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package jalview.viewmodel.seqfeatures; |
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import java.awt.Color; |
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import java.beans.PropertyChangeListener; |
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import java.beans.PropertyChangeSupport; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.Comparator; |
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import java.util.HashMap; |
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import java.util.HashSet; |
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import java.util.Hashtable; |
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import java.util.Iterator; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.Set; |
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import java.util.concurrent.ConcurrentHashMap; |
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import jalview.api.AlignViewportI; |
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import jalview.api.FeatureColourI; |
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import jalview.api.FeaturesDisplayedI; |
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import jalview.datamodel.AlignedCodonFrame; |
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import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.MappedFeatures; |
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import jalview.datamodel.SearchResultMatchI; |
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import jalview.datamodel.SearchResults; |
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import jalview.datamodel.SearchResultsI; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.datamodel.features.FeatureMatcherSetI; |
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import jalview.datamodel.features.SequenceFeatures; |
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import jalview.renderer.seqfeatures.FeatureRenderer; |
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import jalview.schemes.FeatureColour; |
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import jalview.util.ColorUtils; |
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import jalview.util.Platform; |
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| 82% |
Uncovered Elements: 115 (639) |
Complexity: 188 |
Complexity Density: 0.5 |
|
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public abstract class FeatureRendererModel |
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implements jalview.api.FeatureRenderer |
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{ |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.25 |
|
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public static class FeatureSettingsBean |
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{ |
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public final String featureType; |
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public final FeatureColourI featureColour; |
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public final FeatureMatcherSetI filter; |
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public final Boolean show; |
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| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
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public FeatureSettingsBean(String type, FeatureColourI colour,... |
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FeatureMatcherSetI theFilter, Boolean isShown) |
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{ |
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featureType = type; |
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featureColour = colour; |
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filter = theFilter; |
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show = isShown; |
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} |
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} |
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protected float transparency = 1.0f; |
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protected Map<String, FeatureColourI> featureColours = new ConcurrentHashMap<>(); |
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protected Map<String, Boolean> featureGroups = new ConcurrentHashMap<>(); |
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protected Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>(); |
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protected String[] renderOrder; |
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Map<String, Float> featureOrder = null; |
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protected AlignViewportI av; |
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private PropertyChangeSupport changeSupport = new PropertyChangeSupport( |
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this); |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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303268 |
@Override... |
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public AlignViewportI getViewport() |
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{ |
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303280 |
return av; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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2 |
public FeatureRendererSettings getSettings()... |
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{ |
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return new FeatureRendererSettings(this); |
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} |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
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32 |
public void transferSettings(FeatureRendererSettings fr)... |
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{ |
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this.renderOrder = fr.renderOrder; |
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this.featureGroups = fr.featureGroups; |
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this.featureColours = fr.featureColours; |
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this.transparency = fr.transparency; |
