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package jalview.viewmodel.styles; |
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import java.awt.Color; |
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import java.util.List; |
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import jalview.api.ViewStyleI; |
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@author |
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| 85.9% |
Uncovered Elements: 39 (276) |
Complexity: 101 |
Complexity Density: 0.58 |
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public class ViewStyle implements ViewStyleI |
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{ |
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private boolean abovePIDThreshold = false; |
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int charHeight; |
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int charWidth; |
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int idWidth = -1; |
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private boolean colourAppliesToAllGroups; |
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boolean centreColumnLabels = false; |
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private boolean showdbrefs; |
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private boolean shownpfeats; |
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private boolean colourByReferenceSeq = false; |
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boolean conservationColourSelected = false; |
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boolean byConsensusSecondaryStructureSelected = false; |
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private boolean displayReferenceSeq = false; |
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private int increment; |
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private int consensusSecondaryStructureThreshold; |
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boolean renderGaps = true; |
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private boolean rightAlignIds = false; |
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boolean scaleAboveWrapped = false; |
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boolean scaleLeftWrapped = true; |
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boolean scaleRightWrapped = true; |
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boolean seqNameItalics; |
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private boolean showAnnotation = true; |
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boolean showBoxes = true; |
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boolean showColourText = false; |
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boolean showHiddenMarkers = true; |
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boolean showJVSuffix = true; |
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boolean showSeqFeaturesHeight; |
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boolean showSequenceFeatures = false; |
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boolean showText = true; |
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protected boolean showUnconserved = false; |
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Color textColour = Color.black; |
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Color textColour2 = Color.white; |
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int threshold; |
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int thresholdTextColour = 0; |
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boolean upperCasebold = false; |
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private String fontName; |
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private int fontSize; |
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private boolean scaleProteinAsCdna = true; |
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private boolean proteinFontAsCdna = true; |
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@param |
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| 100% |
Uncovered Elements: 0 (47) |
Complexity: 1 |
Complexity Density: 0.02 |
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public ViewStyle(ViewStyleI vs)... |
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{ |
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setAbovePIDThreshold(vs.getAbovePIDThreshold()); |
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setCentreColumnLabels(vs.isCentreColumnLabels()); |
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setCharHeight(vs.getCharHeight()); |
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setCharWidth(vs.getCharWidth()); |
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setColourAppliesToAllGroups(vs.getColourAppliesToAllGroups()); |
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setColourByReferenceSeq(vs.isColourByReferenceSeq()); |
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setColourText(vs.getColourText()); |
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setByConsensusSecondaryStructureSelected( |
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vs.getByConsensusSecondaryStructureSelected()); |
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setConsensusSecondaryStructureThreshold( |
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vs.getConsensusSecondaryStructureThreshold()); |
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setConservationColourSelected(vs.isConservationColourSelected()); |
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setConservationSelected(vs.getConservationSelected()); |
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setDisplayReferenceSeq(vs.isDisplayReferenceSeq()); |
