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package jalview.io; |
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import jalview.api.AlignExportSettingsI; |
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import jalview.api.AlignViewportI; |
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import jalview.api.AlignmentViewPanel; |
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import jalview.api.ComplexAlignFile; |
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import jalview.api.FeatureRenderer; |
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import jalview.api.FeatureSettingsModelI; |
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import jalview.api.FeaturesDisplayedI; |
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import jalview.bin.BuildDetails; |
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import jalview.datamodel.AlignExportSettingsAdapter; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.Annotation; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.HiddenSequences; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo; |
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import jalview.json.binding.biojson.v1.AlignmentPojo; |
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import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo; |
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import jalview.json.binding.biojson.v1.AnnotationPojo; |
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import jalview.json.binding.biojson.v1.ColourSchemeMapper; |
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import jalview.json.binding.biojson.v1.SequenceFeaturesPojo; |
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import jalview.json.binding.biojson.v1.SequenceGrpPojo; |
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import jalview.json.binding.biojson.v1.SequencePojo; |
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import jalview.renderer.seqfeatures.FeatureColourFinder; |
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import jalview.schemes.ColourSchemeProperty; |
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import jalview.schemes.JalviewColourScheme; |
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import jalview.schemes.ResidueColourScheme; |
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import jalview.util.ColorUtils; |
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import jalview.util.Format; |
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import jalview.viewmodel.seqfeatures.FeaturesDisplayed; |
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import java.awt.Color; |
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import java.io.IOException; |
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import java.io.Reader; |
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import java.util.ArrayList; |
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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.Vector; |
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import org.json.simple.JSONArray; |
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import org.json.simple.JSONObject; |
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import org.json.simple.parser.JSONParser; |
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| 83.2% |
Uncovered Elements: 78 (463) |
Complexity: 109 |
Complexity Density: 0.36 |
|
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public class JSONFile extends AlignFile implements ComplexAlignFile |
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{ |
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private static String version = new BuildDetails().getVersion(); |
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private String webstartUrl = "http://www.jalview.org/services/launchApp"; |
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private String application = "Jalview"; |
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private String globalColourScheme; |
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private boolean showSeqFeatures; |
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private Hashtable<String, Sequence> seqMap; |
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private FeaturesDisplayedI displayedFeatures; |
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private FeatureRenderer fr; |
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private HiddenColumns hiddenColumns; |
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private List<String> hiddenSeqRefs; |
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private ArrayList<SequenceI> hiddenSequences; |
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|
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private final static String TCOFFEE_SCORE = "TCoffeeScore"; |
96 |
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|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
97 |
4 |
public JSONFile()... |
98 |
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{ |
99 |
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super(); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
102 |