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this.featureOrder = fr.featureOrder; |
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} |
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@param |
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| 73.9% |
Uncovered Elements: 6 (23) |
Complexity: 5 |
Complexity Density: 0.29 |
|
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public void transferSettings(jalview.api.FeatureRenderer _fr)... |
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{ |
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FeatureRenderer fr = (FeatureRenderer) _fr; |
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FeatureRendererSettings frs = new FeatureRendererSettings(fr); |
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this.renderOrder = frs.renderOrder; |
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this.featureGroups = frs.featureGroups; |
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this.featureColours = frs.featureColours; |
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this.featureFilters = frs.featureFilters; |
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this.transparency = frs.transparency; |
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this.featureOrder = frs.featureOrder; |
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if (av != null && av != fr.getViewport()) |
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{ |
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|
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4 |
if (_fr.getFeaturesDisplayed() != null) |
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{ |
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4 |
FeaturesDisplayedI fd = getFeaturesDisplayed(); |
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4 |
if (fd == null) |
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{ |
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4 |
setFeaturesDisplayedFrom(_fr.getFeaturesDisplayed()); |
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} |
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else |
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{ |
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synchronized (fd) |
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{ |
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fd.clear(); |
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for (String type : _fr.getFeaturesDisplayed() |
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.getVisibleFeatures()) |
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{ |
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fd.setVisible(type); |
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} |
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} |
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} |
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} |
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} |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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4 |
public void setFeaturesDisplayedFrom(FeaturesDisplayedI featuresDisplayed)... |
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{ |
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av.setFeaturesDisplayed(new FeaturesDisplayed(featuresDisplayed)); |
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} |
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| 100% |
Uncovered Elements: 0 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
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18 |
@Override... |
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public void setVisible(String featureType) |
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{ |
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FeaturesDisplayedI fdi = av.getFeaturesDisplayed(); |
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18 |
if (fdi == null) |
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{ |
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5 |
av.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); |
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} |
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18 |
if (!fdi.isRegistered(featureType)) |
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{ |
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pushFeatureType(Arrays.asList(new String[] { featureType })); |
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} |
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18 |
fdi.setVisible(featureType); |
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} |
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|
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| 81.2% |
Uncovered Elements: 3 (16) |
Complexity: 4 |
Complexity Density: 0.4 |
|
194 |
1 |
@Override... |
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public void setAllVisible(List<String> featureTypes) |
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{ |
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1 |
FeaturesDisplayedI fdi = av.getFeaturesDisplayed(); |
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1 |
if (fdi == null) |
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{ |
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1 |
av.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); |
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} |
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1 |
List<String> nft = new ArrayList<>(); |
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1 |
for (String featureType : featureTypes) |
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{ |
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1 |
if (!fdi.isRegistered(featureType)) |
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{ |
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1 |
nft.add(featureType); |
208 |
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} |
209 |
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} |
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1 |
if (nft.size() > 0) |
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{ |
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1 |
pushFeatureType(nft); |
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} |