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setFontName(vs.getFontName()); |
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setFontSize(vs.getFontSize()); |
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setFontStyle(vs.getFontStyle()); |
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setIdWidth(vs.getIdWidth()); |
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setIncrement(vs.getIncrement()); |
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setRenderGaps(vs.isRenderGaps()); |
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setRightAlignIds(vs.isRightAlignIds()); |
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setScaleAboveWrapped(vs.getScaleAboveWrapped()); |
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setScaleLeftWrapped(vs.getScaleLeftWrapped()); |
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setScaleProteinAsCdna(vs.isScaleProteinAsCdna()); |
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setProteinFontAsCdna(vs.isProteinFontAsCdna()); |
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setScaleRightWrapped(vs.getScaleRightWrapped()); |
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setSeqNameItalics(vs.isSeqNameItalics()); |
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setShowAnnotation(vs.isShowAnnotation()); |
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setShowBoxes(vs.getShowBoxes()); |
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setShowColourText(vs.isShowColourText()); |
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setShowDBRefs(vs.isShowDBRefs()); |
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setShowHiddenMarkers(vs.getShowHiddenMarkers()); |
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setShowJVSuffix(vs.getShowJVSuffix()); |
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setShowNPFeats(vs.isShowNPFeats()); |
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setShowSequenceFeaturesHeight(vs.isShowSequenceFeaturesHeight()); |
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setShowSequenceFeatures(vs.isShowSequenceFeatures()); |
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setShowComplementFeatures(vs.isShowComplementFeatures()); |
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setShowComplementFeaturesOnTop(vs.isShowComplementFeaturesOnTop()); |
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setShowText(vs.getShowText()); |
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setShowUnconserved(vs.getShowUnconserved()); |
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setTextColour(vs.getTextColour()); |
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setTextColour2(vs.getTextColour2()); |
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setThreshold(vs.getThreshold()); |
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setThresholdTextColour(vs.getThresholdTextColour()); |
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setUpperCasebold(vs.isUpperCasebold()); |
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setWrapAlignment(vs.getWrapAlignment()); |
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setWrappedWidth(vs.getWrappedWidth()); |
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setSecondaryStructureSources(vs.getSecondaryStructureSources()); |
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setShowStructureProvider(vs.isShowStructureProvider()); |
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} |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
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public ViewStyle()... |
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{ |
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} |
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| 0% |
Uncovered Elements: 10 (10) |
Complexity: 3 |
Complexity Density: 0.38 |
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@Override... |
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public boolean equals(Object other) |
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if (other == null || !(other instanceof ViewStyle)) |
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{ |
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return false; |
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} |
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ViewStyle vs = (ViewStyle) other; |
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boolean match = (getAbovePIDThreshold() == vs.getAbovePIDThreshold() |
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&& isCentreColumnLabels() == vs.isCentreColumnLabels() |
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&& getCharHeight() == vs.getCharHeight() |
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&& getCharWidth() == vs.getCharWidth() |
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&& getColourAppliesToAllGroups() == vs |
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.getColourAppliesToAllGroups() |
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&& isColourByReferenceSeq() == vs.isColourByReferenceSeq() |
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&& getColourText() == vs.getColourText() |
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&& isConservationColourSelected() == vs |
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.isConservationColourSelected() |
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&& getByConsensusSecondaryStructureSelected() == vs |
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.getByConsensusSecondaryStructureSelected() |
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&& getConservationSelected() == vs.getConservationSelected() |
