1 package compbio.data.sequence;
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4 * Enumeration defining two constraints for SMERFS columns score calculation.
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5 * MAX_SCORE gives the highest core of all the windows the column belongs to.
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6 * MID_SCORE gives the window score to the column in the middle.
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8 * @author Agnieszka Golicz & Peter Troshin
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10 public enum SMERFSConstraints {
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12 MAX_SCORE, MID_SCORE;
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15 * Default column scoring schema
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17 public static final SMERFSConstraints DEFAULT_COLUMN_SCORE = SMERFSConstraints.MID_SCORE;
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20 * Default window size value for SMERFS algorithm
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22 public static final int DEFAULT_WINDOW_SIZE = 7;
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25 * Default gap threshold value for SMERFS algorithm
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27 public static final double DEFAULT_GAP_THRESHOLD = 0.1;
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29 public static SMERFSConstraints getSMERFSColumnScore(String score) {
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31 score = score.trim().toLowerCase();
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32 if (score.equalsIgnoreCase(SMERFSConstraints.MAX_SCORE.toString())) {
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33 return SMERFSConstraints.MAX_SCORE;
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35 if (score.equalsIgnoreCase(SMERFSConstraints.MID_SCORE.toString())) {
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36 return SMERFSConstraints.MID_SCORE;
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