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1 |
fdi.setAllVisible(featureTypes); |
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} |
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@param |
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| 100% |
Uncovered Elements: 0 (11) |
Complexity: 3 |
Complexity Density: 0.43 |
|
223 |
18 |
private void pushFeatureType(List<String> types)... |
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{ |
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|
226 |
18 |
int ts = types.size(); |
227 |
18 |
String neworder[] = new String[(renderOrder == null ? 0 |
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: renderOrder.length) + ts]; |
229 |
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types.toArray(neworder); |
230 |
18 |
if (renderOrder != null) |
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{ |
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12 |
System.arraycopy(neworder, 0, neworder, renderOrder.length, ts); |
233 |
12 |
System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length); |
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} |
235 |
18 |
renderOrder = neworder; |
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} |
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protected Map<String, float[][]> minmax = new Hashtable<>(); |
239 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
240 |
28 |
public Map<String, float[][]> getMinMax()... |
241 |
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{ |
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28 |
return minmax; |
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} |
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247 |
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248 |
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@param |
249 |
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@return |
250 |
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251 |
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| 0% |
Uncovered Elements: 12 (12) |
Complexity: 4 |
Complexity Density: 0.5 |
|
252 |
0 |
protected final byte[] normaliseScore(SequenceFeature sequenceFeature)... |
253 |
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{ |
254 |
0 |
float[] mm = minmax.get(sequenceFeature.type)[0]; |
255 |
0 |
final byte[] r = new byte[] { 0, (byte) 255 }; |
256 |
0 |
if (mm != null) |
257 |
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{ |
258 |
0 |
if (r[0] != 0 || mm[0] < 0.0) |
259 |
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{ |
260 |
0 |
r[0] = 1; |
261 |
0 |
r[1] = (byte) ((int) 128.0 |
262 |
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+ 127.0 * (sequenceFeature.score / mm[1])); |
263 |
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} |
264 |
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else |
265 |
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{ |
266 |
0 |
r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1])); |
267 |
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} |
268 |
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} |
269 |
0 |
return r; |
270 |
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} |
271 |
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272 |
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boolean newFeatureAdded = false; |
273 |
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|
274 |
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boolean findingFeatures = false; |
275 |
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|
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|
| 33.3% |
Uncovered Elements: 6 (9) |
Complexity: 5 |
Complexity Density: 1 |
|
276 |
6661 |
protected boolean updateFeatures()... |
277 |
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{ |
278 |
6661 |
if (av.getFeaturesDisplayed() == null || renderOrder == null |
279 |
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|| newFeatureAdded) |
280 |
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{ |
281 |
0 |
findAllFeatures(); |
282 |
0 |
if (av.getFeaturesDisplayed().getVisibleFeatureCount() < 1) |
283 |
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{ |
284 |
0 |
return false; |
285 |
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} |
286 |
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} |
287 |
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288 |
6661 |
return true; |
289 |
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} |
290 |
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291 |
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292 |
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293 |
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294 |
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295 |
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|
| 87.5% |
Uncovered Elements: 1 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
296 |
19 |
protected void findAllFeatures()... |
297 |
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{ |
298 |
19 |
synchronized (firing) |
299 |
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{ |
300 |
19 |
if (firing.equals(Boolean.FALSE)) |
301 |
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{ |
302 |
19 |
firing = Boolean.TRUE; |
303 |
19 |
findAllFeatures(true); |
304 |
19 |
notifyFeaturesChanged(); |
305 |
19 |
firing = Boolean.FALSE; |
306 |
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} |
307 |
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} |
308 |
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} |
309 |
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|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
310 |
85 |
@Override... |
311 |
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public void notifyFeaturesChanged() |
312 |
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{ |
313 |
85 |
changeSupport.firePropertyChange("changeSupport", null, null); |
314 |
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} |
315 |
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|
|
|
| 100% |
Uncovered Elements: 0 (14) |
Complexity: 4 |
Complexity Density: 0.4 |
|
316 |
18 |
@Override... |
317 |
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public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, |
