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package jalview.ext.ensembl; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import java.util.ArrayList; |
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import java.util.List; |
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import com.stevesoft.pat.Regex; |
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@author |
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| 42.9% |
Uncovered Elements: 16 (28) |
Complexity: 13 |
Complexity Density: 0.87 |
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public class EnsemblProtein extends EnsemblSeqProxy |
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{ |
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private static final Regex ACCESSION_REGEX = new Regex( |
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"(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)"); |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public EnsemblProtein()... |
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{ |
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super(); |
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} |
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@param |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public EnsemblProtein(String d)... |
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{ |
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super(d); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public String getDbName() |
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{ |
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return "ENSEMBL (Protein)"; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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protected EnsemblSeqType getSourceEnsemblType() |
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{ |
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return EnsemblSeqType.PROTEIN; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public boolean isDnaCoding() |
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{ |
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return false; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public String getTestQuery() |
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{ |
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return "ENSP00000288602"; |
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} |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
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@Override... |
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protected void addFeaturesAndProduct(String accId, AlignmentI alignment) |
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{ |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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0 |
@Override... |
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protected EnsemblFeatureType[] getFeaturesToFetch() |
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{ |
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return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq, |
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String accId) |
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{ |
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return new ArrayList<>(); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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5 |
@Override... |
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public Regex getAccessionValidator() |
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{ |
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return ACCESSION_REGEX; |
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} |
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| 87.5% |
Uncovered Elements: 1 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
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6 |
@Override... |
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public String getAccessionIdFromQuery(String query) |
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{ |
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String accId = super.getAccessionIdFromQuery(query); |
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if (accId != null && accId.length() >= 12) |
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{ |
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char[] chars = accId.toCharArray(); |
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chars[chars.length - 12] = 'P'; |
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accId = new String(chars); |
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} |
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return accId; |
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} |
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} |