6 |
public JSONFile(FileParse source) throws IOException... |
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{ |
104 |
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super(source); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public JSONFile(String inFile, DataSourceType sourceType)... |
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throws IOException |
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{ |
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super(inFile, sourceType); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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6 |
@Override... |
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public void parse() throws IOException |
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{ |
116 |
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parse(getReader()); |
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} |
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| 88.7% |
Uncovered Elements: 8 (71) |
Complexity: 15 |
Complexity Density: 0.27 |
|
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@Override... |
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public String print(SequenceI[] sqs, boolean jvsuffix) |
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{ |
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String jsonOutput = null; |
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try |
125 |
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{ |
126 |
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AlignmentPojo jsonAlignmentPojo = new AlignmentPojo(); |
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AlignExportSettingsI exportSettings = getExportSettings(); |
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132 |
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if (exportSettings == null) |
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{ |
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exportSettings = new AlignExportSettingsAdapter(true); |
135 |
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} |
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137 |
4 |
int count = 0; |
138 |
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for (SequenceI seq : sqs) |
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{ |
140 |
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StringBuilder name = new StringBuilder(); |
141 |
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name.append(seq.getName()).append("/").append(seq.getStart()) |
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.append("-").append(seq.getEnd()); |
143 |
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SequencePojo jsonSeqPojo = new SequencePojo(); |
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jsonSeqPojo.setId(String.valueOf(seq.hashCode())); |
145 |
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jsonSeqPojo.setOrder(++count); |
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jsonSeqPojo.setEnd(seq.getEnd()); |
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jsonSeqPojo.setStart(seq.getStart()); |
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jsonSeqPojo.setName(name.toString()); |
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jsonSeqPojo.setSeq(seq.getSequenceAsString()); |
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jsonAlignmentPojo.getSeqs().add(jsonSeqPojo); |
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} |
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jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme); |
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jsonAlignmentPojo.getAppSettings().put("application", application); |
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jsonAlignmentPojo.getAppSettings().put("version", version); |
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jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl); |
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jsonAlignmentPojo.getAppSettings().put("showSeqFeatures", |
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String.valueOf(showSeqFeatures)); |
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|
159 |
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String[] hiddenSections = getHiddenSections(); |
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if (hiddenSections != null) |
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{ |
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if (hiddenSections[0] != null |
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&& exportSettings.isExportHiddenColumns()) |
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{ |
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jsonAlignmentPojo.getAppSettings().put("hiddenCols", |
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String.valueOf(hiddenSections[0])); |
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} |
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if (hiddenSections[1] != null |
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&& exportSettings.isExportHiddenSequences()) |
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{ |
