void setShowUnconserved(boolean showunconserved);
+ /**
+ * @return true if a reference sequence is set and should be displayed
+ */
boolean isDisplayReferenceSeq();
+ /**
+ * @return set the flag for displaying reference sequences when they are
+ * available
+ */
void setDisplayReferenceSeq(boolean displayReferenceSeq);
+ /**
+ * @return true if colourschemes should render according to reference sequence
+ * rather than consensus if available
+ */
boolean isColourByReferenceSeq();
void setSeqNameItalics(boolean default1);
void setRightAlignIds(boolean rightAlignIds);
+ /**
+ * Returns true if annotation panel should be shown below alignment
+ *
+ * @return
+ */
boolean isShowAnnotation();
+ /**
+ * Set flag for whether annotation panel should be shown below alignment
+ *
+ * @param b
+ */
void setShowAnnotation(boolean b);
- void setShowSeqFeaturesHeight(boolean selected);
-
- boolean isShowSequenceFeaturesHeight();
+ void setShowSequenceFeaturesHeight(boolean selected);
+ /**
+ * @return true set flag for deciding if colourschemes should render according
+ * to reference sequence rather than consensus if available
+ */
void setColourByReferenceSeq(boolean colourByReferenceSeq);
Color getTextColour();
boolean isShowColourText();
- boolean isShowSeqFeaturesHeight();
+ boolean isShowSequenceFeaturesHeight();
void setConservationColourSelected(boolean conservationColourSelected);