Package com.googlecode.gaal.suffix.api.IntervalTree

Examples of com.googlecode.gaal.suffix.api.IntervalTree.Interval

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    private void visualizeEmbeddedSuffixes(String fileName, String caption, String label) throws IOException {
        buffer.append(String.format(LATEX_INPUT, fileName));
        Writer out = new FileWriter(DOC_PATH + fileName);
        LinearizedSuffixTree lst = new LinearizedSuffixTreeImpl(corpus.sequence(), corpus.alphabetSize());
        int windowSize = 5;
        Interval interval = findInterval(lst, "in");
        LaTeXVisualizer.visualizeEmbeddedSuffixes(out, caption, label, lst, interval, windowSize, corpus);
        out.flush();
        out.close();
    }
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    private void visualizeWindow(String fileName, String caption, String label) throws IOException {
        buffer.append(String.format(LATEX_INPUT, fileName));
        Writer out = new FileWriter(DOC_PATH + fileName);
        LinearizedSuffixTree lst = new LinearizedSuffixTreeImpl(corpus.sequence(), corpus.alphabetSize());
        int windowSize = 5;
        Interval interval = findInterval(lst, "in");
        LaTeXVisualizer.visualizeWindow(out, caption, label, lst, interval, windowSize, corpus);
        out.flush();
        out.close();
    }
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    private void visualizeEmbeddedSuffixesInWindow(String fileName, String caption, String label) throws IOException {
        buffer.append(String.format(LATEX_INPUT, fileName));
        Writer out = new FileWriter(DOC_PATH + fileName);
        LinearizedSuffixTree lst = new LinearizedSuffixTreeImpl(corpus.sequence(), corpus.alphabetSize());
        int windowSize = 5;
        Interval interval = findInterval(lst, "in");
        LaTeXVisualizer.visualizeEmbeddedSuffixesInWindow(out, caption, label, lst, interval, windowSize, corpus);
        out.flush();
        out.close();
    }
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    private void visualizeEmbeddedSuffixTable(String fileName, String caption, String label) throws IOException {
        buffer.append(String.format(LATEX_INPUT, fileName));
        Writer out = new FileWriter(DOC_PATH + fileName);
        LinearizedSuffixTree lst = new LinearizedSuffixTreeImpl(corpus.sequence(), corpus.alphabetSize());
        int windowSize = 5;
        Interval interval = findInterval(lst, "in");
        EmbeddedSuffixTree est = EmbeddedSuffixTreeImpl.create(lst, interval, windowSize, corpus);
        LaTeXVisualizer.visualizeEmbeddedSuffixTable(out, caption, label, est, corpus);
        out.flush();
        out.close();
    }
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    private void visualizeEmbeddedLcpTable(String fileName, String caption, String label) throws IOException {
        buffer.append(String.format(LATEX_INPUT, fileName));
        Writer out = new FileWriter(DOC_PATH + fileName);
        LinearizedSuffixTree lst = new LinearizedSuffixTreeImpl(corpus.sequence(), corpus.alphabetSize());
        int windowSize = 5;
        Interval interval = findInterval(lst, "in");
        EmbeddedSuffixTree est = EmbeddedSuffixTreeImpl.create(lst, interval, windowSize, corpus);
        LaTeXVisualizer.visualizeLcpInSuffixTable(out, caption, label, est, corpus, true);
        out.flush();
        out.close();
    }
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    private void visualizeEmbeddedSuffixTree(String fileName, String caption, String label) throws IOException {
        buffer.append(String.format(LATEX_INPUT, fileName));
        Writer out = new FileWriter(DOC_PATH + fileName);
        LinearizedSuffixTree lst = new LinearizedSuffixTreeImpl(corpus.sequence(), corpus.alphabetSize());
        int windowSize = 5;
        Interval interval = findInterval(lst, "in");
        EmbeddedSuffixTree est = EmbeddedSuffixTreeImpl.create(lst, interval, windowSize, corpus);
        LaTeXVisualizer.visualizeEmbeddedSuffixTree(out, caption, label, est, corpus);
        out.flush();
        out.close();
    }
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    private void visualizeEmbeddedIntervalTree(String fileName, String caption, String label) throws IOException {
        buffer.append(String.format(LATEX_INPUT, fileName));
        Writer out = new FileWriter(DOC_PATH + fileName);
        LinearizedSuffixTree lst = new LinearizedSuffixTreeImpl(corpus.sequence(), corpus.alphabetSize());
        int windowSize = 5;
        Interval interval = findInterval(lst, "in");
        EmbeddedSuffixTree est = EmbeddedSuffixTreeImpl.create(lst, interval, windowSize, corpus);
        LaTeXVisualizer.visualizeIntervalTree(out, caption, label, est, null, corpus);
        out.flush();
        out.close();
    }
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            T sa, Map<Interval, Integer> styleMap) {
        int[] suffixTable = sa.getSuffixTable();
        Iterator<? extends Interval> iterator = sa.preorderIterator();
        boolean[][] usedCells = new boolean[suffixTable.length][sequence.size()];
        while (iterator.hasNext()) {
            Interval node = iterator.next();
            Integer style = styleMap.get(node);
            if (style != null) {
                NodeStyle nodeStyle = TikzConstants.CELL_STYLES[style];
                for (int i = node.left(); i <= node.right(); i++) {
                    IntSequence subSequence = sequence.subSequence(suffixTable[i], suffixTable[i] + node.lcp());
                    for (int j = 0; j < subSequence.size(); j++) {
                        if (!usedCells[i][j]) {
                            usedCells[i][j] = true;
                            drawing.drawCell(i, j, symbolTable.toToken(subSequence.get(j)).toString(), nodeStyle);
                        }
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    }