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jsonAlignmentPojo.getAppSettings().put("hiddenSeqs", |
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String.valueOf(hiddenSections[1])); |
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} |
174 |
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} |
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176 |
4 |
if (exportSettings.isExportAnnotations()) |
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{ |
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jsonAlignmentPojo |
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.setAlignAnnotation(annotationToJsonPojo(annotations)); |
180 |
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} |
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else |
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{ |
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184 |
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185 |
0 |
if (globalColourScheme |
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.equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString()) |
187 |
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|| globalColourScheme.equalsIgnoreCase( |
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JalviewColourScheme.TCoffee.toString())) |
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{ |
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jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE); |
191 |
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} |
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} |
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4 |
if (exportSettings.isExportFeatures()) |
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{ |
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jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs)); |
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} |
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|
199 |
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if (exportSettings.isExportGroups() && seqGroups != null |
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&& seqGroups.size() > 0) |
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{ |
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for (SequenceGroup seqGrp : seqGroups) |
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{ |
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SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo(); |
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seqGrpPojo.setGroupName(seqGrp.getName()); |
206 |
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seqGrpPojo.setColourScheme(ColourSchemeProperty |
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.getColourName(seqGrp.getColourScheme())); |
208 |
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seqGrpPojo.setColourText(seqGrp.getColourText()); |
209 |
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seqGrpPojo.setDescription(seqGrp.getDescription()); |
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seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes()); |
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seqGrpPojo.setDisplayText(seqGrp.getDisplayText()); |
212 |
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seqGrpPojo.setEndRes(seqGrp.getEndRes()); |
213 |
3 |
seqGrpPojo.setStartRes(seqGrp.getStartRes()); |
214 |
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seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved()); |
215 |
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for (SequenceI seq : seqGrp.getSequences()) |
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{ |
217 |
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seqGrpPojo.getSequenceRefs() |
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.add(String.valueOf(seq.hashCode())); |
219 |
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} |
220 |
3 |
jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo); |
221 |
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} |
222 |
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} |
223 |
4 |
org.json.JSONObject generatedJSon = new org.json.JSONObject( |
224 |
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jsonAlignmentPojo); |
225 |
4 |
jsonOutput = generatedJSon.toString(); |
226 |
4 |
return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend", |
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"xEnd"); |
228 |
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} catch (Exception e) |
229 |
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{ |
230 |
0 |
e.printStackTrace(); |
231 |
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} |
232 |
0 |
return jsonOutput; |
233 |
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} |
234 |
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|
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|
| 96.3% |
Uncovered Elements: 1 (27) |
Complexity: 7 |
Complexity Density: 0.41 |
|
235 |
4 |
public String[] getHiddenSections()... |
236 |
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{ |
237 |
4 |
String[] hiddenSections = new String[2]; |
238 |
4 |
if (getViewport() == null) |
239 |