318 |
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int column) |
319 |
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{ |
320 |
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|
321 |
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|
322 |
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|
323 |
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|
324 |
18 |
List<SequenceFeature> result = new ArrayList<>(); |
325 |
18 |
if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null) |
326 |
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{ |
327 |
1 |
return result; |
328 |
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} |
329 |
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|
330 |
17 |
Set<String> visibleFeatures = getFeaturesDisplayed() |
331 |
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.getVisibleFeatures(); |
332 |
17 |
String[] visibleTypes = visibleFeatures |
333 |
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.toArray(new String[visibleFeatures.size()]); |
334 |
17 |
List<SequenceFeature> features = sequence.findFeatures(column, column, |
335 |
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visibleTypes); |
336 |
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|
337 |
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338 |
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|
339 |
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|
340 |
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|
341 |
17 |
for (SequenceFeature sf : features) |
342 |
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{ |
343 |
33 |
if (getColour(sf) != null) |
344 |
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{ |
345 |
23 |
result.add(sf); |
346 |
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} |
347 |
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} |
348 |
17 |
return result; |
349 |
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} |
350 |
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351 |
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352 |
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|
353 |
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|
354 |
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@param |
355 |
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|
356 |
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|
357 |
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|
358 |
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|
|
| 93.4% |
Uncovered Elements: 4 (61) |
Complexity: 13 |
Complexity Density: 0.35 |
|
359 |
133 |
@Override... |
360 |
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public synchronized void findAllFeatures(boolean newMadeVisible) |
361 |
|
{ |
362 |
133 |
newFeatureAdded = false; |
363 |
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|
364 |
133 |
if (findingFeatures) |
365 |
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{ |
366 |
0 |
newFeatureAdded = true; |
367 |
0 |
return; |
368 |
|
} |
369 |
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|
370 |
133 |
findingFeatures = true; |
371 |
133 |
if (av.getFeaturesDisplayed() == null) |
372 |
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{ |
373 |
61 |
av.setFeaturesDisplayed(new FeaturesDisplayed()); |
374 |
|
} |
375 |
133 |
FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed(); |
376 |
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|
377 |
133 |
Set<String> oldfeatures = new HashSet<>(); |
378 |
133 |
if (renderOrder != null) |
379 |
|
{ |
380 |
352 |
for (int i = 0; i < renderOrder.length; i++) |
381 |
|
{ |
382 |
296 |
if (renderOrder[i] != null) |
383 |
|
{ |
384 |
296 |
oldfeatures.add(renderOrder[i]); |
385 |
|
} |
386 |
|
} |
387 |
|
} |
388 |
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|
389 |
133 |
AlignmentI alignment = av.getAlignment(); |
390 |
133 |
List<String> allfeatures = new ArrayList<>(); |
391 |
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|
392 |
1078 |
for (int i = 0; i < alignment.getHeight(); i++) |
393 |
|
{ |
394 |
945 |
SequenceI asq = alignment.getSequenceAt(i); |
395 |
945 |
for (String group : asq.getFeatures().getFeatureGroups(true)) |
396 |
|
{ |
397 |
813 |
boolean groupDisplayed = true; |
398 |
813 |
if (group != null) |
399 |
|
{ |
400 |
791 |
if (featureGroups.containsKey(group)) |
401 |
|
{ |
402 |
706 |
groupDisplayed = featureGroups.get(group); |
403 |
|
} |
404 |
|
else |
405 |
|
{ |
406 |
85 |
groupDisplayed = newMadeVisible; |
407 |
85 |
featureGroups.put(group, groupDisplayed); |
408 |
|
} |
409 |
|
} |
410 |
813 |
if (groupDisplayed) |
411 |
|
{ |
412 |
812 |
Set<String> types = asq.getFeatures() |
413 |
|
.getFeatureTypesForGroups(true, group); |
414 |
812 |
for (String type : types) |
415 |
|
{ |
416 |
2033 |
if (!allfeatures.contains(type)) |
417 |
|
{ |
418 |
355 |
allfeatures.add(type); |
419 |
|
} |
420 |
2033 |
updateMinMax(asq, type, true); |
421 |
|
} |
422 |
|
} |
423 |
|
} |
424 |
|
} |
425 |
|
|
426 |
|
|
427 |
|
|
428 |
133 |
if (newMadeVisible) |
429 |
|
{ |
430 |
131 |
for (String type : allfeatures) |
431 |
|
{ |
432 |
345 |
if (!oldfeatures.contains(type)) |
433 |
|
{ |
434 |
151 |
featuresDisplayed.setVisible(type); |
435 |
151 |
setOrder(type, 0); |
436 |
|
} |
437 |
|
} |
438 |
|
} |
439 |
|
|
440 |
133 |
updateRenderOrder(allfeatures); |
441 |
133 |
findingFeatures = false; |
442 |
|
} |
443 |
|
|
444 |
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|
445 |
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|
446 |
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|
447 |
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|
448 |
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|
449 |
|
@param |
450 |
|
@param |
451 |
|
@param |
452 |
|
|
|
|
| 88.5% |
Uncovered Elements: 3 (26) |
Complexity: 6 |
Complexity Density: 0.38 |
|
453 |
2033 |
protected void updateMinMax(SequenceI seq, String featureType,... |
454 |
|
boolean positional) |
455 |
|
{ |
456 |
2033 |
float min = seq.getFeatures().getMinimumScore(featureType, positional); |
457 |
2033 |
if (Float.isNaN(min)) |
458 |
|
{ |
459 |
26 |
return; |
460 |
|
} |
461 |
|
|
462 |
2007 |
float max = seq.getFeatures().getMaximumScore(featureType, positional); |
463 |
|
|
464 |
|
|
465 |
|
|
466 |
|
|
467 |
|
|
468 |
