import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.datamodel.AlignmentAnnotation;
import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.datamodel.AlignmentAnnotation;
// tmp = ((max - tmp) * (size - cons2[j][23])) / size;
tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size;
// tmp = ((max - tmp) * (size - cons2[j][23])) / size;
tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size;
- // System.out.println(tmp+ " " + j);
- quality.setElementAt(new Double(tmp), j);
+ // jalview.bin.Console.outPrintln(tmp+ " " + j);
+ quality.setElementAt(Double.valueOf(tmp), j);
- quality2.annotations[i] = new Annotation(" ", description,
- ' ', value, new Color(minR + (maxR * vprop),
+ quality2.annotations[i] = new Annotation(" ", description, ' ',
+ value, new Color(minR + (maxR * vprop),