*/
public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
{
- List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+ List<SequenceI[]> seqvectors = new ArrayList<>();
for (PDBEntry pdb : pdbEntries)
{
- List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
+ List<SequenceI> choosenSeqs = new ArrayList<>();
for (SequenceI sq : alignment.getSequences())
{
Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
normaliseSequenceLogo = state;
}
+ public void setNormaliseHMMSequenceLogo(boolean state)
+ {
+ normaliseHMMSequenceLogo = state;
+ }
+
/**
*
* @return true if alignment characters should be displayed
return validCharWidth;
}
- private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
fr.setTransparency(featureSettings.getTransparency());
}
+ @Override
+ public boolean isNormaliseHMMSequenceLogo()
+ {
+ // TODO Auto-generated method stub
+ return normaliseHMMSequenceLogo;
+ }
+
}