2007 |
if (minmax == null) |
469 |
|
{ |
470 |
0 |
minmax = new Hashtable<>(); |
471 |
|
} |
472 |
2007 |
synchronized (minmax) |
473 |
|
{ |
474 |
2007 |
float[][] mm = minmax.get(featureType); |
475 |
2007 |
int index = positional ? 0 : 1; |
476 |
2007 |
if (mm == null) |
477 |
|
{ |
478 |
270 |
mm = new float[][] { null, null }; |
479 |
270 |
minmax.put(featureType, mm); |
480 |
|
} |
481 |
2007 |
if (mm[index] == null) |
482 |
|
{ |
483 |
270 |
mm[index] = new float[] { min, max }; |
484 |
|
} |
485 |
|
else |
486 |
|
{ |
487 |
1737 |
mm[index][0] = Math.min(mm[index][0], min); |
488 |
1737 |
mm[index][1] = Math.max(mm[index][1], max); |
489 |
|
} |
490 |
|
} |
491 |
|
} |
492 |
|
|
493 |
|
protected Boolean firing = Boolean.FALSE; |
494 |
|
|
495 |
|
|
496 |
|
|
497 |
|
|
498 |
|
|
499 |
|
|
500 |
|
|
501 |
|
|
502 |
|
|
503 |
|
|
504 |
|
@param |
505 |
|
|
|
|
| 81.8% |
Uncovered Elements: 14 (77) |
Complexity: 26 |
Complexity Density: 0.58 |
|
506 |
133 |
private void updateRenderOrder(List<String> allFeatures)... |
507 |
|
{ |
508 |
133 |
List<String> allfeatures = new ArrayList<>(allFeatures); |
509 |
133 |
String[] oldRender = renderOrder; |
510 |
133 |
renderOrder = new String[allfeatures.size()]; |
511 |
133 |
boolean initOrders = (featureOrder == null); |
512 |
133 |
int opos = 0; |
513 |
133 |
if (oldRender != null && oldRender.length > 0) |
514 |
|
{ |
515 |
350 |
for (int j = 0; j < oldRender.length; j++) |
516 |
|
{ |
517 |
296 |
if (oldRender[j] != null) |
518 |
|
{ |
519 |
296 |
if (initOrders) |
520 |
|
{ |
521 |
9 |
setOrder(oldRender[j], |
522 |
|
(1 - (1 + (float) j) / oldRender.length)); |
523 |
|
} |
524 |
296 |
if (allfeatures.contains(oldRender[j])) |
525 |
|
{ |
526 |
204 |
renderOrder[opos++] = oldRender[j]; |
527 |
|
|
528 |
204 |
allfeatures.remove(oldRender[j]); |
529 |
204 |
if (minmax != null) |
530 |
|
{ |
531 |
204 |
float[][] mmrange = minmax.get(oldRender[j]); |
532 |
204 |
if (mmrange != null) |
533 |
|
{ |
534 |
202 |
FeatureColourI fc = featureColours.get(oldRender[j]); |
535 |
202 |
if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled() |
536 |
|
&& !fc.isColourByAttribute()) |
537 |
|
{ |
538 |
0 |
fc.updateBounds(mmrange[0][0], mmrange[0][1]); |
539 |
|
} |
540 |
|
} |
541 |
|
} |
542 |
|
} |
543 |
|
} |
544 |
|
} |
545 |
|
} |
546 |
133 |
if (allfeatures.size() == 0) |
547 |
|
{ |
548 |
|
|
549 |
54 |
return; |
550 |
|
} |
551 |
79 |
int i = allfeatures.size() - 1; |
552 |
79 |
int iSize = i; |
553 |
79 |
boolean sort = false; |
554 |
79 |
String[] newf = new String[allfeatures.size()]; |
555 |
79 |
float[] sortOrder = new float[allfeatures.size()]; |
556 |
79 |
for (String newfeat : allfeatures) |
557 |
|
{ |
558 |
151 |
newf[i] = newfeat; |
559 |
151 |
if (minmax != null) |
560 |
|
{ |
561 |
|
|
562 |
151 |
float[][] mmrange = minmax.get(newf[i]); |
563 |
151 |
if (mmrange != null) |
564 |
|
{ |
565 |
142 |
FeatureColourI fc = featureColours.get(newf[i]); |
566 |
142 |
if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled() |
567 |
|
&& !fc.isColourByAttribute()) |
568 |
|
{ |
569 |
0 |
fc.updateBounds(mmrange[0][0], mmrange[0][1]); |
570 |
|
} |
571 |
|
} |
572 |
|
} |
573 |
151 |
if (initOrders || !featureOrder.containsKey(newf[i])) |
574 |
|
{ |
575 |
0 |
int denom = initOrders ? allfeatures.size() : featureOrder.size(); |
576 |
|
|
577 |
|
|
578 |
0 |
setOrder(newf[i], i / (float) denom); |
579 |
|
} |
580 |
|
|
581 |
151 |
sortOrder[i] = 2 - featureOrder.get(newf[i]).floatValue(); |
582 |
151 |
if (i < iSize) |
583 |
|
{ |
584 |
|
|
585 |
72 |
sort = sort || sortOrder[i] > sortOrder[i + 1]; |
586 |
|
} |
587 |
151 |
i--; |
588 |
|
} |
589 |
79 |
if (iSize > 1 && sort) |
590 |
|
{ |
591 |
0 |
jalview.util.QuickSort.sort(sortOrder, newf); |
592 |
|
} |
593 |
79 |
sortOrder = null; |
594 |
79 |
System.arraycopy(newf, 0, renderOrder, opos, newf.length); |
595 |
|
} |
596 |
|
|
597 |
|
|
598 |
|
|
599 |
|
|
600 |
|
|
601 |
|
@param |
602 |
|
@return |
603 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
604 |
10157 |
@Override... |
605 |
|
public FeatureColourI getFeatureStyle(String featureType) |
606 |
|
{ |
607 |
10157 |
FeatureColourI fc = featureColours.get(featureType); |
608 |
10157 |
if (fc == null) |
609 |
|
{ |
610 |
89 |
Color col = ColorUtils.createColourFromName(featureType); |
611 |
89 |
fc = new FeatureColour(col); |
612 |
89 |
featureColours.put(featureType, fc); |
613 |
|
} |
614 |
10157 |
return fc; |
615 |
|
} |
616 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
617 |
4652 |
@Override... |
618 |
|
public Color getColour(SequenceFeature feature) |
619 |
|
{ |
620 |
4652 |
FeatureColourI fc = getFeatureStyle(feature.getType()); |
621 |
4652 |
return getColor(feature, fc); |
622 |
|
} |
623 |
|
|
624 |
|
|
625 |
|
|
626 |
|
|
627 |
|
|
628 |
|
@param |
629 |
|
@return |
630 |
|
|
|
|
| 60% |
Uncovered Elements: 2 (5) |
Complexity: 3 |
Complexity Density: 3 |
|
631 |
175574 |
public boolean showFeatureOfType(String type)... |
632 |
|
{ |
633 |
175586 |
return type == null ? false |
634 |
175610 |
: (av.getFeaturesDisplayed() == null ? true |
635 |
|
: av.getFeaturesDisplayed().isVisible(type)); |
636 |
|
} |
637 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
638 |
100 |
@Override... |
639 |
|
public void setColour(String featureType, FeatureColourI col) |
640 |
|
{ |
641 |
100 |
featureColours.put(featureType, col); |
642 |
|
} |
643 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
644 |
69 |
@Override... |
645 |
|
public void setTransparency(float value) |
646 |
|
{ |
647 |
69 |
transparency = value; |
648 |
|
} |
649 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
650 |
6573 |
@Override... |
651 |
|
public float getTransparency() |
652 |
|
{ |
653 |
6573 |
return transparency; |
654 |
|
} |
655 |
|
|
656 |
|
|
657 |
|
|
658 |
|
|
659 |
|
|
660 |
|
@param |
661 |
|
|
662 |
|
@param |
663 |
|
|
664 |
|
|
665 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
666 |
165 |
public float setOrder(String type, float position)... |
667 |
|
{ |
668 |
165 |
if (featureOrder == null) |
669 |
|
{ |
670 |
62 |
featureOrder = new Hashtable<>(); |
671 |
|
} |
672 |
165 |
featureOrder.put(type, Float.valueOf(position)); |
673 |
165 |
return position; |
674 |
|
} |
675 |
|
|
676 |
|
|
677 |
|
|
678 |
|
|
679 |
|
@param |
680 |
|
@return |
