Package com.googlecode.gaal.data.api

Examples of com.googlecode.gaal.data.api.IntSequence

68
69
70
71
72
73
74
75
76
77
78
79
80
81
        }
    }

    public void visualizeSuffixes(Drawing drawing) {
        for (int i = 0; i < sequence.size(); i++) {
            IntSequence subSequence = sequence.subSequence(i, sequence.size());
            drawing.drawCell(0, i, Integer.toString(i), TikzConstants.RED_CELL);

            for (int j = 0; j < subSequence.size(); j++) {
                drawing.drawCell(j + 1, i, symbolTable.toToken(subSequence.get(j)).toString(), Integer.toString(i + j),
                        TikzConstants.LIGHT_BLUE_CELL);
            }
        }
    }
View Full Code Here
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
            }
        }
    }

    public void visualizeEmbeddedSuffixes(Drawing drawing, SuffixArray sa, Interval interval, int windowSize) {
        IntSequence indices = interval.indices();
        int lcp = interval.lcp();
        for (int i = 0; i < interval.size(); i++) {
            int start = indices.get(i);
            drawing.drawCell(0, i, Integer.toString(start), TikzConstants.RED_CELL);
            IntSequence subSequence = sequence.subSequence(start, sequence.size());
            for (int k = 0; k < subSequence.size(); k++) {
                if (k < lcp) {
                    drawing.drawCell(k + 1, i, symbolTable.toToken(subSequence.get(k)).toString(),
                            Integer.toString(start + k), TikzConstants.LIGHT_BLUE_CELL);
                } else {
                    drawing.drawCell(k + 1, i, symbolTable.toToken(subSequence.get(k)).toString(),
                            Integer.toString(start + k), TikzConstants.BLUE_CELL);
                }
            }
        }
    }
View Full Code Here
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
            }
        }
    }

    public void visualizeWindow(Drawing drawing, SuffixArray sa, Interval interval, int windowSize) {
        IntSequence indices = interval.indices();
        int lcp = interval.lcp();
        for (int i = 0; i < interval.size(); i++) {
            int start = indices.get(i) + lcp;
            drawing.drawCell(0, i, Integer.toString(start), TikzConstants.RED_CELL);
            IntSequence subSequence = sequence.subSequence(start, sequence.size());
            for (int k = 0; k < subSequence.size(); k++) {
                if (k < windowSize) {
                    drawing.drawCell(k + 1, i, symbolTable.toToken(subSequence.get(k)).toString(),
                            Integer.toString(start + k), TikzConstants.GREEN_CELL);
                } else {
                    drawing.drawCell(k + 1, i, symbolTable.toToken(subSequence.get(k)).toString(),
                            Integer.toString(start + k), TikzConstants.LIGHT_BLUE_CELL);
                }
            }
        }
    }
View Full Code Here
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
            }
        }
    }

    public void visualizeEmbeddedSuffixesInWindow(Drawing drawing, SuffixArray sa, Interval interval, int windowSize) {
        IntSequence indices = interval.indices();
        int lcp = interval.lcp();
        int[] inverseSuffixTable = sa.getInverseSuffixTable();
        SortedMap<Integer, Integer> embeddedSuffixTableIndices = new TreeMap<Integer, Integer>();
        int counter = 0;
        for (int i = 0; i < interval.size(); i++) {
            int start = indices.get(i) + lcp;
            for (int j = start; j < start + windowSize && j < sequence.size(); j++) {
                drawing.drawCell(0, counter, Integer.toString(j), TikzConstants.RED_CELL);
                drawing.drawCell(1, counter, Integer.toString(inverseSuffixTable[j]), TikzConstants.GREEN_CELL);
                IntSequence subSequence = sequence.subSequence(j, sequence.size());
                Integer startIndex = embeddedSuffixTableIndices.get(inverseSuffixTable[j]);
                if (startIndex == null || startIndex < start) {
                    embeddedSuffixTableIndices.put(inverseSuffixTable[j], start);
                }
                for (int k = 0; k < subSequence.size(); k++) {
                    drawing.drawCell(k + 2, counter, symbolTable.toToken(subSequence.get(k)).toString(),
                            Integer.toString(j + k), TikzConstants.LIGHT_BLUE_CELL);
                }
                counter++;
            }
        }
View Full Code Here
145
146
147
148
149
150
151
152
153
154
155
156
157
158
    public void visualizeEmbeddedSuffixTable(Drawing drawing, SuffixArray sa) {
        int[] inverseSuffixTable = sa.getInverseSuffixTable();
        int[] suffixTable = sa.getSuffixTable();
        for (int i = 0; i < suffixTable.length; i++) {
            IntSequence subSequence = sequence.subSequence(suffixTable[i], sequence.size());
            drawing.drawCell(0, i, String.format("%d", suffixTable[i]), TikzConstants.RED_CELL);
            drawing.drawCell(1, i, Integer.toString(inverseSuffixTable[suffixTable[i]]), TikzConstants.GREEN_CELL);
            for (int j = 0; j < subSequence.size(); j++) {
                drawing.drawCell(j + 2, i, symbolTable.toToken(subSequence.get(j)).toString(),
                        Integer.toString(suffixTable[i] + j), TikzConstants.LIGHT_BLUE_CELL);
            }
        }
    }
View Full Code Here
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
    public void visualizeLcpInSuffixTable(Drawing drawing, SuffixArray sa) {
        int[] suffixTable = sa.getSuffixTable();
        int[] lcpTable = sa.getLcpTable();
        for (int i = 0; i < suffixTable.length; i++) {
            IntSequence subSequence = sequence.subSequence(suffixTable[i], sequence.size());
            int lcp = lcpTable[i];
            drawing.drawCell(0, i, Integer.toString(lcp), TikzConstants.GREEN_CELL);

