private String alignmentOutput;
+ private boolean suppressTextbox;
+
+ private boolean discardAlignments;
+
/**
* Creates a new PairwiseAlignPanel object.
*
float[][] alignmentScores = new float[seqs.length][seqs.length];
double totscore = 0D;
int count = seqs.length;
+ suppressTextbox = count<10;
+ discardAlignments = count<15;
boolean first = true;
for (int i = 1; i < count; i++)
{
// fill diagonal alignmentScores with Float.NaN
- alignmentScores[i-1][i-1] = Float.NaN;
+ alignmentScores[i - 1][i - 1] = Float.NaN;
for (int j = 0; j < i; j++)
{
AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
}
as.calcScoreMatrix();
- if (endGaps)
- {
+ if (endGaps)
+ {
as.traceAlignmentWithEndGaps();
- } else {
- as.traceAlignment();
- }
- as.scoreAlignment();
+ }
+ else
+ {
+ as.traceAlignment();
+ }
+ as.scoreAlignment();
if (!first)
{
System.out.println(DASHES);
textarea.append(DASHES);
- sb.append(DASHES);
+ sb.append(DASHES);
}
first = false;
- as.printAlignment(System.out);
+ if (discardAlignments) {
+ as.printAlignment(System.out);
+ }
scores[i][j] = as.getMaxScore() / as.getASeq1().length;
alignmentScores[i][j] = as.getAlignmentScore();
totscore = totscore + scores[i][j];
-
- textarea.append(as.getOutput());
- sb.append(as.getOutput());
- sequences.add(as.getAlignedSeq1());
- sequences.add(as.getAlignedSeq2());
+ if (suppressTextbox)
+ {
+ textarea.append(as.getOutput());
+ sb.append(as.getOutput());
+ }
+ if (discardAlignments)
+ {
+ sequences.add(as.getAlignedSeq1());
+ sequences.add(as.getAlignedSeq2());
+ }
}
}
- alignmentScores[count-1][count-1] = Float.NaN;
+ alignmentScores[count - 1][count - 1] = Float.NaN;
this.scores = scores;
this.alignmentScores = alignmentScores;