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&& isDisplayReferenceSeq() == vs.isDisplayReferenceSeq() |
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&& getFontSize() == vs.getFontSize() |
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&& getFontStyle() == vs.getFontStyle() |
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&& getIdWidth() == vs.getIdWidth() |
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&& getIncrement() == vs.getIncrement() |
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&& getConsensusSecondaryStructureThreshold() == vs |
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.getConsensusSecondaryStructureThreshold() |
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&& isRenderGaps() == vs.isRenderGaps() |
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&& isRightAlignIds() == vs.isRightAlignIds() |
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&& getScaleAboveWrapped() == vs.getScaleAboveWrapped() |
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&& getScaleLeftWrapped() == vs.getScaleLeftWrapped() |
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&& isScaleProteinAsCdna() == vs.isScaleProteinAsCdna() |
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&& isProteinFontAsCdna() == vs.isProteinFontAsCdna() |
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&& getScaleRightWrapped() == vs.getScaleRightWrapped() |
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&& isSeqNameItalics() == vs.isSeqNameItalics() |
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&& isShowAnnotation() == vs.isShowAnnotation() |
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&& getShowBoxes() == vs.getShowBoxes() |
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&& isShowColourText() == vs.isShowColourText() |
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&& isShowDBRefs() == vs.isShowDBRefs() |
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&& getShowHiddenMarkers() == vs.getShowHiddenMarkers() |
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&& getShowJVSuffix() == vs.getShowJVSuffix() |
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&& isShowNPFeats() == vs.isShowNPFeats() |
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&& isShowSequenceFeaturesHeight() == vs |
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.isShowSequenceFeaturesHeight() |
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&& isShowSequenceFeatures() == vs.isShowSequenceFeatures() |
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&& isShowComplementFeatures() == vs.isShowComplementFeatures() |
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&& isShowComplementFeaturesOnTop() == vs |
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.isShowComplementFeaturesOnTop() |
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&& getShowText() == vs.getShowText() |
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&& getShowUnconserved() == vs.getShowUnconserved() |
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&& getThreshold() == vs.getThreshold() |
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&& getThresholdTextColour() == vs.getThresholdTextColour() |
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&& isUpperCasebold() == vs.isUpperCasebold() |
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&& getWrapAlignment() == vs.getWrapAlignment() |
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&& getWrappedWidth() == vs.getWrappedWidth() |
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&& getSecondaryStructureSources() == vs |
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.getSecondaryStructureSources() |
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&& isShowStructureProvider() == vs.isShowStructureProvider()); |
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match = match && String.valueOf(getFontName()) |
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.equals(String.valueOf(vs.getFontName())); |
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match = match && String.valueOf(getTextColour()) |
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.equals(String.valueOf(vs.getTextColour())); |
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match = match && String.valueOf(getTextColour2()) |
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.equals(String.valueOf(vs.getTextColour2())); |
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return match; |
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} |
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| 0% |
Uncovered Elements: 25 (25) |
Complexity: 1 |
Complexity Density: 0.04 |
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@Override... |
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public int hashCode() |
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{ |
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int hash = 0; |
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int m = 1; |
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hash += m++ * Boolean.valueOf(this.abovePIDThreshold).hashCode(); |
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hash += m++ * Boolean.valueOf(this.centreColumnLabels).hashCode(); |
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hash += m++ * Boolean.valueOf(this.colourAppliesToAllGroups).hashCode(); |
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hash += m++ * Boolean.valueOf(this.displayReferenceSeq).hashCode(); |
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hash += m++ * Boolean.valueOf(this.renderGaps).hashCode(); |
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hash += m++ * Boolean.valueOf(this.rightAlignIds).hashCode(); |
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hash += m++ * Boolean.valueOf(this.scaleProteinAsCdna).hashCode(); |