            NodeStyle style = null;
            if (lcp > 0)
                style = TikzConstants.CELL_STYLES[lcp];
            for (int j = 0; j < subSequence.size(); j++) {
                NodeStyle cellStyle;
                if (j < lcp) {
                    cellStyle = style;
                } else {
                    cellStyle = TikzConstants.LIGHT_BLUE_CELL;
                }
                drawing.drawCell(j + 1, i, symbolTable.toToken(subSequence.get(j)).toString(),
                        Integer.toString(suffixTable[i] + j), cellStyle);
            }
        }
    }
View Full Code Here
212
213
214
215
216
217
218
219
220
221
222
223
224
225
    }

    public void visualizeSuffixTable(Drawing drawing, SuffixArray sa) {
        int[] suffixTable = sa.getSuffixTable();
        for (int i = 0; i < suffixTable.length; i++) {
            IntSequence subSequence = sequence.subSequence(suffixTable[i], sequence.size());
            drawing.drawCell(0, i, String.format("%d", suffixTable[i]), TikzConstants.RED_CELL);

            for (int j = 0; j < subSequence.size(); j++) {
                drawing.drawCell(j + 1, i, symbolTable.toToken(subSequence.get(j)).toString(),
                        Integer.toString(suffixTable[i] + j), TikzConstants.LIGHT_BLUE_CELL);
            }
        }
    }
View Full Code Here
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
        }
    }

    private void markInterval(Interval interval, EmbeddedInterval embeddedInterval, int[] styleArray, int length,
            int windowSize) {
        IntSequence indices = interval.indices();
        int lcp = interval.lcp();
        if (length < 1) {
            length = lcp;
        }
        for (int i = 0; i < indices.size(); i++) {
            int style = i;
            if (embeddedInterval != null) {
                IntSequence embeddedIndices = embeddedInterval.indices();
                int minDistance = windowSize + 1;
                for (int k = 0; k < embeddedIndices.size(); k++) {
                    int distance = embeddedIndices.get(k) - indices.get(i) - lcp;
                    if (distance >= 0 && distance < minDistance) {
                        minDistance = distance;
                    }
                }
                if (minDistance > windowSize) {
View Full Code Here
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
            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);
                        }
                    }
                }
            }
        }

        for (int i = 0; i < suffixTable.length; i++) {
            IntSequence subSequence = sequence.subSequence(suffixTable[i], sequence.size());

            for (int j = 0; j < subSequence.size(); j++) {
                if (!usedCells[i][j]) {
                    drawing.drawCell(i, j, symbolTable.toToken(subSequence.get(j)).toString(),
                            TikzConstants.LIGHT_BLUE_CELL);
                }
            }
        }
    }
View Full Code Here
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
                    number);
        }
    }

    public static IntSequence removeIntervening(EmbeddedInterval interval) {
        IntSequence indices = interval.indices();
        IntSequence embeddingIndices = interval.embeddingIndices();
        System.out.format("ind:%s\n", indices);
        System.out.format("emb:%s\n", embeddingIndices);
        BitSet removedIndices = new BitSet(embeddingIndices.size());
        for (int i = 0; i < embeddingIndices.size(); i++) {
            if (!removedIndices.get(i)) {
                int index = indices.get(i);
                int embeddingIndex = embeddingIndices.get(i);
                for (int j = 0; j < embeddingIndices.size(); j++) {
                    if (i != j && !removedIndices.get(j) && embeddingIndices.get(j) == embeddingIndex) {
                        System.out.format("%d=%d\n", embeddingIndices.get(j), embeddingIndex);
                        if (indices.get(j) > index) {
                            System.out.format("removing i=%d\n", i);
                            removedIndices.set(i);
                        } else {
                            System.out.format("removing j=%d\n", j);
View Full Code Here
TOP

Related Classes of com.googlecode.gaal.data.api.IntSequence

  • com.googlecode.gaal.analysis.impl.Aligner
  • com.googlecode.gaal.analysis.impl.ContextExtractorTest
  • com.googlecode.gaal.analysis.impl.IntervalVectorBuilder
  • com.googlecode.gaal.analysis.impl.NaiveDistinctBwtSetBuilder
  • com.googlecode.gaal.analysis.impl.NonSingletonBwtSetBuilder
  • com.googlecode.gaal.analysis.impl.SetBuildersTest
  • com.googlecode.gaal.analysis.impl.SimpleContextFilter
  • com.googlecode.gaal.analysis.impl.SingletonBwtSetBuilder
  • com.googlecode.gaal.data.impl.AbstractCorpus
  • com.googlecode.gaal.data.impl.AbstractSequence
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.