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{ |
240 |
1 |
return null; |
241 |
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} |
242 |
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|
243 |
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|
244 |
3 |
if (getViewport().hasHiddenColumns()) |
245 |
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{ |
246 |
2 |
hiddenSections[0] = getViewport().getAlignment().getHiddenColumns() |
247 |
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.regionsToString(";", "-"); |
248 |
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} |
249 |
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|
250 |
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|
251 |
3 |
HiddenSequences hiddenSeqsObj = getViewport().getAlignment() |
252 |
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.getHiddenSequences(); |
253 |
3 |
if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null) |
254 |
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{ |
255 |
1 |
return hiddenSections; |
256 |
|
} |
257 |
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|
258 |
2 |
SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences; |
259 |
2 |
StringBuilder hiddenSeqsBuilder = new StringBuilder(); |
260 |
2 |
for (SequenceI hiddenSeq : hiddenSeqs) |
261 |
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{ |
262 |
12 |
if (hiddenSeq != null) |
263 |
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{ |
264 |
2 |
hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode()); |
265 |
|
} |
266 |
|
} |
267 |
2 |
if (hiddenSeqsBuilder.length() > 0) |
268 |
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{ |
269 |
2 |
hiddenSeqsBuilder.deleteCharAt(0); |
270 |
|
} |
271 |
2 |
hiddenSections[1] = hiddenSeqsBuilder.toString(); |
272 |
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|
273 |
2 |
return hiddenSections; |
274 |
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} |
275 |
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|
|
|
| 91.7% |
Uncovered Elements: 3 (36) |
Complexity: 7 |
Complexity Density: 0.29 |
|
276 |
4 |
protected List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(... |
277 |
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SequenceI[] sqs) |
278 |
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{ |
279 |
4 |
displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed(); |
280 |
4 |
List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>(); |
281 |
4 |
if (sqs == null) |
282 |
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{ |
283 |
0 |
return sequenceFeaturesPojo; |
284 |
|
} |
285 |
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|
286 |
4 |
FeatureColourFinder finder = new FeatureColourFinder(fr); |
287 |
|
|
288 |
4 |
String[] visibleFeatureTypes = displayedFeatures == null ? null |
289 |
|
: displayedFeatures.getVisibleFeatures().toArray( |
290 |
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new String[displayedFeatures.getVisibleFeatureCount()]); |
291 |
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|
292 |
4 |
for (SequenceI seq : sqs) |
293 |
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{ |
294 |
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|
295 |
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|
296 |
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|
297 |
30 |
List<SequenceFeature> seqFeatures = seq.getFeatures().getAllFeatures( |
298 |
|
visibleFeatureTypes); |
299 |
30 |
for (SequenceFeature sf : seqFeatures) |
300 |
|
{ |
301 |
12 |
SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo( |
302 |
|
String.valueOf(seq.hashCode())); |
303 |
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|
304 |
12 |
String featureColour = (fr == null) ? null : Format |
305 |
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.getHexString(finder.findFeatureColour(Color.white, seq, |
306 |
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seq.findIndex(sf.getBegin()))); |
307 |
12 |
int xStart = sf.getBegin() == 0 ? 0 |
308 |
|
: seq.findIndex(sf.getBegin()) - 1; |
309 |
12 |
int xEnd = sf.getEnd() == 0 ? 0 : seq.findIndex(sf.getEnd()); |
310 |
12 |
jsonFeature.setXstart(xStart); |
311 |
12 |
jsonFeature.setXend(xEnd); |
312 |
12 |
jsonFeature.setType(sf.getType()); |
313 |
12 |
jsonFeature.setDescription(sf.getDescription()); |
314 |
12 |
jsonFeature.setLinks(sf.links); |
315 |
12 |
jsonFeature.setOtherDetails(sf.otherDetails); |
316 |
12 |
jsonFeature.setScore(sf.getScore()); |
317 |
12 |
jsonFeature.setFillColor(featureColour); |
318 |
12 |
jsonFeature.setFeatureGroup(sf.getFeatureGroup()); |
319 |
12 |
sequenceFeaturesPojo.add(jsonFeature); |
320 |
|
} |
321 |
|
} |
322 |
4 |
return sequenceFeaturesPojo; |
323 |
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} |
324 |
|
|
|
|
| 72.5% |
Uncovered Elements: 14 (51) |
Complexity: 9 |
Complexity Density: 0.24 |
|
325 |
4 |
public static List<AlignmentAnnotationPojo> annotationToJsonPojo(... |
326 |
|
Vector<AlignmentAnnotation> annotations) |
327 |
|
{ |
328 |
4 |
List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<>(); |
329 |
4 |
if (annotations == null) |
330 |
|
{ |
331 |
0 |