342 |
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hash += m++ * Boolean.valueOf(this.scaleRightWrapped).hashCode(); |
343 |
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hash += m++ * Boolean.valueOf(this.seqNameItalics).hashCode(); |
344 |
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hash += m++ * Boolean.valueOf(this.showAnnotation).hashCode(); |
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hash += m++ * Boolean.valueOf(this.showBoxes).hashCode(); |
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hash += m++ * Boolean.valueOf(this.showdbrefs).hashCode(); |
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hash += m++ * Boolean.valueOf(this.showJVSuffix).hashCode(); |
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hash += m++ * Boolean.valueOf(this.showSequenceFeatures).hashCode(); |
349 |
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hash += m++ * Boolean.valueOf(this.showUnconserved).hashCode(); |
350 |
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hash += m++ * Boolean.valueOf(this.wrapAlignment).hashCode(); |
351 |
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hash += m++ * this.charHeight; |
352 |
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hash += m++ * this.charWidth; |
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hash += m++ * fontSize; |
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hash += m++ * fontStyle; |
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hash += m++ * idWidth; |
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hash += String.valueOf(this.fontName).hashCode(); |
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return hash; |
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} |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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363 |
23 |
@Override... |
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public boolean isUpperCasebold() |
365 |
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{ |
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return upperCasebold; |
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} |
368 |
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369 |
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@param |
371 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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23 |
@Override... |
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public void setUpperCasebold(boolean upperCasebold) |
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{ |
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this.upperCasebold = upperCasebold; |
377 |
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} |
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boolean wrapAlignment = false; |
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int wrappedWidth; |
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private int fontStyle; |
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private boolean showComplementFeatures; |
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private boolean showComplementFeaturesOnTop; |
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private List<String> secondaryStructureSources = List.of(new String[0]); |
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private boolean showStructureProvider; |
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@return |
406 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
407 |
273 |
@Override... |
408 |
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public boolean getAbovePIDThreshold() |
409 |
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{ |
410 |
273 |
return abovePIDThreshold; |
411 |
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} |
412 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
413 |
273 |
@Override... |
414 |
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public boolean getByConsensusSecondaryStructureSelected() |
415 |
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{ |
416 |
273 |
return byConsensusSecondaryStructureSelected; |
417 |
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} |
418 |
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419 |
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420 |
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421 |
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422 |
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@return |
423 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
424 |
16801 |
@Override... |
425 |
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public int getCharHeight() |
426 |
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{ |
427 |
16801 |
return charHeight; |
428 |
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} |
429 |
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430 |
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431 |
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432 |
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433 |
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@return |
434 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
435 |
108002 |
@Override... |
436 |
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public int getCharWidth() |
437 |
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{ |
438 |
108009 |
return charWidth; |
439 |
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} |
440 |
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441 |
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442 |
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443 |
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444 |
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@return |
