import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Rectangle;
-import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
-import java.util.Vector;
import javax.swing.JInternalFrame;
setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
AlignmentI al = getAlignment();
- al.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+
+ if (Cache.getDefault("NORMALISE_GAPS", true))
+ {
+ al.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+ }
// We must set conservation and consensus before setting colour,
// as Blosum and Clustal require this to be done
showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
false);
+ // for now, use consensus options for Information till it gets its own
+ setShowHMMSequenceLogo(showSequenceLogo);
+ setNormaliseHMMSequenceLogo(normaliseSequenceLogo);
+ setShowInformationHistogram(showConsensusHistogram);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
.getStructureSelectionManager(Desktop.instance);
}
- @Override
- public boolean isNormaliseSequenceLogo()
- {
- return normaliseSequenceLogo;
- }
-
-
- public void setNormaliseSequenceLogo(boolean state)
- {
- normaliseSequenceLogo = state;
- }
-
- public void setNormaliseHMMSequenceLogo(boolean state)
- {
- normaliseHMMSequenceLogo = state;
- }
-
/**
*
* @return true if alignment characters should be displayed
fr.setTransparency(featureSettings.getTransparency());
}
- @Override
- public boolean isNormaliseHMMSequenceLogo()
- {
- return normaliseHMMSequenceLogo;
- }
-
}