+
+ /**
+ * consensus annotation includes all percentage for all symbols in column
+ * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1 compatible)
+ */
+ private boolean includeAllConsensusSymbols=false;
+
+ /**
+ * should conservation rows be shown for groups
+ * DISABLED FOR 2.5 RELEASE (bug 62446)
+ */
+ boolean showGroupConservation = false;
+ /**
+ * should consensus rows be shown for groups
+ * DISABLED FOR 2.5 RELEASE (bug 62446)
+ */
+ boolean showGroupConsensus = false;
+ /**
+ * should consensus profile be rendered by default
+ * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1 compatible)
+ */
+ public boolean showSequenceLogo = false;
+ /**
+ * should consensus histograms be rendered by default
+ */
+ public boolean showConsensusHistogram = true;
+ /**
+ * @return the showConsensusProfile
+ */
+ public boolean isShowSequenceLogo()
+ {
+ return showSequenceLogo;
+ }
+ /**
+ * @param showSequenceLogo the new value
+ public void setShowSequenceLogo(boolean showSequenceLogo)
+ {
+ this.showSequenceLogo = showSequenceLogo;
+ }
+ */
+ /**
+ * @param showGroupConsensus the showGroupConsensus to set
+ */
+ public void setShowGroupConsensus(boolean showGroupConsensus)
+ {
+ this.showGroupConsensus = showGroupConsensus;
+ }
+ /**
+ * @return the includeAllConsensusSymbols
+ */
+ public boolean isIncludeAllConsensusSymbols()
+ {
+ return false;
+ }
+
+ /**
+ *
+ * @return flag to indicate if the consensus histogram should be rendered by default
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ return this.showConsensusHistogram;
+ }