445 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
446 |
326 |
@Override... |
447 |
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public boolean getColourAppliesToAllGroups() |
448 |
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{ |
449 |
326 |
return colourAppliesToAllGroups; |
450 |
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} |
451 |
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452 |
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453 |
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454 |
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455 |
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@return |
456 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
457 |
48486 |
@Override... |
458 |
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public boolean getColourText() |
459 |
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{ |
460 |
48486 |
return showColourText; |
461 |
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} |
462 |
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463 |
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464 |
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465 |
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466 |
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@return |
467 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
468 |
353 |
@Override... |
469 |
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public boolean getConservationSelected() |
470 |
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{ |
471 |
353 |
return conservationColourSelected; |
472 |
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} |
473 |
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474 |
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475 |
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476 |
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477 |
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@return |
478 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
479 |
23 |
@Override... |
480 |
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public int getIncrement() |
481 |
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{ |
482 |
23 |
return increment; |
483 |
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} |
484 |
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485 |
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|
486 |
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|
487 |
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|
488 |
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@return |
489 |
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|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
490 |
174 |
@Override... |
491 |
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public boolean getScaleAboveWrapped() |
492 |
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{ |
493 |
174 |
return scaleAboveWrapped; |
494 |
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} |
495 |
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496 |
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497 |
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|
498 |
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|
499 |
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@return |
500 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
501 |
302 |
@Override... |
502 |
|
public boolean getScaleLeftWrapped() |
503 |
|
{ |
504 |
302 |
return scaleLeftWrapped; |
505 |
|
} |
506 |
|
|
507 |
|
|
508 |
|
|
509 |
|
|
510 |
|
@return |
511 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
512 |
343 |
@Override... |
513 |
|
public boolean getScaleRightWrapped() |
514 |
|
{ |
515 |
343 |
return scaleRightWrapped; |
516 |
|
} |
517 |
|
|
518 |
|
|
519 |
|
|
520 |
|
|
521 |
|
@return |
522 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
523 |
51737 |
@Override... |
524 |
|
public boolean getShowBoxes() |
525 |
|
{ |
526 |
51737 |
return showBoxes; |
527 |
|
} |
528 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
529 |
282 |
@Override... |
530 |
|
public boolean getShowHiddenMarkers() |
531 |
|
{ |
532 |
282 |
return showHiddenMarkers; |
533 |
|
} |
534 |
|
|
535 |
|
|
536 |
|
|
537 |
|
|
538 |
|
@return |
539 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
540 |
5519 |
@Override... |
541 |
|
public boolean getShowJVSuffix() |
542 |
|
{ |
543 |
5519 |
return showJVSuffix; |
544 |
|
} |
545 |
|
|
546 |
|
|
547 |
|
|
548 |
|
|
549 |
|
@return |
550 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
551 |
48716 |
@Override... |
552 |
|
public boolean getShowText() |
553 |
|
{ |
554 |
48716 |
return showText; |
555 |
|
} |
556 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
557 |
48717 |
@Override... |
558 |
|
public boolean getShowUnconserved() |
559 |
|
{ |
560 |
48717 |
return showUnconserved; |
561 |
|
} |
562 |
|
|
563 |
|
|
564 |
|
@return |
565 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
566 |
49955 |
@Override... |
567 |
|
public Color getTextColour() |
568 |
|
{ |
569 |
49956 |
return textColour; |
570 |
|
} |
571 |
|
|
572 |
|
|
573 |
|
@return |
574 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
575 |
31 |
@Override... |
576 |
|
public Color getTextColour2() |
577 |
|
{ |
578 |
31 |
return textColour2; |
579 |
|
} |
580 |
|
|
581 |
|
|
582 |
|
|
583 |
|
|
584 |
|
@return |
585 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
586 |
23 |
@Override... |
587 |
|
public int getThreshold() |
588 |
|
{ |
589 |
23 |
return threshold; |
590 |
|
} |
591 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
592 |
23 |
@Override... |
593 |
|
public int getConsensusSecondaryStructureThreshold() |
594 |
|
{ |
595 |
23 |
