+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager().sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
+ }
+
+ public void setShowSequenceFeaturesHeight(boolean selected)
+ {
+ showSeqFeaturesHeight = selected;
+ }
+
+ public boolean getShowSequenceFeaturesHeight()
+ {
+ return showSeqFeaturesHeight;
+ }
+
+ boolean showUnconserved = false;
+
+ public boolean getShowUnconserved()
+ {
+ return showUnconserved;
+ }
+
+ public void setShowUnconserved(boolean showunconserved)
+ {
+ showUnconserved = showunconserved;
+ }
+
+ /**
+ * return the alignPanel containing the given viewport. Use this to get the
+ * components currently handling the given viewport.
+ *
+ * @param av
+ * @return null or an alignPanel guaranteed to have non-null alignFrame
+ * reference
+ */
+ public AlignmentPanel getAlignPanel()
+ {
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
+ .getSequenceSetId());
+ AlignmentPanel ap = null;
+ for (int p = 0; aps != null && p < aps.length; p++)
+ {
+ if (aps[p].av == this)
+ {
+ return aps[p];
+ }
+ }
+ return null;
+ }
+
+ public boolean getSortByTree()
+ {
+ return sortByTree;
+ }
+
+ public void setSortByTree(boolean sort)
+ {
+ sortByTree = sort;
+ }
+
+ /**
+ * should conservation rows be shown for groups
+ */
+ boolean showGroupConservation = false;
+
+ /**
+ * should consensus rows be shown for groups
+ */
+ boolean showGroupConsensus = false;
+
+ /**
+ * should consensus profile be rendered by default
+ */
+ 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)
+ {
+ if (showSequenceLogo != this.showSequenceLogo)
+ {
+ // TODO: decouple settings setting from calculation when refactoring
+ // annotation update method from alignframe to viewport
+ this.showSequenceLogo = showSequenceLogo;
+ if (consensusThread != null)
+ {
+ consensusThread.updateAnnotation();
+ }
+ }
+ this.showSequenceLogo = showSequenceLogo;
+ }
+
+ /**
+ * @param showConsensusHistogram
+ * the showConsensusHistogram to set
+ */
+ public void setShowConsensusHistogram(boolean showConsensusHistogram)
+ {
+ this.showConsensusHistogram = showConsensusHistogram;
+ }
+
+ /**
+ * @return the showGroupConservation
+ */
+ public boolean isShowGroupConservation()
+ {
+ return showGroupConservation;
+ }
+
+ /**
+ * @param showGroupConservation
+ * the showGroupConservation to set
+ */
+ public void setShowGroupConservation(boolean showGroupConservation)
+ {
+ this.showGroupConservation = showGroupConservation;