protected ColumnSelection colSel = new ColumnSelection();
- public boolean autoCalculateConsensus = true;
+ protected boolean autoCalculateConsensusAndConservation = true;
+
+ public boolean getAutoCalculateConsensusAndConservation()
+ { // BH 2019.07.24
+ return autoCalculateConsensusAndConservation;
+ }
+
+ public void setAutoCalculateConsensusAndConservation(boolean b)
+ {
+ autoCalculateConsensusAndConservation = b;
+ }
protected boolean autoCalculateStrucConsensus = true;
+ public boolean getAutoCalculateStrucConsensus()
+ { // BH 2019.07.24
+ return autoCalculateStrucConsensus;
+ }
+
+ public void setAutoCalculateStrucConsensus(boolean b)
+ {
+ autoCalculateStrucConsensus = b;
+ }
+
protected boolean ignoreGapsInConsensusCalculation = false;
protected ResidueShaderI residueShading = new ResidueShader();
/**
* results of cDNA complement consensus visible portion of view
*/
- protected Hashtable[] hcomplementConsensus = null;
+ protected Hashtable<String, Object>[] hcomplementConsensus = null;
/**
* results of secondary structure base pair consensus for visible portion of
* view
*/
- protected Hashtable[] hStrucConsensus = null;
+ protected Hashtable<String, Object>[] hStrucConsensus = null;
protected Conservation hconservation = null;
}
@Override
- public void setComplementConsensusHash(Hashtable[] hconsensus)
+ public void setComplementConsensusHash(
+ Hashtable<String, Object>[] hconsensus)
{
this.hcomplementConsensus = hconsensus;
}
}
@Override
- public Hashtable[] getComplementConsensusHash()
+ public Hashtable<String, Object>[] getComplementConsensusHash()
{
return hcomplementConsensus;
}
@Override
- public Hashtable[] getRnaStructureConsensusHash()
+ public Hashtable<String, Object>[] getRnaStructureConsensusHash()
{
return hStrucConsensus;
}
@Override
- public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
+ public void setRnaStructureConsensusHash(
+ Hashtable<String, Object>[] hStrucConsensus)
{
this.hStrucConsensus = hStrucConsensus;
// see note in mantis : issue number 8585
if (alignment.isNucleotide()
|| (conservation == null && quality == null)
- || !autoCalculateConsensus)
+ || !autoCalculateConsensusAndConservation)
{
return;
}
public void updateConsensus(final AlignmentViewPanel ap)
{
// see note in mantis : issue number 8585
- if (consensus == null || !autoCalculateConsensus)
+ if (consensus == null || !autoCalculateConsensusAndConservation)
{
return;
}
}
} while (end < max);
- int[][] startEnd = new int[regions.size()][2];
+ // int[][] startEnd = new int[regions.size()][2];
return regions;
}
{
alignment.padGaps();
}
- if (autoCalculateConsensus)
+ if (autoCalculateConsensusAndConservation)
{
updateConsensus(ap);
}
- if (hconsensus != null && autoCalculateConsensus)
+ if (hconsensus != null && autoCalculateConsensusAndConservation)
{
updateConservation(ap);
}
* TODO reorder the annotation rows according to group/sequence ordering on
* alignment
*/
- boolean sortg = true;
+ // boolean sortg = true;
// remove old automatic annotation
// add any new annotation
public void clearSequenceColours()
{
sequenceColours.clear();
- };
+ }
@Override
public AlignViewportI getCodingComplement()