void |
AlignmentListener.alignmentSeqActivityChanged(Alignment alignment,
Sequence sequence) |
void |
AlignmentNamePanel.alignmentSeqActivityChanged(Alignment alignment,
Sequence sequence) |
void |
AlignmentPanel.alignmentSeqActivityChanged(Alignment alignment,
Sequence sequence) |
void |
ColumnAnnotationComponent.alignmentSeqActivityChanged(Alignment alignment,
Sequence sequence) |
void |
DisplayProperties.alignmentSeqActivityChanged(Alignment alignment,
Sequence sequence) |
void |
RulerAnnotationComponent.alignmentSeqActivityChanged(Alignment alignment,
Sequence sequence) |
void |
RulerComponent.alignmentSeqActivityChanged(Alignment alignment,
Sequence sequence) |
void |
AlignmentListener.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 |
ColumnAnnotationComponent.alignmentSeqDeleted(Alignment alignment,
int i,
Sequence sequence) |
void |
DisplayProperties.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 |
Alignment.calcSortValueBasedOnColumnSorts(Sequence seq) |
int |
Alignment.compare(Sequence seq1,
Sequence seq2) |
void |
ColumnAnnotationComponent.displayAnnViewChanged(DisplayProperties dp,
Sequence sequence,
boolean show) |
void |
ConsensusComponent.displayAnnViewChanged(DisplayProperties dp,
Sequence sequence,
boolean show) |
void |
DisplayPropertiesListener.displayAnnViewChanged(DisplayProperties dp,
Sequence sequence,
boolean show) |
void |
RulerAnnotationComponent.displayAnnViewChanged(DisplayProperties dp,
Sequence sequence,
boolean show) |
void |
RulerComponent.displayAnnViewChanged(DisplayProperties dp,
Sequence sequence,
boolean show) |
void |
SequenceAnnComponent.displayAnnViewChanged(DisplayProperties dp,
Sequence sequence,
boolean show) |
void |
SequenceComponent.displayAnnViewChanged(DisplayProperties dp,
Sequence sequence,
boolean show) |
void |
SequenceNameComponent.displayAnnViewChanged(DisplayProperties dp,
Sequence sequence,
boolean show) |
void |
ColumnAnnotationComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence sequence) |
void |
ConsensusComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence sequence) |
void |
DisplayPropertiesListener.displayHighlightsChanged(DisplayProperties dp,
Sequence sequence) |
void |
RulerAnnotationComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence sequence) |
void |
RulerComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence sequence) |
void |
SequenceAnnComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence sequence) |
void |
SequenceComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence sequence) |
void |
SequenceNameComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence sequence) |
void |
ColumnAnnotationComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence[] sequenceArray) |
void |
ConsensusComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence[] sequenceArray) |
void |
DisplayPropertiesListener.displayHighlightsChanged(DisplayProperties dp,
Sequence[] sequenceArray) |
void |
RulerAnnotationComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence[] sequenceArray) |
void |
RulerComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence[] sequenceArray) |
void |
SequenceAnnComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence[] sequenceArray) |
void |
SequenceComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence[] sequenceArray) |
void |
SequenceNameComponent.displayHighlightsChanged(DisplayProperties dp,
Sequence[] sequenceArray) |
void |
ColumnAnnotationComponent.displaySeqSelectChanged(DisplayProperties dp,
Sequence sequence,
boolean select) |
void |
ConsensusComponent.displaySeqSelectChanged(DisplayProperties dp,
Sequence sequence,
boolean select) |
void |
DisplayPropertiesListener.displaySeqSelectChanged(DisplayProperties dp,
Sequence sequence,
boolean select) |
void |
RulerAnnotationComponent.displaySeqSelectChanged(DisplayProperties dp,
Sequence sequence,
boolean select) |
void |
RulerComponent.displaySeqSelectChanged(DisplayProperties dp,
Sequence sequence,
boolean select) |
void |
SequenceAnnComponent.displaySeqSelectChanged(DisplayProperties dp,
Sequence sequence,
boolean select) |
void |
SequenceComponent.displaySeqSelectChanged(DisplayProperties dp,
Sequence sequence,
boolean select) |
void |
SequenceNameComponent.displaySeqSelectChanged(DisplayProperties dp,
Sequence sequence,
boolean select) |
void |
DisplayProperties.fireDisplayHighlightsChanged(Sequence s) |
void |
DisplayProperties.fireDisplayHighlightsChanged(Sequence[] s) |
void |
DisplayProperties.fireSeqSelect(Sequence s) |
boolean |
DisplayProperties.getAnnView(Sequence s) |
java.awt.Color |
ColorScheme.getBackgroundColor(Sequence sequence,
int activityIndex) |
java.awt.Color |
ColorScheme.getForegroundColor(Sequence sequence,
int activityIndex) |
void |
Sequence.ColumnAnnotation.getFormattedAnnotationInfo(Sequence seq,
java.lang.StringBuffer sb) |
java.util.List<Sequence.LineAnnotation> |
DisplayProperties.getHiddenLineAnnotations(Sequence sequence)
Get a list of the line annotations that are hidden for the given sequence
|
int[] |
DisplayProperties.getHighlights(Sequence sequence)
Identify the column positions (activities) that are highlighted in the
given sequence
|
int |
Alignment.getIndex(Sequence s) |
boolean |
DisplayProperties.getSeqSelect(Sequence s) |
SequenceComponent |
AlignmentPanel.getSequenceComponent(Sequence sequence) |
int |
AlignmentPanel.getSequenceIndex(Sequence sequence) |
int[] |
Alignment.getUniqueActivityCounts(int column,
java.lang.String[] encodedActivitiesArray,
Sequence[] seqs) |
java.util.List<Sequence.LineAnnotation> |
DisplayProperties.getVisibleLineAnnotations(Sequence sequence)
Get a list of the line annotations that are visible for the given
sequence.