681 |
|
|
|
|
| 62.5% |
Uncovered Elements: 3 (8) |
Complexity: 3 |
Complexity Density: 0.75 |
|
682 |
160 |
public float getOrder(String type)... |
683 |
|
{ |
684 |
160 |
if (featureOrder != null) |
685 |
|
{ |
686 |
160 |
if (featureOrder.containsKey(type)) |
687 |
|
{ |
688 |
160 |
return featureOrder.get(type).floatValue(); |
689 |
|
} |
690 |
|
} |
691 |
0 |
return -1; |
692 |
|
} |
693 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
694 |
59 |
@Override... |
695 |
|
public Map<String, FeatureColourI> getFeatureColours() |
696 |
|
{ |
697 |
59 |
return featureColours; |
698 |
|
} |
699 |
|
|
700 |
|
|
701 |
|
|
702 |
|
|
703 |
|
@param |
704 |
|
|
705 |
|
@return |
706 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
707 |
13 |
public boolean setFeaturePriority(FeatureSettingsBean[] data)... |
708 |
|
{ |
709 |
13 |
return setFeaturePriority(data, true); |
710 |
|
} |
711 |
|
|
712 |
|
|
713 |
|
|
714 |
|
|
715 |
|
|
716 |
|
@param |
717 |
|
|
718 |
|
@param |
719 |
|
|
720 |
|
@return |
721 |
|
|
722 |
|
|
|
|
| 82.9% |
Uncovered Elements: 7 (41) |
Complexity: 9 |
Complexity Density: 0.36 |
|
723 |
16 |
public boolean setFeaturePriority(FeatureSettingsBean[] data,... |
724 |
|
boolean visibleNew) |
725 |
|
{ |
726 |
|
|
727 |
|
|
728 |
|
|
729 |
16 |
List<String> visibleFeatures = getDisplayedFeatureTypes(); |
730 |
16 |
Map<String, FeatureColourI> visibleColours = new HashMap<>( |
731 |
|
getFeatureColours()); |
732 |
|
|
733 |
16 |
FeaturesDisplayedI av_featuresdisplayed = null; |
734 |
16 |
if (visibleNew) |
735 |
|
{ |
736 |
? |
if ((av_featuresdisplayed = av.getFeaturesDisplayed()) != null) |
737 |
|
{ |
738 |
12 |
av.getFeaturesDisplayed().clear(); |
739 |
|
} |
740 |
|
else |
741 |
|
{ |
742 |
1 |
av.setFeaturesDisplayed( |
743 |
|
av_featuresdisplayed = new FeaturesDisplayed()); |
744 |
|
} |
745 |
|
} |
746 |
|
else |
747 |
|
{ |
748 |
3 |
av_featuresdisplayed = av.getFeaturesDisplayed(); |
749 |
|
} |
750 |
16 |
if (data == null) |
751 |
|
{ |
752 |
0 |
return false; |
753 |
|
} |
754 |
|
|
755 |
|
|
756 |
|
|
757 |
16 |
renderOrder = new String[data.length]; |
758 |
|
|
759 |
16 |
if (data.length > 0) |
760 |
|
{ |
761 |
57 |
for (int i = 0; i < data.length; i++) |
762 |
|
{ |
763 |
41 |
String type = data[i].featureType; |
764 |
41 |
setColour(type, data[i].featureColour); |
765 |
41 |
if (data[i].show) |
766 |
|
{ |
767 |
29 |
av_featuresdisplayed.setVisible(type); |
768 |
|
} |
769 |
|
|
770 |
41 |
renderOrder[data.length - i - 1] = type; |
771 |
|
} |
772 |
|
} |
773 |
|
|
774 |
|
|
775 |
|
|
776 |
|
|
777 |
|
|
778 |
16 |
List<String> reorderedVisibleFeatures = getDisplayedFeatureTypes(); |
779 |
16 |
if (!visibleFeatures.equals(reorderedVisibleFeatures)) |
780 |
|
{ |
781 |
|
|
782 |
|
|
783 |
|
|
784 |
11 |
return true; |
785 |
|
} |
786 |
|
|
787 |
|
|
788 |
|
|
789 |
|
|
790 |
5 |
for (String feature : visibleFeatures) |
791 |
|
{ |
792 |
17 |
if (visibleColours.get(feature) != getFeatureStyle(feature)) |
793 |
|
{ |
794 |
0 |
return true; |
795 |
|
} |
796 |
|
} |
797 |
5 |
return false; |
798 |
|
} |
799 |
|
|
800 |
|
|
801 |
|
@param |
802 |
|
@see |
803 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
804 |
1 |
public void addPropertyChangeListener(PropertyChangeListener listener)... |
805 |
|
{ |
806 |
1 |
changeSupport.addPropertyChangeListener(listener); |
807 |
|
} |
808 |
|
|
809 |
|
|
810 |
|
@param |
811 |
|
@see |
812 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
813 |
1 |
public void removePropertyChangeListener(PropertyChangeListener listener)... |
814 |
|
{ |
815 |
1 |
changeSupport.removePropertyChangeListener(listener); |
816 |
|
} |
817 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
818 |
1 |
public Set<String> getAllFeatureColours()... |
819 |
|
{ |
820 |
1 |
return featureColours.keySet(); |
821 |
|
} |
822 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
823 |
16 |
public void clearRenderOrder()... |
824 |
|
{ |
825 |
16 |
renderOrder = null; |
826 |
|
} |
827 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
828 |
6987 |
public boolean hasRenderOrder()... |
829 |
|
{ |
830 |
6987 |
return renderOrder != null; |
831 |
|
} |
832 |
|
|
833 |
|
|
834 |
|
|
835 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
836 |
255 |
public List<String> getRenderOrder()... |
837 |
|
{ |
838 |
255 |
if (renderOrder == null) |
839 |
|
{ |
840 |
41 |
return Arrays.asList(new String[] {}); |
841 |
|
} |
842 |
214 |
return Arrays.asList(renderOrder); |
843 |
|
} |
844 |
|
|
|
|
| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
845 |
2 |
public int getFeatureGroupsSize()... |
846 |
|
{ |
847 |
2 |
return featureGroups != null ? 0 : featureGroups.size(); |
848 |
|
} |
849 |
|
|
|
|
| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
850 |
164 |
@Override... |
851 |
|
public List<String> getFeatureGroups() |
852 |
|
{ |
853 |
|
|
854 |
|
|
855 |
164 |
return (featureGroups == null) ? Arrays.asList(new String[0]) |
856 |
|
: Arrays.asList(featureGroups.keySet().toArray(new String[0])); |
857 |
|
} |
858 |
|
|
|
|
| 38.5% |
Uncovered Elements: 8 (13) |
Complexity: 4 |
Complexity Density: 0.57 |
|
859 |
42 |
public boolean checkGroupVisibility(String group,... |
860 |
|
boolean newGroupsVisible) |
861 |
|
{ |
862 |
42 |
if (featureGroups == null) |
863 |
|
{ |
864 |
|
|
865 |
|
} |
866 |
42 |
if (featureGroups.containsKey(group)) |
867 |
|
{ |
868 |
42 |
return featureGroups.get(group).booleanValue(); |
869 |
|
} |
870 |
0 |
if (newGroupsVisible) |
871 |
|
{ |
872 |
0 |
featureGroups.put(group, Boolean.valueOf(true)); |
873 |
0 |
return true; |
874 |
|
} |
875 |
0 |
return false; |
876 |
|
} |
877 |
|
|
878 |
|
|
879 |
|
|
880 |
|
|
881 |
|
@param |
882 |
|
|
883 |
|
@return |
884 |
|
|
|
|
| 66.7% |
Uncovered Elements: 4 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
|
885 |
16 |
@Override... |
886 |
|
public List<String> getGroups(boolean visible) |
887 |
|
{ |
888 |
16 |
if (featureGroups != null) |
889 |
|
{ |
890 |
16 |
List<String> gp = new ArrayList<>(); |
891 |
|
|
892 |
16 |
for (String grp : featureGroups.keySet()) |
893 |
|
{ |
894 |
60 |
Boolean state = featureGroups.get(grp); |
895 |
60 |
if (state.booleanValue() == visible) |
896 |
|
{ |
897 |
0 |
gp.add(grp); |
898 |
|
} |
899 |
|
} |
900 |
16 |
return gp; |
901 |
|
} |
902 |