return jsonAnnotations; |
332 |
|
} |
333 |
4 |
for (AlignmentAnnotation annot : annotations) |
334 |
|
{ |
335 |
2 |
AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo(); |
336 |
2 |
alignAnnotPojo.setDescription(annot.description); |
337 |
2 |
alignAnnotPojo.setLabel(annot.label); |
338 |
2 |
if (!Double.isNaN(annot.score)) |
339 |
|
{ |
340 |
0 |
alignAnnotPojo.setScore(annot.score); |
341 |
|
} |
342 |
2 |
alignAnnotPojo.setCalcId(annot.getCalcId()); |
343 |
2 |
alignAnnotPojo.setGraphType(annot.graph); |
344 |
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|
345 |
2 |
AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo(); |
346 |
2 |
annotSetting.setBelowAlignment(annot.belowAlignment); |
347 |
2 |
annotSetting.setCentreColLabels(annot.centreColLabels); |
348 |
2 |
annotSetting.setScaleColLabel(annot.scaleColLabel); |
349 |
2 |
annotSetting.setShowAllColLabels(annot.showAllColLabels); |
350 |
2 |
annotSetting.setVisible(annot.visible); |
351 |
2 |
annotSetting.setHasIcon(annot.hasIcons); |
352 |
2 |
alignAnnotPojo.setAnnotationSettings(annotSetting); |
353 |
2 |
SequenceI refSeq = annot.sequenceRef; |
354 |
2 |
if (refSeq != null) |
355 |
|
{ |
356 |
0 |
alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode())); |
357 |
|
} |
358 |
2 |
for (Annotation annotation : annot.annotations) |
359 |
|
{ |
360 |
70 |
AnnotationPojo annotationPojo = new AnnotationPojo(); |
361 |
70 |
if (annotation != null) |
362 |
|
{ |
363 |
70 |
annotationPojo.setDescription(annotation.description); |
364 |
70 |
annotationPojo.setValue(annotation.value); |
365 |
70 |
annotationPojo |
366 |
|
.setSecondaryStructure(annotation.secondaryStructure); |
367 |
70 |
String displayChar = annotation.displayCharacter == null ? null |
368 |
|
: annotation.displayCharacter; |
369 |
|
|
370 |
70 |
annotationPojo.setDisplayCharacter(displayChar); |
371 |
70 |
if (annotation.colour != null) |
372 |
|
{ |
373 |
0 |
annotationPojo.setColour( |
374 |
|
jalview.util.Format.getHexString(annotation.colour)); |
375 |
|
} |
376 |
70 |
alignAnnotPojo.getAnnotations().add(annotationPojo); |
377 |
|
} |
378 |
|
else |
379 |
|
{ |
380 |
0 |
if (annot.getCalcId() != null |
381 |
|
&& annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE)) |
382 |
|
{ |
383 |
|
|
384 |
|
} |
385 |
|
else |
386 |
|
{ |
387 |
0 |
alignAnnotPojo.getAnnotations().add(annotationPojo); |
388 |
|
} |
389 |
|
} |
390 |
|
} |
391 |
2 |
jsonAnnotations.add(alignAnnotPojo); |
392 |
|
} |
393 |
4 |
return jsonAnnotations; |
394 |
|
} |
395 |
|
|
|
|
| 80.5% |
Uncovered Elements: 31 (159) |
Complexity: 34 |
Complexity Density: 0.34 |
|
396 |
6 |
@SuppressWarnings("unchecked")... |
397 |
|
public JSONFile parse(Reader jsonAlignmentString) |
398 |
|
{ |
399 |
6 |
try |
400 |
|
{ |
401 |
6 |
JSONParser jsonParser = new JSONParser(); |
402 |
6 |
JSONObject alignmentJsonObj = (JSONObject) jsonParser |
403 |
|
.parse(jsonAlignmentString); |
404 |
6 |
JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs"); |
405 |
6 |
JSONArray alAnnotJsonArray = (JSONArray) alignmentJsonObj |
406 |
|
.get("alignAnnotation"); |
407 |
6 |
JSONArray jsonSeqArray = (JSONArray) alignmentJsonObj |
408 |
|
.get("seqFeatures"); |
409 |
6 |
JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj |
410 |
|
.get("seqGroups"); |
411 |
6 |
JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj |
412 |
|
.get("appSettings"); |
413 |
|
|
414 |
6 |
if (jvSettingsJsonObj != null) |
415 |
|
{ |
416 |
6 |
globalColourScheme = (String) jvSettingsJsonObj |
417 |
|
.get("globalColorScheme"); |
418 |
6 |
Boolean showFeatures = Boolean.valueOf( |
419 |
|
jvSettingsJsonObj.get("showSeqFeatures").toString()); |
420 |
6 |
setShowSeqFeatures(showFeatures); |
421 |
6 |
parseHiddenSeqRefsAsList(jvSettingsJsonObj); |
422 |
6 |
parseHiddenCols(jvSettingsJsonObj); |
423 |
|
} |
424 |
|
|
425 |
6 |
hiddenSequences = new ArrayList<>(); |
426 |
6 |
seqMap = new Hashtable<>(); |
427 |
6 |
for (Iterator<JSONObject> sequenceIter = seqJsonArray |
428 |
48 |
.iterator(); sequenceIter.hasNext();) |
429 |
|
{ |
430 |
42 |
JSONObject sequence = sequenceIter.next(); |
431 |
42 |
String sequcenceString = sequence.get("seq").toString(); |
432 |
42 |
String sequenceName = sequence.get("name").toString(); |
433 |
42 |
String seqUniqueId = sequence.get("id").toString(); |
434 |
42 |
int start = Integer.valueOf(sequence.get("start").toString()); |
435 |
42 |
int end = Integer.valueOf(sequence.get("end").toString()); |
436 |
42 |
Sequence seq = new Sequence(sequenceName, sequcenceString, start, |
437 |
|
end); |
438 |
42 |
if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId)) |
439 |
|
{ |
440 |
2 |
hiddenSequences.add(seq); |
441 |
|
} |
442 |
42 |
seqs.add(seq); |
443 |
42 |
seqMap.put(seqUniqueId, seq); |
444 |
|
} |
445 |
|
|
446 |
6 |
parseFeatures(jsonSeqArray); |
447 |
|
|
448 |
6 |
for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray |
449 |
11 |
.iterator(); seqGrpIter.hasNext();) |
450 |
|
{ |
451 |
5 |
JSONObject seqGrpObj = seqGrpIter.next(); |
452 |
5 |
String grpName = seqGrpObj.get("groupName").toString(); |
453 |
5 |
String colourScheme = seqGrpObj.get("colourScheme").toString(); |
454 |
5 |
