public abstract class AlignmentViewport implements AlignViewportI,
CommandListener, VamsasSource
{
- protected ViewportRanges ranges;
+ final protected ViewportRanges ranges;
protected ViewStyleI viewStyle = new ViewStyle();
protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
/**
+ * alignment displayed in the viewport. Please use get/setter
+ */
+ protected AlignmentI alignment;
+
+ public AlignmentViewport(AlignmentI al)
+ {
+ setAlignment(al);
+ ranges = new ViewportRanges(al);
+ }
+
+ /**
* @param name
* @see jalview.api.ViewStyleI#setFontName(java.lang.String)
*/
viewStyle.setSeqNameItalics(default1);
}
- /**
- * alignment displayed in the viewport. Please use get/setter
- */
- protected AlignmentI alignment;
+
@Override
public AlignmentI getAlignment()
}
/**
- * If this is a protein alignment and there are mappings to cDNA, add the cDNA
- * consensus annotation.
+ * If this is a protein alignment and there are mappings to cDNA, adds the
+ * cDNA consensus annotation and returns true, else returns false.
*/
- public void initComplementConsensus()
+ public boolean initComplementConsensus()
{
if (!alignment.isNucleotide())
{
"PID for cDNA", new Annotation[1], 0f, 100f,
AlignmentAnnotation.BAR_GRAPH);
initConsensus(complementConsensus);
+ return true;
}
}
}
+ return false;
}
private void initConsensus(AlignmentAnnotation aa)