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1 package de.mpiwg.anteater.results.impl;
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2
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3 import java.util.ArrayList;
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4 import java.util.List;
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5
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6 import de.mpiwg.anteater.AnteaterConfiguration;
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7 import de.mpiwg.anteater.results.AResultManager;
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8 import de.mpiwg.anteater.results.AnnotationTag;
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9 import de.mpiwg.anteater.results.SpeciesScientificResult;
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10 import de.mpiwg.anteater.text.TextType;
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11
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12 public class ScientificNameResultManager extends AResultManager<SpeciesScientificResult> {
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13
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14 public final static String SCIENTIFIC_NAME_TAG_Start = "<species_scientific name=\"";
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15 public final static String SCIENTIFIC_NAME_ID_ATTR = "\" ncbiID=\"";
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16 public final static String SCIENTIFIC_NAME_TAG_End = "\" >";
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17 public final static String SCIENTIFIC_NAME_TAG_CLOSE = "</species_scientific>";
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18 public final static String TAG_TYPE = "scientific_name";
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19
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20 public ScientificNameResultManager(AnteaterConfiguration configuration) {
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21 super(configuration);
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22 }
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23
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24 @Override
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25 protected List<AnnotationTag> getSpecificSummaryTags(
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26 List<SpeciesScientificResult> results, int textIndex) {
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27 return getTags(results, textIndex, TextType.TYPE_SUMMARY);
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28 }
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29
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30 @Override
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31 protected List<AnnotationTag> getSpecificSuppleInfTags(
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32 List<SpeciesScientificResult> results, int textIndex) {
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33 return getTags(results, textIndex, TextType.TYPE_SUPLINF);
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34 }
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35
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36 protected List<AnnotationTag> getTags(List<SpeciesScientificResult> results, int textIndex, int type) {
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37 List<AnnotationTag> tags = new ArrayList<AnnotationTag>();
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38
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39 // get applicants for text
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40 List<SpeciesScientificResult> namesOfSum = new ArrayList<SpeciesScientificResult>();
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41 for (SpeciesScientificResult r : results) {
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42 if (r.getResult().getType() == type
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43 && r.getResult().getTextIdx() == textIndex)
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44 namesOfSum.add(r);
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45 }
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46
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47
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48 for (SpeciesScientificResult name : namesOfSum) {
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49 tags.add(new AnnotationTag(SCIENTIFIC_NAME_TAG_Start + name.getFinding().getScientificName() + SCIENTIFIC_NAME_ID_ATTR + (name.getFinding().getNcbiId() != null ? name.getFinding().getNcbiId() : "") + SCIENTIFIC_NAME_TAG_End, name.getFinding().getStart(), SCIENTIFIC_NAME_TAG_CLOSE, name.getFinding().getStart()
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50 + name.getFinding().getLength(), TAG_TYPE));
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51 }
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52
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53 return tags;
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54 }
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55
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56 }
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