String description = (seqGrpObj.get("description") == null) ? null |
455 |
|
: seqGrpObj.get("description").toString(); |
456 |
5 |
boolean displayBoxes = Boolean |
457 |
|
.valueOf(seqGrpObj.get("displayBoxes").toString()); |
458 |
5 |
boolean displayText = Boolean |
459 |
|
.valueOf(seqGrpObj.get("displayText").toString()); |
460 |
5 |
boolean colourText = Boolean |
461 |
|
.valueOf(seqGrpObj.get("colourText").toString()); |
462 |
5 |
boolean showNonconserved = Boolean |
463 |
|
.valueOf(seqGrpObj.get("showNonconserved").toString()); |
464 |
5 |
int startRes = Integer |
465 |
|
.valueOf(seqGrpObj.get("startRes").toString()); |
466 |
5 |
int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString()); |
467 |
5 |
JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs"); |
468 |
|
|
469 |
5 |
ArrayList<SequenceI> grpSeqs = new ArrayList<>(); |
470 |
5 |
if (sequenceRefs.size() > 0) |
471 |
|
{ |
472 |
5 |
Iterator<String> seqHashIter = sequenceRefs.iterator(); |
473 |
25 |
while (seqHashIter.hasNext()) |
474 |
|
{ |
475 |
20 |
String seqHash = seqHashIter.next(); |
476 |
20 |
Sequence sequence = seqMap.get(seqHash); |
477 |
20 |
if (sequence != null) |
478 |
|
{ |
479 |
20 |
grpSeqs.add(sequence); |
480 |
|
} |
481 |
|
} |
482 |
|
} |
483 |
5 |
SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null, |
484 |
|
displayBoxes, displayText, colourText, startRes, endRes); |
485 |
5 |
seqGrp.setColourScheme(ColourSchemeMapper |
486 |
|
.getJalviewColourScheme(colourScheme, seqGrp)); |
487 |
5 |
seqGrp.setShowNonconserved(showNonconserved); |
488 |
5 |
seqGrp.setDescription(description); |
489 |
5 |
this.seqGroups.add(seqGrp); |
490 |
|
|
491 |
|
} |
492 |
|
|
493 |
6 |
for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray |
494 |
10 |
.iterator(); alAnnotIter.hasNext();) |
495 |
|
{ |
496 |
4 |
JSONObject alAnnot = alAnnotIter.next(); |
497 |
4 |
JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations"); |
498 |
4 |
Annotation[] annotations = new Annotation[annotJsonArray.size()]; |
499 |
4 |
int count = 0; |
500 |
4 |
for (Iterator<JSONObject> annotIter = annotJsonArray |
501 |
144 |
.iterator(); annotIter.hasNext();) |
502 |
|
{ |
503 |
140 |
JSONObject annot = annotIter.next(); |
504 |
140 |
if (annot == null) |
505 |
|
{ |
506 |
0 |
annotations[count] = null; |
507 |
|
} |
508 |
|
else |
509 |
|
{ |
510 |
140 |
float val = annot.get("value") == null ? null |
511 |
|
: Float.valueOf(annot.get("value").toString()); |
512 |
140 |
String desc = annot.get("description") == null ? null |
513 |
|
: annot.get("description").toString(); |
514 |
140 |
char ss = annot.get("secondaryStructure") == null |
515 |
|
|| annot.get("secondaryStructure").toString() |
516 |
|
.equalsIgnoreCase("u0000") ? ' ' |
517 |
|
: annot.get("secondaryStructure") |
518 |
|
.toString().charAt(0); |
519 |
140 |
String displayChar = annot.get("displayCharacter") == null ? "" |
520 |
|
: annot.get("displayCharacter").toString(); |
521 |
|
|
522 |
140 |
annotations[count] = new Annotation(displayChar, desc, ss, val); |
523 |
140 |
if (annot.get("colour") != null) |
524 |
|
{ |
525 |
0 |
Color color = ColorUtils |
526 |
|
.parseColourString(annot.get("colour").toString()); |
527 |
0 |
annotations[count].colour = color; |
528 |
|
} |
529 |
|
} |
530 |
140 |
++count; |
531 |
|
} |
532 |
|
|
533 |
4 |
AlignmentAnnotation alignAnnot = new AlignmentAnnotation( |
534 |
|
alAnnot.get("label").toString(), |
535 |
|
alAnnot.get("description").toString(), annotations); |
536 |
4 |
alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 |
537 |
|
: Integer.valueOf(alAnnot.get("graphType").toString()); |
538 |
|
|
539 |
4 |
JSONObject diplaySettings = (JSONObject) alAnnot |
540 |
|
.get("annotationSettings"); |
541 |
4 |
if (diplaySettings != null) |
542 |
|
{ |
543 |
|
|
544 |
2 |
alignAnnot.scaleColLabel = (diplaySettings |
545 |
|
.get("scaleColLabel") == null) ? false |
546 |
|
: Boolean.valueOf(diplaySettings |
547 |
|
.get("scaleColLabel").toString()); |
548 |
2 |
alignAnnot.showAllColLabels = (diplaySettings |
549 |
|
.get("showAllColLabels") == null) ? true |
550 |
|
: Boolean.valueOf(diplaySettings |
551 |
|
.get("showAllColLabels").toString()); |
552 |
2 |
alignAnnot.centreColLabels = (diplaySettings |
553 |
|
.get("centreColLabels") == null) ? true |
554 |
|
: Boolean.valueOf(diplaySettings |
555 |
|
.get("centreColLabels").toString()); |
556 |
2 |
alignAnnot.belowAlignment = (diplaySettings |
557 |
|
.get("belowAlignment") == null) ? false |
558 |
|
: Boolean.valueOf(diplaySettings |
559 |
|
.get("belowAlignment").toString()); |
560 |
2 |
alignAnnot.visible = (diplaySettings.get("visible") == null) |
561 |
|
? true |
562 |
|
: Boolean.valueOf( |
563 |
|
diplaySettings.get("visible").toString()); |
564 |
2 |
alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) |
565 |
|
? true |
566 |
|
: Boolean.valueOf( |
567 |
|
diplaySettings.get("hasIcon").toString()); |
568 |
|
|
569 |
|
} |
570 |
4 |
if (alAnnot.get("score") != null) |
571 |
|
{ |
572 |
2 |
alignAnnot.score = Double |
573 |
|
.valueOf(alAnnot.get("score").toString()); |
574 |
|
} |
575 |
|
|
576 |
4 |
String calcId = (alAnnot.get("calcId") == null) ? "" |
577 |
|
: alAnnot.get("calcId").toString(); |
578 |
4 |