return consensusSecondaryStructureThreshold; |
596 |
|
} |
597 |
|
|
598 |
|
|
599 |
|
@return |
600 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
601 |
48487 |
@Override... |
602 |
|
public int getThresholdTextColour() |
603 |
|
{ |
604 |
48487 |
return thresholdTextColour; |
605 |
|
} |
606 |
|
|
607 |
|
|
608 |
|
|
609 |
|
|
610 |
|
@return |
611 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
612 |
8707 |
@Override... |
613 |
|
public boolean getWrapAlignment() |
614 |
|
{ |
615 |
8707 |
return wrapAlignment; |
616 |
|
} |
617 |
|
|
618 |
|
|
619 |
|
|
620 |
|
|
621 |
|
@return |
622 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
623 |
25 |
@Override... |
624 |
|
public int getWrappedWidth() |
625 |
|
{ |
626 |
25 |
return wrappedWidth; |
627 |
|
} |
628 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
629 |
23 |
@Override... |
630 |
|
public boolean isColourByReferenceSeq() |
631 |
|
{ |
632 |
23 |
return colourByReferenceSeq; |
633 |
|
} |
634 |
|
|
635 |
|
|
636 |
|
@return |
637 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
638 |
29 |
@Override... |
639 |
|
public boolean isConservationColourSelected() |
640 |
|
{ |
641 |
29 |
return conservationColourSelected; |
642 |
|
} |
643 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
644 |
23 |
@Override... |
645 |
|
public boolean isDisplayReferenceSeq() |
646 |
|
{ |
647 |
23 |
return displayReferenceSeq; |
648 |
|
} |
649 |
|
|
650 |
|
|
651 |
|
@return |
652 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
653 |
957 |
@Override... |
654 |
|
public boolean isRenderGaps() |
655 |
|
{ |
656 |
957 |
return renderGaps; |
657 |
|
} |
658 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
659 |
2077 |
@Override... |
660 |
|
public boolean isRightAlignIds() |
661 |
|
{ |
662 |
2077 |
return rightAlignIds; |
663 |
|
} |
664 |
|
|
665 |
|
|
666 |
|
@return |
667 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
668 |
785 |
@Override... |
669 |
|
public boolean isSeqNameItalics() |
670 |
|
{ |
671 |
785 |
return seqNameItalics; |
672 |
|
} |
673 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
674 |
1049 |
@Override... |
675 |
|
public boolean isShowAnnotation() |
676 |
|
{ |
677 |
1049 |
return showAnnotation; |
678 |
|
} |
679 |
|
|
680 |
|
|
681 |
|
@return |
682 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
683 |
253 |
@Override... |
684 |
|
public boolean isShowColourText() |
685 |
|
{ |
686 |
253 |
return showColourText; |
687 |
|
} |
688 |
|
|
689 |
|
|
690 |
|
@return |
691 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
692 |
23 |
@Override... |
693 |
|
public boolean isShowSequenceFeaturesHeight() |
694 |
|
{ |
695 |
23 |
return showSeqFeaturesHeight; |
696 |
|
} |
697 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
698 |
32816 |
@Override... |
699 |
|
public boolean isShowSequenceFeatures() |
700 |
|
{ |
701 |
32816 |
return showSequenceFeatures; |
702 |
|
} |
703 |
|
|
704 |
|
|
705 |
|
|
706 |
|
|
707 |
|
|
708 |
|
@param |
709 |
|
|
710 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
711 |
37 |
@Override... |
712 |
|
public void setAbovePIDThreshold(boolean b) |
713 |
|
{ |
714 |
37 |
abovePIDThreshold = b; |
715 |
|
} |
716 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
717 |
29 |
@Override... |
718 |
|
public void setByConsensusSecondaryStructureSelected(boolean b) |
719 |
|
{ |
720 |
29 |
byConsensusSecondaryStructureSelected = b; |
721 |
|
} |
722 |
|
|
723 |
|
|
724 |
|
|
725 |
|
|
726 |
|
@param |
727 |
|
|
728 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
729 |
304 |
@Override... |
730 |
|
public void setCharHeight(int h) |
731 |
|
{ |
732 |
304 |
this.charHeight = h; |
733 |
|
} |
734 |
|
|
735 |
|
|
736 |
|
|
737 |
|
|
738 |
|
@param |
739 |
|
|
740 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
741 |
305 |
@Override... |
742 |
|
public void setCharWidth(int w) |
743 |
|
{ |
744 |
305 |
this.charWidth = w; |
745 |
|
} |
746 |
|
|
747 |
|
|
748 |
|
@param |
749 |
|
|
750 |
|
|
751 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
752 |
316 |
@Override... |
753 |
|
public void setColourAppliesToAllGroups(boolean b) |
754 |
|
{ |
755 |
316 |
colourAppliesToAllGroups = b; |
756 |
|
} |
757 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
758 |
23 |
@Override... |
759 |
|
public void setColourByReferenceSeq(boolean colourByReferenceSeq) |
760 |
|
{ |
761 |
23 |
this.colourByReferenceSeq = colourByReferenceSeq; |
762 |
|
} |
763 |
|
|
764 |
|
|
765 |
|
|
766 |
|
|
767 |
|
@param |
768 |
|
|
769 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
770 |
29 |
@Override... |
771 |
|
public void setColourText(boolean state) |
772 |
|
{ |
773 |
29 |
showColourText = state; |
774 |
|
} |
775 |
|
|
776 |
|
|
777 |
|
@param |
778 |
|
|
779 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
780 |
23 |
@Override... |
781 |
|
public void setConservationColourSelected( |
782 |
|
boolean conservationColourSelected) |
783 |
|
{ |
784 |
23 |
this.conservationColourSelected = conservationColourSelected; |
785 |
|
} |
786 |
|
|
787 |
|
|
788 |
|
|
789 |
|
|
790 |
|
@param |
791 |
|
|
792 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
793 |
36 |
@Override... |
794 |
|
public void setConservationSelected(boolean b) |
795 |
|
{ |
796 |
36 |
conservationColourSelected = b; |
797 |
|
} |
798 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
799 |
23 |
@Override... |
800 |
|
public void setDisplayReferenceSeq(boolean displayReferenceSeq) |
801 |
|
{ |
802 |
23 |
this.displayReferenceSeq = displayReferenceSeq; |
803 |
|
} |
804 |
|
|
805 |
|
|
806 |
|
|
807 |
|
@param |
808 |
|
|
809 |
|
|
810 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
811 |
29 |
@Override... |
812 |
|
public void setIncrement(int inc) |
813 |
|
{ |
