Modifier and Type | Class and Description |
---|---|
class |
ConsensusSequence |
Modifier and Type | Method and Description |
---|---|
Sequence[] |
DisplayProperties.getAllSelectedSequences() |
Sequence[] |
DisplayProperties.getAllSelectedSequences(boolean inViewOrder) |
Sequence[] |
Alignment.getAllSequences() |
Sequence |
Alignment.getSequence(int index) |
Sequence |
Alignment.getSequence(java.lang.String sequenceName) |
Sequence[] |
Alignment.getSequencesInAlignment() |
Modifier and Type | Method and Description |
---|---|
void |
DisplayProperties.alignmentSeqActivityChanged(Alignment alignment,
Sequence sequence) |
void |
DisplayProperties.alignmentSeqDeleted(Alignment alignment,
int i,
Sequence sequence) |
void |
Alignment.calcSortValueBasedOnColumnSorts(Sequence seq) |
int |
Alignment.compare(Sequence seq1,
Sequence seq2) |
void |
DisplayProperties.fireDisplayHighlightsChanged(Sequence s) |
void |
DisplayProperties.fireDisplayHighlightsChanged(Sequence[] s) |
void |
DisplayProperties.fireSeqSelect(Sequence sequence) |
int[] |
DisplayProperties.getHighlights(Sequence sequence) |
int |
Alignment.getIndex(Sequence sequence) |
int[] |
Alignment.getUniqueActivityCounts(int column,
java.lang.String[] encodedActivitiesArray,
Sequence[] sequences) |
boolean |
DisplayProperties.isSeqHighlight(Sequence s,
int idx) |
boolean |
DisplayProperties.isSequenceSelected(Sequence s) |
void |
DisplayProperties.sequenceActivityChanged(Sequence sequence) |
void |
DisplayProperties.sequenceAnnotationChanged(Sequence sequence) |
void |
DisplayProperties.sequenceColorChanged(Sequence sequence) |
void |
DisplayProperties.sequenceLineAnnotationsChanged(Sequence aaseq) |
void |
DisplayProperties.sequenceNameChanged(Sequence sequence,
java.lang.String oldName) |
void |
DisplayProperties.setIsSequenceSelected(Sequence sequence,
boolean isSelected) |
void |
DisplayProperties.setSeqHidden(Sequence s,
boolean hidden) |
void |
DisplayProperties.setSeqHighlight(Sequence s,
int idx,
boolean highlight) |
void |
DisplayProperties.setSeqHighlight(Sequence s,
int idx,
boolean highlight,
boolean notify) |
Constructor and Description |
---|
Alignment(int encodingLength,
AlignmentFrame owner,
Sequence[] sequencesInAlignment) |
ConsensusSequence(AlignmentFrame owner,
DisplayProperties displayProperties,
Sequence[] seqs) |
Constructor and Description |
---|
AlignmentSorter(Alignment alignment,
java.util.Comparator<Sequence> comparator) |
Modifier and Type | Method and Description |
---|---|
void |
AlignmentListener.alignmentSeqActivityChanged(Alignment alignment,
Sequence sequence) |
void |
AlignmentListener.alignmentSeqDeleted(Alignment alignment,
int i,
Sequence sequence) |
void |
DisplayPropertiesListener.displayAnnViewChanged(DisplayProperties displayProperties,
Sequence sequence,
boolean show) |
void |
DisplayPropertiesListener.displayHighlightsChanged(DisplayProperties displayProperties,
Sequence sequence) |
void |
DisplayPropertiesListener.displayHighlightsChanged(DisplayProperties displayProperties,
Sequence[] sequenceArray) |
void |
DisplayPropertiesListener.displaySeqSelectChanged(DisplayProperties displayProperties,
Sequence sequence,
boolean select) |
void |
SequenceListener.sequenceActivityChanged(Sequence sequence) |
void |
SequenceListener.sequenceAnnotationChanged(Sequence sequence) |
void |
SequenceListener.sequenceColorChanged(Sequence sequence) |
void |
SequenceListener.sequenceLineAnnotationsChanged(Sequence sequence) |
void |
SequenceListener.sequenceNameChanged(Sequence sequence,
java.lang.String oldName) |
Modifier and Type | Field and Description |
---|---|
protected Sequence |
EditSeqAnnBaseDialog.sequence |
Modifier and Type | Method and Description |
---|---|
Sequence |
SequenceComponent.getSequence() |
Sequence |
SequenceNameComponent.getSequence() |
Modifier and Type | Method and Description |
---|---|
void |
AlignmentFrame.alignmentSeqActivityChanged(Alignment alignment,
Sequence sequence) |
void |
AlignmentNamePanel.alignmentSeqActivityChanged(Alignment alignment,
Sequence sequence) |
void |
AlignmentPanel.alignmentSeqActivityChanged(Alignment alignment,
Sequence sequence) |
void |
RulerAnnotationComponent.alignmentSeqActivityChanged(Alignment alignment,
Sequence sequence) |
void |
RulerComponent.alignmentSeqActivityChanged(Alignment alignment,
Sequence sequence) |
void |
AlignmentFrame.alignmentSeqDeleted(Alignment alignment,
int i,
Sequence sequence) |
void |
AlignmentNamePanel.alignmentSeqDeleted(Alignment alignment,
int i,
Sequence sequence) |
void |
AlignmentPanel.alignmentSeqDeleted(Alignment alignment,
int i,
Sequence sequence) |
void |
RulerAnnotationComponent.alignmentSeqDeleted(Alignment alignment,
int i,
Sequence sequence) |
void |
RulerComponent.alignmentSeqDeleted(Alignment alignment,
int i,
Sequence sequence) |
void |
AlignmentFrame.displayAnnViewChanged(DisplayProperties displayProperties,
Sequence sequence,