0 |
return null; |
903 |
|
} |
904 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
905 |
126 |
@Override... |
906 |
|
public void setGroupVisibility(String group, boolean visible) |
907 |
|
{ |
908 |
126 |
featureGroups.put(group, Boolean.valueOf(visible)); |
909 |
|
} |
910 |
|
|
|
|
| 0% |
Uncovered Elements: 14 (14) |
Complexity: 6 |
Complexity Density: 0.75 |
|
911 |
0 |
@Override... |
912 |
|
public void setGroupVisibility(List<String> toset, boolean visible) |
913 |
|
{ |
914 |
0 |
if (toset != null && toset.size() > 0 && featureGroups != null) |
915 |
|
{ |
916 |
0 |
boolean rdrw = false; |
917 |
0 |
for (String gst : toset) |
918 |
|
{ |
919 |
0 |
Boolean st = featureGroups.get(gst); |
920 |
0 |
featureGroups.put(gst, Boolean.valueOf(visible)); |
921 |
0 |
if (st != null) |
922 |
|
{ |
923 |
0 |
rdrw = rdrw || (visible != st.booleanValue()); |
924 |
|
} |
925 |
|
} |
926 |
0 |
if (rdrw) |
927 |
|
{ |
928 |
|
|
929 |
|
} |
930 |
|
} |
931 |
|
} |
932 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
933 |
22 |
@Override... |
934 |
|
public Map<String, FeatureColourI> getDisplayedFeatureCols() |
935 |
|
{ |
936 |
22 |
Map<String, FeatureColourI> fcols = new Hashtable<>(); |
937 |
22 |
if (getViewport().getFeaturesDisplayed() == null) |
938 |
|
{ |
939 |
5 |
return fcols; |
940 |
|
} |
941 |
17 |
Set<String> features = getViewport().getFeaturesDisplayed() |
942 |
|
.getVisibleFeatures(); |
943 |
17 |
for (String feature : features) |
944 |
|
{ |
945 |
26 |
fcols.put(feature, getFeatureStyle(feature)); |
946 |
|
} |
947 |
17 |
return fcols; |
948 |
|
} |
949 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
950 |
6846 |
@Override... |
951 |
|
public FeaturesDisplayedI getFeaturesDisplayed() |
952 |
|
{ |
953 |
6846 |
return av.getFeaturesDisplayed(); |
954 |
|
} |
955 |
|
|
956 |
|
|
957 |
|
|
958 |
|
|
959 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (13) |
Complexity: 3 |
Complexity Density: 0.33 |
|
960 |
106 |
@Override... |
961 |
|
public List<String> getDisplayedFeatureTypes() |
962 |
|
{ |
963 |
106 |
List<String> typ = getRenderOrder(); |
964 |
106 |
List<String> displayed = new ArrayList<>(); |
965 |
106 |
FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed(); |
966 |
106 |
if (feature_disp != null) |
967 |
|
{ |
968 |
105 |
synchronized (feature_disp) |
969 |
|
{ |
970 |
105 |
for (String type : typ) |
971 |
|
{ |
972 |
303 |
if (feature_disp.isVisible(type)) |
973 |
|
{ |
974 |
285 |
displayed.add(type); |
975 |
|
} |
976 |
|
} |
977 |
|
} |
978 |
|
} |
979 |
106 |
return displayed; |
980 |
|
} |
981 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
982 |
10 |
@Override... |
983 |
|
public List<String> getDisplayedFeatureGroups() |
984 |
|
{ |
985 |
10 |
List<String> _gps = new ArrayList<>(); |
986 |
10 |
for (String gp : getFeatureGroups()) |
987 |
|
{ |
988 |
13 |
if (checkGroupVisibility(gp, false)) |
989 |
|
{ |
990 |
11 |
_gps.add(gp); |
991 |
|
} |
992 |
|
} |
993 |
10 |
return _gps; |
994 |
|
} |
995 |
|
|
996 |
|
|
997 |
|
|
998 |
|
|
999 |
|
|
1000 |
|
@param |
1001 |
|
@return |
1002 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1003 |
38627 |
public boolean featureGroupNotShown(final SequenceFeature sequenceFeature)... |
1004 |
|
{ |
1005 |
38628 |
return featureGroups != null && sequenceFeature.featureGroup != null |
1006 |
|
&& sequenceFeature.featureGroup.length() != 0 |
1007 |
|
&& featureGroups.containsKey(sequenceFeature.featureGroup) |
1008 |
|
&& !featureGroups.get(sequenceFeature.featureGroup) |
1009 |
|
.booleanValue(); |
1010 |
|
} |
1011 |
|
|
1012 |
|
|
1013 |
|
@inheritDoc |
1014 |
|
|
|
|
| 78.6% |
Uncovered Elements: 3 (14) |
Complexity: 5 |
Complexity Density: 0.5 |
|
1015 |
62 |
@Override... |
1016 |
|
public List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence, |
1017 |
|
int fromResNo, int toResNo) |
1018 |
|
{ |
1019 |
62 |
List<SequenceFeature> result = new ArrayList<>(); |
1020 |
62 |
if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null) |
1021 |
|
{ |
1022 |
0 |
return result; |
1023 |
|
} |
1024 |
|
|
1025 |
|
|
1026 |
|
|
1027 |
|
|
1028 |
|
|
1029 |
|
|
1030 |
62 |
List<String> visibleFeatures = getDisplayedFeatureTypes(); |
1031 |
62 |
String[] visibleTypes = visibleFeatures |
1032 |
|
.toArray(new String[visibleFeatures.size()]); |
1033 |
62 |
List<SequenceFeature> features = sequence.getFeatures() |
1034 |
|
.findFeatures(fromResNo, toResNo, visibleTypes); |
1035 |
|
|
1036 |
62 |
for (SequenceFeature sf : features) |
1037 |
|
{ |
1038 |
73 |
if (!featureGroupNotShown(sf) && getColour(sf) != null) |
1039 |
|
{ |
1040 |
73 |
result.add(sf); |
1041 |
|
} |
1042 |
|
} |
1043 |
62 |
return result; |
1044 |
|
} |
1045 |
|
|
1046 |
|
|
1047 |
|
|
1048 |
|
|
1049 |
|
|
1050 |
|
|
1051 |
|
|
1052 |
|
|
1053 |
|
@param |
1054 |
|
|
|
|
| 92% |
Uncovered Elements: 2 (25) |
Complexity: 12 |
Complexity Density: 0.8 |
|
1055 |
1116 |
public void filterFeaturesForDisplay(List<SequenceFeature> features)... |
1056 |
|
{ |
1057 |
|
|
1058 |
|
|
1059 |
|
|
1060 |
1116 |
if (Platform.isJS()) |
1061 |
|
{ |
1062 |
0 |
return; |
1063 |
|
} |
1064 |
|
|
1065 |
|
|
1066 |
|
|
1067 |
|
|
1068 |
|
|
1069 |
|
|
1070 |
1116 |
if (features.isEmpty() || transparency != 1f |
1071 |
|
|| !featureFilters.isEmpty()) |
1072 |
|
{ |
1073 |
2 |
return; |
1074 |
|
} |
1075 |
|
|
1076 |
1114 |
SequenceFeatures.sortFeatures(features, true); |
1077 |
1114 |
SequenceFeature lastFeature = null; |
1078 |
|
|
1079 |
1114 |
Iterator<SequenceFeature> it = features.iterator(); |
1080 |
15867 |
while (it.hasNext()) |
1081 |
|
{ |
1082 |
14753 |
SequenceFeature sf = it.next(); |
1083 |
14753 |
if (featureGroupNotShown(sf)) |
1084 |
|
{ |
1085 |
2 |
it.remove(); |
1086 |
2 |
continue; |
1087 |
|
} |
1088 |
|
|
1089 |
|
|
1090 |
|
|
1091 |
|
|
1092 |
|
|
1093 |
|
|
1094 |
|
|
1095 |
14751 |
if (lastFeature != null && sf.getBegin() == lastFeature.getBegin() |
1096 |
|
&& sf.getEnd() == lastFeature.getEnd() |
1097 |
|
&& sf.isContactFeature() == lastFeature.isContactFeature() |
1098 |
|
&& sf.getType().equals(lastFeature.getType())) |
1099 |
|
{ |
1100 |
3 |
it.remove(); |
1101 |
|
} |
1102 |
14751 |
lastFeature = sf; |
1103 |
|
} |
1104 |
|
} |
1105 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1106 |
15 |
@Override... |
1107 |
|
public Map<String, FeatureMatcherSetI> getFeatureFilters() |
