplayName() methods of the various classes

getScore

public static java.lang.Object getScore(SeqFeatureI feature)

getGenomicLength

public static java.lang.Object getGenomicLength(SeqFeatureI feature)

getMatchLength

public static java.lang.Object getMatchLength(SeqFeatureI feature)

getGenomicRange

public static java.lang.Object getGenomicRange(SeqFeatureI feature)

getMatchRange

public static java.lang.Object getMatchRange(SeqFeatureI feature)

getType

public static java.lang.Object getType(SeqFeatureI feature)

getBioType

public static java.lang.String getBioType(SeqFeatureI feature)

getTier

public static java.lang.Object getTier(SeqFeatureI feature)

getPropertyType

public static java.lang.String getPropertyType(SeqFeatureI feature)

Changed return from Object to String since FeatureProperty.getDisplayType is a String - rename this getVisualType?

getHitFeature

protected static SeqFeatureI getHitFeature(SeqFeatureI feature)