&& selectionGroup.getSize() > 0;
AlignmentView view = viewport.getAlignmentView(isSelection);
// String[] seqStrings = viewport.getViewAsString(true);
- String[] seqStrings = view.getSequenceStrings(viewport
- .getGapCharacter());
+ String[] seqStrings = view
+ .getSequenceStrings(viewport.getGapCharacter());
SequenceI[] seqs;
if (isSelection)
{
- seqs = (SequenceI[]) view.getAlignmentAndHiddenColumns(viewport
- .getGapCharacter())[0];
+ seqs = (SequenceI[]) view
+ .getAlignmentAndHiddenColumns(viewport.getGapCharacter())[0];
}
else
{
if (!first)
{
- System.out.println(DASHES);
+ jalview.bin.Console.outPrintln(DASHES);
textarea.append(DASHES);
}
first = false;
as.printAlignment(System.out);
- scores[i][j] = as.getMaxScore()
- / as.getASeq1().length;
+ scores[i][j] = as.getMaxScore() / as.getASeq1().length;
totscore = totscore + scores[i][j];
textarea.append(as.getOutput());
for (int i = 0; i < seqs.length; i++)
{
- System.out.println(String.format("%3d %s", i + 1,
- seqs[i].getDisplayId(true)));
+ jalview.bin.Console.outPrintln(
+ String.format("%3d %s", i + 1, seqs[i].getDisplayId(true)));
}
/*
{
System.out.print(String.format("%7d", i + 1));
}
- System.out.println();
+ jalview.bin.Console.outPrintln();
for (int i = 0; i < seqs.length; i++)
{
*/
System.out.print(String.format("%7.3f", scores[i][j] / totscore));
}
- System.out.println();
+ jalview.bin.Console.outPrintln();
}
- System.out.println("\n");
+ jalview.bin.Console.outPrintln("\n");
}
/**