alignAnnot.setCalcId(calcId); |
579 |
4 |
String seqHash = (alAnnot.get("sequenceRef") != null) |
580 |
|
? alAnnot.get("sequenceRef").toString() |
581 |
|
: null; |
582 |
|
|
583 |
4 |
Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null; |
584 |
4 |
if (sequence != null) |
585 |
|
{ |
586 |
0 |
alignAnnot.sequenceRef = sequence; |
587 |
0 |
sequence.addAlignmentAnnotation(alignAnnot); |
588 |
0 |
if (alignAnnot.label.equalsIgnoreCase("T-COFFEE")) |
589 |
|
{ |
590 |
0 |
alignAnnot.createSequenceMapping(sequence, sequence.getStart(), |
591 |
|
false); |
592 |
0 |
sequence.addAlignmentAnnotation(alignAnnot); |
593 |
0 |
alignAnnot.adjustForAlignment(); |
594 |
|
} |
595 |
|
} |
596 |
4 |
alignAnnot.validateRangeAndDisplay(); |
597 |
4 |
this.annotations.add(alignAnnot); |
598 |
|
|
599 |
|
} |
600 |
|
} catch (Exception e) |
601 |
|
{ |
602 |
0 |
e.printStackTrace(); |
603 |
|
} |
604 |
6 |
return this; |
605 |
|
} |
606 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
607 |
6 |
public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)... |
608 |
|
{ |
609 |
6 |
hiddenSeqRefs = new ArrayList<>(); |
610 |
6 |
String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs"); |
611 |
6 |
if (hiddenSeqs != null && !hiddenSeqs.isEmpty()) |
612 |
|
{ |
613 |
4 |
String[] seqRefs = hiddenSeqs.split(";"); |
614 |
4 |
for (String seqRef : seqRefs) |
615 |
|
{ |
616 |
4 |
hiddenSeqRefs.add(seqRef); |
617 |
|
} |
618 |
|
} |
619 |
|
} |
620 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 3 |
Complexity Density: 0.43 |
|
621 |
6 |
public void parseHiddenCols(JSONObject jvSettingsJson)... |
622 |
|
{ |
623 |
6 |
String hiddenCols = (String) jvSettingsJson.get("hiddenCols"); |
624 |
6 |
if (hiddenCols != null && !hiddenCols.isEmpty()) |
625 |
|
{ |
626 |
4 |
hiddenColumns = new HiddenColumns(); |
627 |
4 |
String[] rangeStrings = hiddenCols.split(";"); |
628 |
4 |
for (String rangeString : rangeStrings) |
629 |
|
{ |
630 |
8 |
String[] range = rangeString.split("-"); |
631 |
8 |
hiddenColumns.hideColumns(Integer.valueOf(range[0]), |
632 |
|
Integer.valueOf(range[1])); |
633 |
|
} |
634 |
|
} |
635 |
|
} |
636 |
|
|
|
|
| 77.1% |
Uncovered Elements: 8 (35) |
Complexity: 8 |
Complexity Density: 0.35 |
|
637 |
6 |
@SuppressWarnings("unchecked")... |
638 |
|
private void parseFeatures(JSONArray jsonSeqFeatures) |
639 |
|
{ |
640 |
6 |
if (jsonSeqFeatures != null) |
641 |
|
{ |
642 |
6 |
displayedFeatures = new FeaturesDisplayed(); |
643 |
6 |
for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures |
644 |
26 |
.iterator(); seqFeatureItr.hasNext();) |
645 |
|
{ |
646 |
20 |
JSONObject jsonFeature = seqFeatureItr.next(); |
647 |
20 |
Long begin = (Long) jsonFeature.get("xStart"); |
648 |
20 |
Long end = (Long) jsonFeature.get("xEnd"); |
649 |
20 |
String type = (String) jsonFeature.get("type"); |
650 |
20 |
String featureGrp = (String) jsonFeature.get("featureGroup"); |
651 |
20 |
String description = (String) jsonFeature.get("description"); |
652 |
20 |
String seqRef = (String) jsonFeature.get("sequenceRef"); |
653 |
20 |
Float score = Float.valueOf(jsonFeature.get("score").toString()); |
654 |
|
|
655 |
20 |
Sequence seq = seqMap.get(seqRef); |
656 |
|
|
657 |
|
|
658 |
|
|
659 |
|
|
660 |
20 |
int featureBegin = begin.intValue() == 0 ? 0 : seq |
661 |
|
.findPosition(begin.intValue()); |
662 |
20 |
int featureEnd = end.intValue() == 0 ? 0 : seq.findPosition(end |
663 |
|
.intValue()) - 1; |
664 |
|
|
665 |
20 |
SequenceFeature sequenceFeature = new SequenceFeature(type, |
666 |
|
description, featureBegin, featureEnd, score, featureGrp); |
667 |
|
|
668 |
20 |
JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links"); |
669 |
20 |
if (linksJsonArray != null && linksJsonArray.size() > 0) |
670 |
|
{ |
671 |
0 |
Iterator<String> linkList = linksJsonArray.iterator(); |
672 |
0 |
while (linkList.hasNext()) |
673 |
|
{ |
674 |
0 |
String link = linkList.next(); |
675 |
0 |
sequenceFeature.addLink(link); |
676 |
|
} |
677 |
|
} |
678 |
|
|
679 |
20 |
seq.addSequenceFeature(sequenceFeature); |
680 |
20 |
displayedFeatures.setVisible(type); |
681 |
|
} |
682 |
|
} |
683 |
|
} |
684 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
685 |
4 |
@Override... |
686 |
|
public String getGlobalColourScheme() |
687 |
|
{ |
688 |
4 |
return globalColourScheme; |
689 |
|
} |
690 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
691 |
0 |
public void setGlobalColorScheme(String globalColourScheme)... |
692 |
|
{ |
693 |
0 |
this.globalColourScheme = globalColourScheme; |
694 |
|
} |
695 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
696 |
2 |
@Override... |
697 |
|
public FeaturesDisplayedI getDisplayedFeatures() |
698 |
|
{ |
699 |
2 |
return displayedFeatures; |
700 |
|
} |
701 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
702 |
3 |
public void setDisplayedFeatures(FeaturesDisplayedI displayedFeatures)... |
703 |
|
{ |
704 |
3 |
this.displayedFeatures = displayedFeatures; |
705 |
|
} |
706 |
|
|
|
|
| 95.2% |
Uncovered Elements: 1 (21) |
Complexity: 5 |
Complexity Density: 0.33 |
|
707 |
4 |
@Override... |
708 |
|
public void configureForView(AlignmentViewPanel avpanel) |
709 |
|
{ |
710 |
4 |
if (avpanel == null) |
