public interface AlignViewportI extends ViewStyleI
{
- int getCharWidth();
-
int getEndRes();
- int getCharHeight();
-
/**
* calculate the height for visible annotation, revalidating bounds where
* necessary ABSTRACT GUI METHOD
void updateGroupAnnotationSettings(boolean applyGlobalSettings,
boolean preserveNewGroupSettings);
- /**
- * @return true if a reference sequence is set and should be displayed
- */
- public boolean isDisplayReferenceSeq();
-
- /**
- * @return set the flag for displaying reference sequences when they are
- * available
- */
- public void setDisplayReferenceSeq(boolean displayReferenceSeq);
-
- /**
- * @return true if colourschemes should render according to reference sequence
- * rather than consensus if available
- */
- public boolean isColourByReferenceSeq();
-
- /**
- * @return true set flag for deciding if colourschemes should render according
- * to reference sequence rather than consensus if available
- */
- public void setColourByReferenceSeq(boolean colourByReferenceSeq);
-
void setSequenceColour(SequenceI seq, Color col);
Color getSequenceColour(SequenceI seq);
String getSequenceSetId();
- boolean isShowSequenceFeatures();
-
- void setShowSequenceFeatures(boolean b);
-
- /**
- *
- * @param flag
- * indicating if annotation panel shown below alignment
- *
- */
- void setShowAnnotation(boolean b);
-
- /**
- * flag indicating if annotation panel shown below alignment
- *
- * @return
- */
- boolean isShowAnnotation();
-
- boolean isRightAlignIds();
-
- void setRightAlignIds(boolean rightAlignIds);
-
boolean areFeaturesDisplayed();
- void setShowSequenceFeaturesHeight(boolean selected);
-
- boolean isShowSequenceFeaturesHeight();
-
void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI);
void alignmentChanged(AlignmentViewPanel ap);