protected AlignmentAnnotation[] groupConservation;
- protected AlignmentAnnotation hmmConsensus;
+ protected AlignmentAnnotation informationContent;
/**
* results of alignment consensus analysis for visible portion of view
}
@Override
+ public AlignmentAnnotation getAlignmentInformationAnnotation()
+ {
+ return informationContent;
+ }
+
+ @Override
public AlignmentAnnotation getAlignmentGapAnnotation()
{
return gapcounts;
protected boolean showConsensusHistogram = true;
/**
+ * should hmm profile be rendered by default
+ */
+ protected boolean showHMMSequenceLogo = false;
+
+ /**
+ * should hmm profile be rendered normalised to row height
+ */
+ protected boolean normaliseHMMSequenceLogo = false;
+
+ /**
+ * should information histograms be rendered by default
+ */
+ protected boolean showInformationHistogram = true;
+
+ /**
* @return the showConsensusProfile
*/
@Override
}
/**
+ * @return the showInformationProfile
+ */
+ @Override
+ public boolean isShowHMMSequenceLogo()
+ {
+ return showHMMSequenceLogo;
+ }
+
+ /**
* @param showSequenceLogo
* the new value
*/
this.showSequenceLogo = showSequenceLogo;
}
+ public void setShowHMMSequenceLogo(boolean showHMMSequenceLogo)
+ {
+ if (showHMMSequenceLogo != this.showHMMSequenceLogo)
+ {
+ this.showHMMSequenceLogo = showHMMSequenceLogo;
+ }
+ this.showHMMSequenceLogo = showHMMSequenceLogo;
+ }
+
/**
* @param showConsensusHistogram
* the showConsensusHistogram to set
}
/**
+ * @param showInformationHistogram
+ * the showInformationHistogram to set
+ */
+ public void setShowInformationHistogram(boolean showInformationHistogram)
+ {
+ this.showInformationHistogram = showInformationHistogram;
+ }
+
+ /**
* @return the showGroupConservation
*/
public boolean isShowGroupConservation()
}
/**
+ *
+ * @return flag to indicate if the information content histogram should be
+ * rendered by default
+ */
+ @Override
+ public boolean isShowInformationHistogram()
+ {
+ return this.showInformationHistogram;
+ }
+
+ /**
* when set, updateAlignment will always ensure sequences are of equal length
*/
private boolean padGaps = false;
return ignoreGapsInConsensusCalculation;
}
+ @Override
public boolean isIgnoreBelowBackground()
{
return ignoreBelowBackGroundFrequencyCalculation;