+ boolean showSeqFeaturesHeight;
+ /**
+ * checks current SelectionGroup against record of last hash value, and updates record.
+ * @return true if SelectionGroup changed since last call
+ */
+ boolean isSelectionGroupChanged() {
+ int hc=(selectionGroup==null) ? -1 : selectionGroup.hashCode();
+ if (hc!=sgrouphash)
+ {
+ sgrouphash = hc;
+ return true;
+ }
+ return false;
+ }
+ /**
+ * checks current colsel against record of last hash value, and updates record.
+ * @return true if colsel changed since last call
+ */
+ boolean isColSelChanged() {
+ int hc=(colSel==null) ? -1 : colSel.hashCode();
+ if (hc!=colselhash)
+ {
+ colselhash = hc;
+ return true;
+ }
+ return false;
+ }
+ public void sendSelection()
+ {
+ 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)
+ {
+ 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;
+ }
+ /**
+ * @return the showGroupConsensus
+ */
+ public boolean isShowGroupConsensus()
+ {
+ return showGroupConsensus;
+ }
+ /**
+ * @param showGroupConsensus the showGroupConsensus to set
+ */
+ public void setShowGroupConsensus(boolean showGroupConsensus)
+ {
+ this.showGroupConsensus = showGroupConsensus;
+ }
+ /**
+ * @return the includeAllConsensusSymbols
+ */
+ public boolean isIncludeAllConsensusSymbols()
+ {
+ return includeAllConsensusSymbols;
+ }
+ /**
+ * @param includeAllConsensusSymbols the includeAllConsensusSymbols to set
+ */
+ public void setIncludeAllConsensusSymbols(boolean includeAllConsensusSymbols)
+ {
+ this.includeAllConsensusSymbols = includeAllConsensusSymbols;
+ }
+
+ /**
+ *
+ * @return flag to indicate if the consensus histogram should be rendered by default
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ return this.showConsensusHistogram;
+ }
+