    private Interval findInterval(IntervalTree<? extends Interval> tree, String label) {
        Iterator<? extends Interval> iterator = tree.preorderIterator();
        while (iterator.hasNext()) {
            Interval interval = iterator.next();
            if (corpus.toString(interval.label(), "").equals(label)) {
                return interval;
            }
        }
        return null;
    }
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        return null;
    }

    private <T extends SuffixArray & IntervalTree<? extends Interval>> void visualizeInterval(Writer out, T tree,
            String[] labels, int labelIndex, int length, int windowSize) throws IOException {
        Interval interval = findInterval(tree, labels[labelIndex]);
        if (labelIndex == labels.length - 1) {
            LaTeXVisualizer.visualizeInterval(out, null, null, tree, interval, length, windowSize, corpus);
        } else {
            EmbeddedSuffixTree est = EmbeddedSuffixTreeImpl.create(tree, interval, 5, corpus);
            visualizeInterval(out, est, labels, labelIndex + 1, length, windowSize);
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Related Classes of com.googlecode.gaal.suffix.api.IntervalTree.Interval

  • com.googlecode.gaal.analysis.impl.Analyser
  • com.googlecode.gaal.analysis.impl.ConcurrentEmbeddedContextExtractor$ContextIterator
  • com.googlecode.gaal.analysis.impl.ContextExtractorTest
  • com.googlecode.gaal.analysis.impl.RecursiveIntervalExtractor$RecursiveIntervalIterator
  • com.googlecode.gaal.analysis.impl.SimpleContextFilter
  • com.googlecode.gaal.suffix.algorithm.impl.ExtendedLcpTableBuilderImpl
  • com.googlecode.gaal.suffix.impl.EnhancedSuffixArrayImplTest
  • com.googlecode.gaal.suffix.impl.EnhancedSuffixArrayImplTest$IntervalImpl
  • com.googlecode.gaal.suffix.impl.LinearizedSuffixTreeImplTest
  • com.googlecode.gaal.vis.TableVisualizer
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