|
boolean |
DisplayProperties.isSeqHighlight(Sequence s,
int idx) |
void |
Alignment.sequenceActivityChanged(Sequence sequence) |
void |
ColumnAnnotationComponent.sequenceActivityChanged(Sequence aaseq) |
void |
ConsensusComponent.sequenceActivityChanged(Sequence aaseq) |
void |
DisplayProperties.sequenceActivityChanged(Sequence sequence) |
void |
SequenceAnnComponent.sequenceActivityChanged(Sequence aaseq) |
void |
SequenceComponent.sequenceActivityChanged(Sequence sequence) |
void |
SequenceListener.sequenceActivityChanged(Sequence aaseq) |
void |
SequenceNameComponent.sequenceActivityChanged(Sequence aaseq) |
void |
Alignment.sequenceAnnotationChanged(Sequence sequence) |
void |
ColumnAnnotationComponent.sequenceAnnotationChanged(Sequence sequence) |
void |
ConsensusComponent.sequenceAnnotationChanged(Sequence sequence) |
void |
DisplayProperties.sequenceAnnotationChanged(Sequence sequence) |
void |
SequenceAnnComponent.sequenceAnnotationChanged(Sequence sequence) |
void |
SequenceComponent.sequenceAnnotationChanged(Sequence sequence) |
void |
SequenceListener.sequenceAnnotationChanged(Sequence sequence) |
void |
SequenceNameComponent.sequenceAnnotationChanged(Sequence sequence) |
void |
Alignment.sequenceColorChanged(Sequence sequence) |
void |
ColumnAnnotationComponent.sequenceColorChanged(Sequence sequence) |
void |
ConsensusComponent.sequenceColorChanged(Sequence sequence) |
void |
DisplayProperties.sequenceColorChanged(Sequence sequence) |
void |
SequenceAnnComponent.sequenceColorChanged(Sequence sequence) |
void |
SequenceComponent.sequenceColorChanged(Sequence sequence) |
void |
SequenceListener.sequenceColorChanged(Sequence sequence) |
void |
SequenceNameComponent.sequenceColorChanged(Sequence sequence) |
void |
Alignment.sequenceColumnAnnotationsChanged(Sequence sequence,
int column) |
void |
ColumnAnnotationComponent.sequenceColumnAnnotationsChanged(Sequence sequence,
int column) |
void |
ConsensusComponent.sequenceColumnAnnotationsChanged(Sequence sequence,
int column) |
void |
DisplayProperties.sequenceColumnAnnotationsChanged(Sequence sequence,
int column) |
void |
SequenceAnnComponent.sequenceColumnAnnotationsChanged(Sequence sequence,
int column) |
void |
SequenceComponent.sequenceColumnAnnotationsChanged(Sequence sequence,
int column) |
void |
SequenceListener.sequenceColumnAnnotationsChanged(Sequence sequence,
int column) |
void |
SequenceNameComponent.sequenceColumnAnnotationsChanged(Sequence sequence,
int column) |
void |
Alignment.sequenceLineAnnotationsChanged(Sequence aaseq) |
void |
ColumnAnnotationComponent.sequenceLineAnnotationsChanged(Sequence aaseq) |
void |
ConsensusComponent.sequenceLineAnnotationsChanged(Sequence aaseq) |
void |
DisplayProperties.sequenceLineAnnotationsChanged(Sequence aaseq) |
void |
SequenceAnnComponent.sequenceLineAnnotationsChanged(Sequence aaseq) |
void |
SequenceComponent.sequenceLineAnnotationsChanged(Sequence aaseq) |
void |
SequenceListener.sequenceLineAnnotationsChanged(Sequence aaseq) |
void |
SequenceNameComponent.sequenceLineAnnotationsChanged(Sequence sequence) |
void |
Alignment.sequenceNameChanged(Sequence sequence,
java.lang.String oldName) |
void |
ColumnAnnotationComponent.sequenceNameChanged(Sequence sequence,
java.lang.String oldName) |
void |
ConsensusComponent.sequenceNameChanged(Sequence sequence,
java.lang.String oldName) |
void |
DisplayProperties.sequenceNameChanged(Sequence sequence,
java.lang.String oldName) |
void |
SequenceAnnComponent.sequenceNameChanged(Sequence sequence,
java.lang.String oldName) |
void |
SequenceComponent.sequenceNameChanged(Sequence sequence,
java.lang.String oldName) |
void |
SequenceListener.sequenceNameChanged(Sequence sequence,
java.lang.String oldName) |
void |
SequenceNameComponent.sequenceNameChanged(Sequence sequence,
java.lang.String oldName) |
void |
DisplayProperties.setAnnView(Sequence s,
boolean show) |
void |
DisplayProperties.setHiddenLineAnnotation(Sequence sequence,
Sequence.LineAnnotation lineAnnotation) |
void |
Alignment.setRefSequence(Sequence sequence) |
void |
AlignmentNamePanel.setRefSequence(Sequence seq) |
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) |
void |
DisplayProperties.setSeqSelect(Sequence s,
boolean select) |
void |
Sequence.LineAnnotation.setSequence(Sequence sequence) |
void |
SequenceAnnComponent.setSequence(Sequence sequence) |
void |
SequenceComponent.setSequence(Sequence sequence) |
void |
SequenceNameComponent.setSequence(Sequence sequence) |
void |
DisplayProperties.setVisibleLineAnnotation(Sequence sequence,
Sequence.LineAnnotation lineAnnotation) |