1108 |
|
{ |
1109 |
15 |
return featureFilters; |
1110 |
|
} |
1111 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1112 |
0 |
@Override... |
1113 |
|
public void setFeatureFilters(Map<String, FeatureMatcherSetI> filters) |
1114 |
|
{ |
1115 |
0 |
featureFilters = filters; |
1116 |
|
} |
1117 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1118 |
168 |
@Override... |
1119 |
|
public FeatureMatcherSetI getFeatureFilter(String featureType) |
1120 |
|
{ |
1121 |
168 |
return featureFilters.get(featureType); |
1122 |
|
} |
1123 |
|
|
|
|
| 60% |
Uncovered Elements: 2 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
1124 |
23 |
@Override... |
1125 |
|
public void setFeatureFilter(String featureType, |
1126 |
|
FeatureMatcherSetI filter) |
1127 |
|
{ |
1128 |
23 |
if (filter == null || filter.isEmpty()) |
1129 |
|
{ |
1130 |
0 |
featureFilters.remove(featureType); |
1131 |
|
} |
1132 |
|
else |
1133 |
|
{ |
1134 |
23 |
featureFilters.put(featureType, filter); |
1135 |
|
} |
1136 |
|
} |
1137 |
|
|
1138 |
|
|
1139 |
|
|
1140 |
|
|
1141 |
|
|
1142 |
|
|
1143 |
|
@param |
1144 |
|
@param |
1145 |
|
@return |
1146 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
1147 |
19782 |
public Color getColor(SequenceFeature sf, FeatureColourI fc)... |
1148 |
|
{ |
1149 |
|
|
1150 |
|
|
1151 |
|
|
1152 |
19782 |
if (featureGroupNotShown(sf)) |
1153 |
|
{ |
1154 |
8 |
return null; |
1155 |
|
} |
1156 |
|
|
1157 |
|
|
1158 |
|
|
1159 |
|
|
1160 |
19774 |
if (!featureMatchesFilters(sf)) |
1161 |
|
{ |
1162 |
6 |
return null; |
1163 |
|
} |
1164 |
|
|
1165 |
19768 |
return fc.getColor(sf); |
1166 |
|
} |
1167 |
|
|
1168 |
|
|
1169 |
|
|
1170 |
|
|
1171 |
|
|
1172 |
|
|
1173 |
|
@param |
1174 |
|
@return |
1175 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
1176 |
19812 |
protected boolean featureMatchesFilters(SequenceFeature sf)... |
1177 |
|
{ |
1178 |
19812 |
FeatureMatcherSetI filter = featureFilters.get(sf.getType()); |
1179 |
19812 |
return filter == null ? true : filter.matches(sf); |
1180 |
|
} |
1181 |
|
|
1182 |
|
|
1183 |
|
|
1184 |
|
|
1185 |
|
|
1186 |
|
@param |
1187 |
|
@return |
1188 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1189 |
0 |
public boolean isGroupVisible(String group)... |
1190 |
|
{ |
1191 |
0 |
if (!featureGroups.containsKey(group)) |
1192 |
|
{ |
1193 |
0 |
return true; |
1194 |
|
} |
1195 |
0 |
return featureGroups.get(group); |
1196 |
|
} |
1197 |
|
|
1198 |
|
|
1199 |
|
|
1200 |
|
|
1201 |
|
|
1202 |
|
@param |
1203 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1204 |
66 |
public void orderFeatures(Comparator<String> order)... |
1205 |
|
{ |
1206 |
66 |
Arrays.sort(renderOrder, order); |
1207 |
|
} |
1208 |
|
|
|
|
| 83.6% |
Uncovered Elements: 9 (55) |
Complexity: 9 |
Complexity Density: 0.23 |
|
1209 |
2 |
@Override... |
1210 |
|
public MappedFeatures findComplementFeaturesAtResidue( |
1211 |
|
final SequenceI sequence, final int pos) |
1212 |
|
{ |
1213 |
2 |
SequenceI ds = sequence.getDatasetSequence(); |
1214 |
2 |
if (ds == null) |
1215 |
|
{ |
1216 |
0 |
ds = sequence; |
1217 |
|
} |
1218 |
2 |
final char residue = ds.getCharAt(pos - ds.getStart()); |
1219 |
|
|
1220 |
2 |
List<SequenceFeature> found = new ArrayList<>(); |
1221 |
2 |
List<AlignedCodonFrame> mappings = this.av.getAlignment() |
1222 |
|
.getCodonFrame(sequence); |
1223 |
|
|
1224 |
|
|
1225 |
|
|
1226 |
|
|
1227 |
|
|
1228 |
2 |
if (mappings.isEmpty()) |
1229 |
|
{ |
1230 |
2 |
mappings = this.av.getCodingComplement().getAlignment() |
1231 |
|
.getCodonFrame(sequence); |
1232 |
|
} |
1233 |
|
|
1234 |
|
|
1235 |
|
|
1236 |
|
|
1237 |
|
|
1238 |
2 |
SequenceToSequenceMapping mapping = null; |
1239 |
2 |
SequenceI mapFrom = null; |
1240 |
|
|
1241 |
2 |
for (AlignedCodonFrame acf : mappings) |
1242 |
|
{ |
1243 |
2 |
mapping = acf.getCoveringCodonMapping(ds); |
1244 |
2 |
if (mapping == null) |
1245 |
|
{ |
1246 |
0 |
continue; |
1247 |
|
} |
1248 |
2 |
SearchResultsI sr = new SearchResults(); |
1249 |
2 |
mapping.markMappedRegion(ds, pos, sr); |
1250 |
2 |
for (SearchResultMatchI match : sr.getResults()) |
1251 |
|
{ |
1252 |
2 |
int fromRes = match.getStart(); |
1253 |
2 |
int toRes = match.getEnd(); |
1254 |
2 |
mapFrom = match.getSequence(); |
1255 |
2 |
List<SequenceFeature> fs = findFeaturesAtResidue(mapFrom, fromRes, |
1256 |
|
toRes); |
1257 |
2 |
for (SequenceFeature sf : fs) |
1258 |
|
{ |
1259 |
3 |
if (!found.contains(sf)) |
1260 |
|
{ |
1261 |
3 |
found.add(sf); |
1262 |
|
} |
1263 |
|
} |
1264 |
|
} |
1265 |
|
|
1266 |
|
|
1267 |
|
|
1268 |
|
|
1269 |
2 |
if (!found.isEmpty()) |
1270 |
|
{ |
1271 |
2 |
break; |
1272 |
|
} |
1273 |
|
} |
1274 |
2 |
if (found.isEmpty()) |
1275 |
|
{ |
1276 |
0 |
return null; |
1277 |
|
} |
1278 |
|
|
1279 |
|
|
1280 |
|
|
1281 |
|
|
1282 |
|
|
1283 |
2 |
List<SequenceFeature> result = new ArrayList<>(); |
1284 |
2 |
final int toAdd = found.size(); |
1285 |
2 |
int added = 0; |
1286 |
2 |
for (String type : renderOrder) |
1287 |
|
{ |
1288 |
3 |
for (SequenceFeature sf : found) |
1289 |
|
{ |
1290 |
4 |
if (type.equals(sf.getType())) |
1291 |
|
{ |
1292 |
3 |
result.add(sf); |
1293 |
3 |
added++; |
1294 |
|
} |
1295 |
4 |
if (added == toAdd) |
1296 |
|
{ |
1297 |
2 |
break; |
1298 |
|
} |
1299 |
|
} |
1300 |
|
} |
1301 |
|
|
1302 |
2 |
return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue, |
1303 |
|
result); |
1304 |
|
} |
1305 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (22) |
Complexity: 8 |
Complexity Density: 0.67 |
|
1306 |
46 |
@Override... |
1307 |
|
public boolean isVisible(SequenceFeature feature) |
1308 |
|
{ |
1309 |
46 |
if (feature == null) |
1310 |
|
{ |
1311 |
1 |
return false; |
1312 |
|
} |
1313 |
45 |
if (getFeaturesDisplayed() == null |
1314 |
|
|| !getFeaturesDisplayed().isVisible(feature.getType())) |
1315 |
|
{ |
1316 |
1 |
return false; |
1317 |
|
} |
1318 |
44 |
if (featureGroupNotShown(feature)) |
1319 |
|
{ |
1320 |
2 |
return false; |
1321 |
|
} |
1322 |
42 |
FeatureColourI fc = featureColours.get(feature.getType()); |
1323 |
42 |
if (fc != null && fc.isOutwithThreshold(feature)) |
1324 |
|
{ |
1325 |
4 |
return false; |
1326 |
|
} |
1327 |
38 |
if (!featureMatchesFilters(feature)) |
1328 |
|
{ |
1329 |
3 |
return false; |
1330 |
|
} |
1331 |
35 |
return true; |
1332 |
|
} |
1333 |
|
} |