814 |
29 |
increment = inc; |
815 |
|
} |
816 |
|
|
817 |
|
|
818 |
|
|
819 |
|
@param |
820 |
|
|
821 |
|
|
822 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
823 |
29 |
@Override... |
824 |
|
public void setConsensusSecondaryStructureThreshold(int val) |
825 |
|
{ |
826 |
29 |
consensusSecondaryStructureThreshold = val; |
827 |
|
} |
828 |
|
|
829 |
|
|
830 |
|
|
831 |
|
|
832 |
|
@param |
833 |
|
|
834 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
835 |
29 |
@Override... |
836 |
|
public void setRenderGaps(boolean state) |
837 |
|
{ |
838 |
29 |
renderGaps = state; |
839 |
|
} |
840 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
841 |
301 |
@Override... |
842 |
|
public void setRightAlignIds(boolean rightAlignIds) |
843 |
|
{ |
844 |
301 |
this.rightAlignIds = rightAlignIds; |
845 |
|
} |
846 |
|
|
847 |
|
|
848 |
|
|
849 |
|
|
850 |
|
@param |
851 |
|
|
852 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
853 |
32 |
@Override... |
854 |
|
public void setScaleAboveWrapped(boolean b) |
855 |
|
{ |
856 |
32 |
scaleAboveWrapped = b; |
857 |
|
} |
858 |
|
|
859 |
|
|
860 |
|
|
861 |
|
|
862 |
|
@param |
863 |
|
|
864 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
865 |
34 |
@Override... |
866 |
|
public void setScaleLeftWrapped(boolean b) |
867 |
|
{ |
868 |
34 |
scaleLeftWrapped = b; |
869 |
|
} |
870 |
|
|
871 |
|
|
872 |
|
|
873 |
|
|
874 |
|
@param |
875 |
|
|
876 |
|
|
877 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
878 |
32 |
@Override... |
879 |
|
public void setScaleRightWrapped(boolean b) |
880 |
|
{ |
881 |
32 |
scaleRightWrapped = b; |
882 |
|
} |
883 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
884 |
295 |
@Override... |
885 |
|
public void setSeqNameItalics(boolean italics) |
886 |
|
{ |
887 |
295 |
seqNameItalics = italics; |
888 |
|
} |
889 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
890 |
309 |
@Override... |
891 |
|
public void setShowAnnotation(boolean b) |
892 |
|
{ |
893 |
309 |
showAnnotation = b; |
894 |
|
} |
895 |
|
|
896 |
|
|
897 |
|
|
898 |
|
|
899 |
|
@param |
900 |
|
|
901 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
902 |
29 |
@Override... |
903 |
|
public void setShowBoxes(boolean state) |
904 |
|
{ |
905 |
29 |
showBoxes = state; |
906 |
|
} |
907 |
|
|
908 |
|
|
909 |
|
@param |
910 |
|
|
911 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
912 |
23 |
@Override... |
913 |
|
public void setShowColourText(boolean showColourText) |
914 |
|
{ |
915 |
23 |
this.showColourText = showColourText; |
916 |
|
} |
917 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
918 |
23 |
@Override... |
919 |
|
public void setShowHiddenMarkers(boolean show) |
920 |
|
{ |
921 |
23 |
showHiddenMarkers = show; |
922 |
|
} |
923 |
|
|
924 |
|
|
925 |
|
|
926 |
|
|
927 |
|
@param |
928 |
|
|
929 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
930 |
302 |
@Override... |
931 |
|
public void setShowJVSuffix(boolean b) |
932 |
|
{ |
933 |
302 |
showJVSuffix = b; |
934 |
|
} |
935 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
936 |
23 |
@Override... |
937 |
|
public void setShowSequenceFeaturesHeight(boolean selected) |
938 |
|
{ |
939 |
23 |
showSeqFeaturesHeight = selected; |
940 |
|
|
941 |
|
} |
942 |
|
|
943 |
|
|
944 |
|
|
945 |
|
|
946 |
|
@param |
947 |
|
|
948 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
949 |
64 |
@Override... |
950 |
|
public void setShowSequenceFeatures(boolean b) |
951 |
|
{ |
952 |
64 |
showSequenceFeatures = b; |
953 |
|
} |
954 |
|
|
955 |
|
|
956 |
|
|
957 |
|
|
958 |
|
@param |
959 |
|
|
960 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
961 |
29 |
@Override... |
962 |
|
public void setShowText(boolean state) |
963 |
|
{ |
964 |
29 |
showText = state; |
965 |
|
} |
966 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
967 |
301 |
@Override... |
968 |
|
public void setShowUnconserved(boolean showunconserved) |
969 |
|
{ |
970 |
301 |
showUnconserved = showunconserved; |
971 |
|
} |
972 |
|
|
973 |
|
|
974 |
|
@param |
975 |
|
|
976 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
977 |
29 |
@Override... |
978 |
|
public void setTextColour(Color textColour) |
979 |
|
{ |
980 |
29 |
this.textColour = textColour; |
981 |
|
} |
982 |
|
|
983 |
|
|
984 |
|
@param |
985 |
|
|
986 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
987 |
29 |
@Override... |
988 |
|
public void setTextColour2(Color textColour2) |
989 |
|
{ |
990 |
29 |
this.textColour2 = textColour2; |
991 |
|
} |
992 |
|
|
993 |
|
|
994 |
|
|
995 |
|
|
996 |
|
@param |
997 |
|
|
998 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
999 |
46 |
@Override... |
1000 |
|
public void setThreshold(int thresh) |
1001 |
|
{ |
1002 |
46 |
threshold = thresh; |
1003 |
|
} |
1004 |
|
|
1005 |
|
|
1006 |
|
@param |
1007 |
|
|
1008 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1009 |
29 |
@Override... |
1010 |
|
public void setThresholdTextColour(int thresholdTextColour) |
1011 |
|
{ |
1012 |
29 |
this.thresholdTextColour = thresholdTextColour; |
1013 |
|
} |
1014 |
|
|
1015 |
|
|
1016 |
|
|
1017 |
|
|
1018 |
|
@param |
1019 |
|
|
1020 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1021 |
311 |
@Override... |
1022 |
|
public void setWrapAlignment(boolean state) |
1023 |
|
{ |
1024 |
311 |
wrapAlignment = state; |
1025 |
|
} |
1026 |
|
|
1027 |
|
|
1028 |
|
|
1029 |
|
|
1030 |
|
@param |
1031 |
|
|
1032 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1033 |
103 |
@Override... |
1034 |
|
public void setWrappedWidth(int w) |
1035 |
|
{ |
1036 |
103 |
this.wrappedWidth = w; |
1037 |
|
} |
1038 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1039 |
0 |
@Override... |
1040 |
|
public boolean sameStyle(ViewStyleI that) |
1041 |
|
{ |
1042 |
0 |
return this.equals(that); |