711 |
|
{ |
712 |
1 |
return; |
713 |
|
} |
714 |
3 |
super.configureForView(avpanel); |
715 |
3 |
AlignViewportI viewport = avpanel.getAlignViewport(); |
716 |
3 |
AlignmentI alignment = viewport.getAlignment(); |
717 |
3 |
AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); |
718 |
|
|
719 |
3 |
seqGroups = alignment.getGroups(); |
720 |
3 |
fr = avpanel.cloneFeatureRenderer(); |
721 |
|
|
722 |
|
|
723 |
3 |
if (annots != null) |
724 |
|
{ |
725 |
3 |
for (AlignmentAnnotation annot : annots) |
726 |
|
{ |
727 |
14 |
if (annot != null && !annot.autoCalculated) |
728 |
|
{ |
729 |
2 |
annotations.add(annot); |
730 |
|
} |
731 |
|
} |
732 |
|
} |
733 |
3 |
globalColourScheme = ColourSchemeProperty |
734 |
|
.getColourName(viewport.getGlobalColourScheme()); |
735 |
3 |
setDisplayedFeatures(viewport.getFeaturesDisplayed()); |
736 |
3 |
showSeqFeatures = viewport.isShowSequenceFeatures(); |
737 |
|
|
738 |
|
} |
739 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
740 |
2 |
@Override... |
741 |
|
public boolean isShowSeqFeatures() |
742 |
|
{ |
743 |
2 |
return showSeqFeatures; |
744 |
|
} |
745 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
746 |
6 |
public void setShowSeqFeatures(boolean showSeqFeatures)... |
747 |
|
{ |
748 |
6 |
this.showSeqFeatures = showSeqFeatures; |
749 |
|
} |
750 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
751 |
0 |
public Vector<AlignmentAnnotation> getAnnotations()... |
752 |
|
{ |
753 |
0 |
return annotations; |
754 |
|
} |
755 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
756 |
3 |
@Override... |
757 |
|
public HiddenColumns getHiddenColumns() |
758 |
|
{ |
759 |
3 |
return hiddenColumns; |
760 |
|
} |
761 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
762 |
0 |
public void setHiddenColumns(HiddenColumns hidden)... |
763 |
|
{ |
764 |
0 |
this.hiddenColumns = hidden; |
765 |
|
} |
766 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
|
767 |
4 |
@Override... |
768 |
|
public SequenceI[] getHiddenSequences() |
769 |
|
{ |
770 |
4 |
if (hiddenSequences == null || hiddenSequences.isEmpty()) |
771 |
|
{ |
772 |
1 |
return new SequenceI[] {}; |
773 |
|
} |
774 |
3 |
synchronized (hiddenSequences) |
775 |
|
{ |
776 |
3 |
return hiddenSequences.toArray(new SequenceI[hiddenSequences.size()]); |
777 |
|
} |
778 |
|
} |
779 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
780 |
0 |
public void setHiddenSequences(ArrayList<SequenceI> hiddenSequences)... |
781 |
|
{ |
782 |
0 |
this.hiddenSequences = hiddenSequences; |
783 |
|
} |
784 |
|
|
|
|
| 0% |
Uncovered Elements: 20 (20) |
Complexity: 10 |
Complexity Density: 1 |
|
785 |
|
public class JSONExportSettings |
786 |
|
{ |
787 |
|
private boolean exportSequence; |
788 |
|
|
789 |
|
private boolean exportSequenceFeatures; |
790 |
|
|
791 |
|
private boolean exportAnnotations; |
792 |
|
|
793 |
|
private boolean exportGroups; |
794 |
|
|
795 |
|
private boolean exportJalviewSettings; |
796 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
797 |
0 |
public boolean isExportSequence()... |
798 |
|
{ |
799 |
0 |
return exportSequence; |
800 |
|
} |
801 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
802 |
0 |
public void setExportSequence(boolean exportSequence)... |
803 |
|
{ |
804 |
0 |
this.exportSequence = exportSequence; |
805 |
|
} |
806 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
807 |
0 |
public boolean isExportSequenceFeatures()... |
808 |
|
{ |
809 |
0 |
return exportSequenceFeatures; |
810 |
|
} |
811 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
812 |
0 |
public void setExportSequenceFeatures(boolean exportSequenceFeatures)... |
813 |
|
{ |
814 |
0 |
this.exportSequenceFeatures = exportSequenceFeatures; |
815 |
|
} |
816 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
817 |
0 |
public boolean isExportAnnotations()... |
818 |
|
{ |
819 |
0 |
return exportAnnotations; |
820 |
|
} |
821 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
822 |
0 |
public void setExportAnnotations(boolean exportAnnotations)... |
823 |
|
{ |
824 |
0 |
this.exportAnnotations = exportAnnotations; |
825 |
|
} |
826 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
827 |
0 |
public boolean isExportGroups()... |
828 |
|
{ |
829 |
0 |
return exportGroups; |
830 |
|
} |
831 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
832 |
0 |
public void setExportGroups(boolean exportGroups)... |
833 |
|
{ |
834 |
0 |
this.exportGroups = exportGroups; |
835 |
|
} |
836 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
837 |
0 |
public boolean isExportJalviewSettings()... |
838 |
|
{ |
839 |
0 |
return exportJalviewSettings; |
840 |
|
} |
841 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
842 |
0 |
public void setExportJalviewSettings(boolean exportJalviewSettings)... |
843 |
|
{ |
844 |
0 |
this.exportJalviewSettings = exportJalviewSettings; |
845 |
|
} |
846 |
|
} |
847 |
|
|
848 |
|
|
849 |
|
|
850 |
|
|
851 |
|
|
852 |
|
|
853 |
|
|
854 |
|
|
855 |
|
|
856 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
857 |
0 |
@Override... |
858 |
|
public FeatureSettingsModelI getFeatureColourScheme() |
859 |
|
{ |
860 |
0 |
return new PDBFeatureSettings(); |
861 |
|
} |
862 |
|
} |