boolean show) |
void |
ConsensusComponent.displayAnnViewChanged(DisplayProperties displayProperties,
Sequence sequence,
boolean show) |
void |
RulerAnnotationComponent.displayAnnViewChanged(DisplayProperties dp,
Sequence sequence,
boolean show) |
void |
RulerComponent.displayAnnViewChanged(DisplayProperties displayProperties,
Sequence sequence,
boolean show) |
void |
SequenceComponent.displayAnnViewChanged(DisplayProperties displayProperties,
Sequence sequence,
boolean show) |
void |
SequenceNameComponent.displayAnnViewChanged(DisplayProperties displayProperties,
Sequence sequence,
boolean show) |
void |
AlignmentFrame.displayHighlightsChanged(DisplayProperties displayProperties,
Sequence sequence) |
void |
ConsensusComponent.displayHighlightsChanged(DisplayProperties displayProperties,
Sequence sequence) |
void |
RulerAnnotationComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence sequence) |
void |
RulerComponent.displayHighlightsChanged(DisplayProperties displayProperties,
Sequence sequence) |
void |
SequenceComponent.displayHighlightsChanged(DisplayProperties displayProperties,
Sequence sequence) |
void |
SequenceNameComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence sequence) |
void |
AlignmentFrame.displayHighlightsChanged(DisplayProperties displayProperties,
Sequence[] sequenceArray) |
void |
ConsensusComponent.displayHighlightsChanged(DisplayProperties displayProperties,
Sequence[] sequenceArray) |
void |
RulerAnnotationComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence[] sequenceArray) |
void |
RulerComponent.displayHighlightsChanged(DisplayProperties displayProperties,
Sequence[] sequenceArray) |
void |
SequenceComponent.displayHighlightsChanged(DisplayProperties displayProperties,
Sequence[] sequenceArray) |
void |
SequenceNameComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence[] sequenceArray) |
void |
AlignmentFrame.displaySeqSelectChanged(DisplayProperties displayProperties,
Sequence sequence,
boolean select) |
void |
ConsensusComponent.displaySeqSelectChanged(DisplayProperties displayProperties,
Sequence sequence,
boolean select) |
void |
RulerAnnotationComponent.displaySeqSelectChanged(DisplayProperties dp,
Sequence sequence,
boolean select) |
void |
RulerComponent.displaySeqSelectChanged(DisplayProperties displayProperties,
Sequence sequence,
boolean select) |
void |
SequenceComponent.displaySeqSelectChanged(DisplayProperties displayProperties,
Sequence sequence,
boolean select) |
void |
SequenceNameComponent.displaySeqSelectChanged(DisplayProperties dp,
Sequence sequence,
boolean select) |
SequenceComponent |
AlignmentPanel.getSequenceComponent(Sequence sequence) |
int |
AlignmentPanel.getSequenceIndex(Sequence sequence) |
void |
ConsensusComponent.sequenceActivityChanged(Sequence sequence) |
void |
SequenceComponent.sequenceActivityChanged(Sequence sequence) |
void |
SequenceNameComponent.sequenceActivityChanged(Sequence aaseq) |
void |
ConsensusComponent.sequenceAnnotationChanged(Sequence sequence) |
void |
SequenceComponent.sequenceAnnotationChanged(Sequence sequence) |
void |
SequenceNameComponent.sequenceAnnotationChanged(Sequence sequence) |
void |
ConsensusComponent.sequenceColorChanged(Sequence sequence) |
void |
SequenceComponent.sequenceColorChanged(Sequence sequence) |
void |
SequenceNameComponent.sequenceColorChanged(Sequence sequence) |
void |
ConsensusComponent.sequenceColumnAnnotationsChanged(Sequence sequence,
int column) |
void |
ConsensusComponent.sequenceLineAnnotationsChanged(Sequence aaseq) |
void |
SequenceComponent.sequenceLineAnnotationsChanged(Sequence sequence) |
void |
SequenceNameComponent.sequenceLineAnnotationsChanged(Sequence sequence) |
void |
ConsensusComponent.sequenceNameChanged(Sequence sequence,
java.lang.String oldName) |
void |
SequenceComponent.sequenceNameChanged(Sequence sequence,
java.lang.String oldName) |
void |
SequenceNameComponent.sequenceNameChanged(Sequence sequence,
java.lang.String oldName) |
void |
SequenceComponent.setSequence(Sequence sequence) |
void |
SequenceNameComponent.setSequence(Sequence sequence) |
Constructor and Description |
---|
ColorSequenceDialog(AlignmentFrame owner,
Sequence sequence) |
EditActivityAnnotationDialog(AlignmentFrame owner,
DisplayProperties displayProperties,
Sequence sequence,
int index) |
EditSeqAnnBaseDialog(AlignmentFrame owner,
java.lang.String title,
DisplayProperties displayProperties,
Sequence sequence) |
EditSequenceDialog(AlignmentFrame owner,
Sequence s) |
EditSequenceDialog(AlignmentFrame owner,
Sequence s,
Alignment alignment,
int mouseRowIndex)
Allows user to create and edit a NEW sequence
|
EditSequenceNameDialog(AlignmentFrame owner,
DisplayProperties props,
Sequence s) |
SequenceComponent(Sequence sequence,
DisplayProperties displayProperties) |
SequenceNameComponent(AlignmentFrame owner,
Sequence sequence,
DisplayProperties displayProperties) |