1043 |
|
} |
1044 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1045 |
29 |
@Override... |
1046 |
|
public String getFontName() |
1047 |
|
{ |
1048 |
29 |
return fontName; |
1049 |
|
} |
1050 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1051 |
29 |
@Override... |
1052 |
|
public int getFontSize() |
1053 |
|
{ |
1054 |
29 |
return fontSize; |
1055 |
|
} |
1056 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1057 |
29 |
@Override... |
1058 |
|
public int getFontStyle() |
1059 |
|
{ |
1060 |
29 |
return fontStyle; |
1061 |
|
} |
1062 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1063 |
310 |
@Override... |
1064 |
|
public void setFontName(String name) |
1065 |
|
{ |
1066 |
310 |
fontName = name; |
1067 |
|
} |
1068 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1069 |
310 |
@Override... |
1070 |
|
public void setFontSize(int size) |
1071 |
|
{ |
1072 |
310 |
fontSize = size; |
1073 |
|
|
1074 |
|
} |
1075 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1076 |
310 |
@Override... |
1077 |
|
public void setFontStyle(int style) |
1078 |
|
{ |
1079 |
310 |
fontStyle = style; |
1080 |
|
} |
1081 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1082 |
2519 |
@Override... |
1083 |
|
public int getIdWidth() |
1084 |
|
{ |
1085 |
2519 |
return idWidth; |
1086 |
|
} |
1087 |
|
|
1088 |
|
|
1089 |
|
@param |
1090 |
|
|
1091 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1092 |
325 |
@Override... |
1093 |
|
public void setIdWidth(int idWidth) |
1094 |
|
{ |
1095 |
325 |
this.idWidth = idWidth; |
1096 |
|
} |
1097 |
|
|
1098 |
|
|
1099 |
|
@return |
1100 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1101 |
253 |
@Override... |
1102 |
|
public boolean isCentreColumnLabels() |
1103 |
|
{ |
1104 |
253 |
return centreColumnLabels; |
1105 |
|
} |
1106 |
|
|
1107 |
|
|
1108 |
|
@param |
1109 |
|
|
1110 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1111 |
301 |
@Override... |
1112 |
|
public void setCentreColumnLabels(boolean centreColumnLabels) |
1113 |
|
{ |
1114 |
301 |
this.centreColumnLabels = centreColumnLabels; |
1115 |
|
} |
1116 |
|
|
1117 |
|
|
1118 |
|
@return |
1119 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1120 |
261 |
@Override... |
1121 |
|
public boolean isShowDBRefs() |
1122 |
|
{ |
1123 |
261 |
return showdbrefs; |
1124 |
|
} |
1125 |
|
|
1126 |
|
|
1127 |
|
@param |
1128 |
|
|
1129 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1130 |
301 |
@Override... |
1131 |
|
public void setShowDBRefs(boolean showdbrefs) |
1132 |
|
{ |
1133 |
301 |
this.showdbrefs = showdbrefs; |
1134 |
|
} |
1135 |
|
|
1136 |
|
|
1137 |
|
@return |
1138 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1139 |
261 |
@Override... |
1140 |
|
public boolean isShowNPFeats() |
1141 |
|
{ |
1142 |
261 |
return shownpfeats; |
1143 |
|
} |
1144 |
|
|
1145 |
|
|
1146 |
|
@param |
1147 |
|
|
1148 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1149 |
301 |
@Override... |
1150 |
|
public void setShowNPFeats(boolean shownpfeats) |
1151 |
|
{ |
1152 |
301 |
this.shownpfeats = shownpfeats; |
1153 |
|
} |
1154 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1155 |
32 |
@Override... |
1156 |
|
public boolean isScaleProteinAsCdna() |
1157 |
|
{ |
1158 |
32 |
return this.scaleProteinAsCdna; |
1159 |
|
} |
1160 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1161 |
301 |
@Override... |
1162 |
|
public void setScaleProteinAsCdna(boolean b) |
1163 |
|
{ |
1164 |
301 |
this.scaleProteinAsCdna = b; |
1165 |
|
} |
1166 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1167 |
23 |
@Override... |
1168 |
|
public boolean isProteinFontAsCdna() |
1169 |
|
{ |
1170 |
23 |
return proteinFontAsCdna; |
1171 |
|
} |
1172 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1173 |
23 |
@Override... |
1174 |
|
public void setProteinFontAsCdna(boolean b) |
1175 |
|
{ |
1176 |
23 |
proteinFontAsCdna = b; |
1177 |
|
} |
1178 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1179 |
29 |
@Override... |
1180 |
|
public void setShowComplementFeatures(boolean b) |
1181 |
|
{ |
1182 |
29 |
showComplementFeatures = b; |
1183 |
|
} |
1184 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1185 |
31129 |
@Override... |
1186 |
|
public boolean isShowComplementFeatures() |
1187 |
|
{ |
1188 |
31129 |
return showComplementFeatures; |
1189 |
|
} |
1190 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1191 |
29 |
@Override... |
1192 |
|
public void setShowComplementFeaturesOnTop(boolean b) |
1193 |
|
{ |
1194 |
29 |
showComplementFeaturesOnTop = b; |
1195 |
|
} |
1196 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1197 |
32 |
@Override... |
1198 |
|
public boolean isShowComplementFeaturesOnTop() |
1199 |
|
{ |
1200 |
32 |
return showComplementFeaturesOnTop; |
1201 |
|
} |
1202 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1203 |
1056 |
@Override... |
1204 |
|
public List<String> getSecondaryStructureSources() |
1205 |
|
{ |
1206 |
1056 |
return secondaryStructureSources; |
1207 |
|
} |
1208 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1209 |
603 |
@Override... |
1210 |
|
public void setSecondaryStructureSources( |
1211 |
|
List<String> secondaryStructureSources) |
1212 |
|
{ |
1213 |
603 |
this.secondaryStructureSources = secondaryStructureSources; |
1214 |
|
} |
1215 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1216 |
301 |
@Override... |
1217 |
|
public void setShowStructureProvider(boolean showStructureProvider) |
1218 |
|
{ |
1219 |
301 |
this.showStructureProvider = showStructureProvider; |
1220 |
|
} |
1221 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1222 |
1629 |
@Override... |
1223 |
|
public boolean isShowStructureProvider() |
1224 |
|
{ |
1225 |
1629 |
return showStructureProvider; |
1226 |
|
} |
1227 |
|
} |