}
IntervalSetBuilder intervalSetBuilder = null;
if (line.hasOption("max")) {
intervalSetBuilder = new NonSingletonBwtSetBuilder();
} else if (line.hasOption("smax")) {
intervalSetBuilder = new SupermaximalSetBuilder();
} else {
intervalSetBuilder = new ProperIntervalSetBuilder();
}
if (line.hasOption('v')) {
System.out.println("alignment options:");
System.out.printf("minimal similarity : %f\n", minSimilarity);
System.out.printf("alignments number: %d\n", alignmentsNumber);
System.out.printf("minimal vector size: %d\n", minVectorSize);
System.out.print("outputing ");
if (intervalSetBuilder instanceof NonSingletonBwtSetBuilder) {
System.out.print("maximal");
} else if (intervalSetBuilder instanceof SupermaximalSetBuilder) {
System.out.print("supermaximal");
} else if (intervalSetBuilder instanceof ProperIntervalSetBuilder) {
System.out.print("all the");
}
System.out.println(" repeats");
}
boolean asLaTeX = false;
if (line.hasOption('x')) {
asLaTeX = true;
}
getAnalyser(line.getOptionValue('s'), line.getOptionValue('t'), corpusSize, regex, srcStopWords,
dstStopWords, srcSeparators, dstSeparators).printRecursiveAlignments(intervalSetBuilder,
minLeftRightContextRatio, minNonEmptyFillerCount, minSimilarity, alignmentsNumber,
minVectorSize, windowSize, srcDepth, srcMaxDepth, dstDepth, dstMaxDepth, asLaTeX);
} else if (line.hasOption('s')
&& (line.hasOption('i') || line.hasOption('r') || line.hasOption('u') || line.hasOption('z'))) {
if (line.hasOption('i')) {
getAnalyser(line.getOptionValue('s'), null, corpusSize, regex, srcStopWords, dstStopWords,
srcSeparators, dstSeparators).printSrcCorpusInfo();
}
if (line.hasOption('r')) {
IntervalSetBuilder intervalSetBuilder = null;
if (line.hasOption("max")) {
intervalSetBuilder = new NonSingletonBwtSetBuilder();
} else if (line.hasOption("smax")) {
intervalSetBuilder = new SupermaximalSetBuilder();
} else {
intervalSetBuilder = new ProperIntervalSetBuilder();
}
getAnalyser(line.getOptionValue('s'), null, corpusSize, regex, srcStopWords, dstStopWords,
srcSeparators, dstSeparators).printSrcRecursiveIntervals(intervalSetBuilder,