All Methods Instance Methods Concrete Methods
Modifier and Type |
Method and Description |
void |
addColumn() |
void |
addColumnFilter(ColumnFilter filter,
int column) |
void |
addColumnSort(ColumnSort sort,
int column) |
void |
addListener(AlignmentListener listener) |
void |
addRulerAnnotation() |
void |
calcSortValueBasedOnColumnSorts(Sequence seq) |
void |
clearLastActivityIndexSelected() |
void |
clearLastColumnIndexSelected() |
void |
clearLastRulerAnnIndexSelected() |
int |
compare(Sequence seq1,
Sequence seq2) |
void |
deselectAllColumns(DisplayProperties p) |
void |
deselectAllColumns(DisplayProperties p,
boolean quickDeselect) |
void |
deselectAllRulerSelections() |
Sequence[] |
getAllSequences() |
ColumnFilter |
getColumnFilter(java.lang.Integer key) |
java.util.Iterator<java.lang.Integer> |
getColumnFilterColumnIterator() |
int |
getColumnFilterCurrentColumn() |
boolean |
getColumnFiltering() |
ColumnSort |
getColumnSort(java.lang.Integer key) |
java.util.Iterator<java.lang.Integer> |
getColumnSortColumnIterator() |
int |
getColumnSortCurrentColumn() |
boolean |
getColumnSorting() |
int |
getColumnsSize()
Returns the total number of columns in the alignment
|
ColumnFilter |
getCurrentColumnFilter() |
ColumnSort |
getCurrentColumnSort() |
int |
getEncodingLength() |
int |
getFirstColumnSelected() |
int |
getFontSize() |
int |
getIndex(Sequence s) |
int |
getLastActivityIndexSelected() |
int |
getLastActivityRowSelected() |
int |
getLastColumnIdxSelected() |
int |
getLastColumnSelected() |
java.lang.String |
getName() |
int |
getNoSequences() |
int |
getNumberOfColumnsSelected() |
Sequence |
getRefSequence() |
Alignment.RulerAnnotation |
getRulerAnnotation(int idx) |
Sequence |
getSequence(int index) |
Sequence |
getSequence(java.lang.String sequenceName) |
java.lang.String[] |
getUniqueActivitiesInColumn(int column) |
int[] |
getUniqueActivityCounts(int column,
java.lang.String[] encodedActivitiesArray) |
int[] |
getUniqueActivityCounts(int column,
java.lang.String[] encodedActivitiesArray,
Sequence[] seqs) |
boolean |
isColumnSelected() |
boolean |
isColumnSelected(int idx) |
boolean |
isRulerAnnotationSelected() |
int |
maxLength() |
void |
removeAllGapColumns() |
void |
removeColumnFilter(int column) |
void |
removeColumnFromEnd() |
void |
removeColumnRange(int from,
int to) |
void |
removeColumnSort(int column) |
void |
removeRulerAnnotationFromEnd() |
void |
removeRulerAnnotationRange(int from,
int to) |
int |
rulerAnnotationsSize() |
void |
sequenceActivityChanged(Sequence sequence) |
void |
sequenceAnnotationChanged(Sequence sequence) |
void |
sequenceColorChanged(Sequence sequence) |
void |
sequenceColumnAnnotationsChanged(Sequence sequence,
int column) |
void |
sequenceLineAnnotationsChanged(Sequence aaseq) |
void |
sequenceNameChanged(Sequence sequence,
java.lang.String oldName) |
void |
setChanged(boolean b) |
void |
setColumnFilterCurrentColumn(int col) |
void |
setColumnFiltering(boolean b) |
void |
setColumnSelected(int idx,
boolean b,
DisplayProperties p) |
void |
setColumnSortCurrentColumn(int col) |
void |
setColumnSorting(boolean b) |
void |
setLastActivityIndexSelected(int row,
int idx) |
void |
setLastColumnIdxSelected(int idx) |
void |
setLastRulerAnnIdxSelected(int idx) |
void |
setRefSequence(Sequence sequence) |
void |
sortBasedOnColumnSorts() |
void |
sortBasedOnSortValue() |
void |
swapSequence(int i,
int j) |