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Public Member Functions | Static Public Member Functions | Public Attributes | Static Public Attributes | Protected Member Functions | Package Functions | Private Member Functions

jalview::datamodel::AlignmentAnnotation Class Reference

Collaboration diagram for jalview::datamodel::AlignmentAnnotation:
Collaboration graph

List of all members.

Public Member Functions

void adjustForAlignment ()
 AlignmentAnnotation (String label, String description, Annotation[] annotations)
 AlignmentAnnotation (String label, String description, double score)
 AlignmentAnnotation (AlignmentAnnotation alignmentAnnotation, ColumnSelection colSel)
 AlignmentAnnotation (String label, String description, Annotation[] annotations, float min, float max, int graphType)
 AlignmentAnnotation (AlignmentAnnotation annotation)
int compactAnnotationArray ()
void createSequenceMapping (SequenceI seqRef, int startRes, boolean alreadyMapped)
String getDescription (boolean seqname)
double getScore ()
GraphLine getThreshold ()
boolean hasScore ()
boolean padAnnotation (int length)
void restrict (int startRes, int endRes)
void setPadGaps (boolean padgaps, char gapchar)
void setScore (double score)
void setSequenceRef (SequenceI sequenceI)
void setThreshold (GraphLine line)
String toString ()

Static Public Member Functions

static int getGraphValueFromString (String string)

Public Attributes

String annotationId
Annotation[] annotations
boolean autoCalculated = false
boolean belowAlignment = true
boolean centreColLabels = false
String description
boolean editable = false
int graph = 0
int graphGroup = -1
int graphHeight = 40
float graphMax
float graphMin
SequenceGroup groupRef = null
boolean hasIcons
boolean hasScore = false
boolean hasText
int height = 0
String label
boolean padGaps = false
boolean scaleColLabel = false
double score = Double.NaN
java.util.Hashtable sequenceMapping
SequenceI sequenceRef
boolean showAllColLabels = false
GraphLine threshold
boolean visible = true

Static Public Attributes

static final int BAR_GRAPH = 1
static final int LINE_GRAPH = 2
static final int NO_GRAPH = 0

Protected Member Functions

void finalize () throws Throwable

Package Functions

void areLabelsSecondaryStructure ()

Private Member Functions

void validateRangeAndDisplay ()

Detailed Description



Definition at line 29 of file AlignmentAnnotation.java.

The documentation for this class was generated from the following file:

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