import jalview.api.FeatureRenderer;
import jalview.api.FeaturesDisplayedI;
import jalview.bin.BuildDetails;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
import jalview.json.binding.biojson.v1.AlignmentPojo;
+import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
import jalview.json.binding.biojson.v1.AnnotationPojo;
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
import jalview.json.binding.biojson.v1.SequenceGrpPojo;
import jalview.json.binding.biojson.v1.SequencePojo;
-import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import java.awt.Color;
public class JSONFile extends AlignFile implements ComplexAlignFile
{
- private ColourSchemeI colourScheme;
-
private static String version = new BuildDetails().getVersion();
private String webstartUrl = "http://www.jalview.org/services/launchApp";
public static final String FILE_DESC = "JSON";
- private String globalColorScheme;
+ private String globalColourScheme;
private boolean showSeqFeatures;
private ArrayList<SequenceI> hiddenSequences;
+ private final static String TCOFFEE_SCORE = "TCoffeeScore";
+
public JSONFile()
{
super();
jsonSeqPojo.setSeq(seq.getSequenceAsString());
jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
}
- jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
+ jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
jsonAlignmentPojo.getAppSettings().put("application", application);
jsonAlignmentPojo.getAppSettings().put("version", version);
jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
jsonAlignmentPojo
.setAlignAnnotation(annotationToJsonPojo(annotations));
}
+ else
+ {
+ // These color schemes require annotation, disable them if annotations
+ // are not exported
+ if (globalColourScheme.equalsIgnoreCase("RNA Helices")
+ || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
+ {
+ jsonAlignmentPojo.setGlobalColorScheme("None");
+ }
+ }
if (exportSettings.isExportFeatures())
{
AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
alignAnnotPojo.setDescription(annot.description);
alignAnnotPojo.setLabel(annot.label);
+ if (!Double.isNaN(annot.score))
+ {
+ alignAnnotPojo.setScore(annot.score);
+ }
+ alignAnnotPojo.setCalcId(annot.getCalcId());
+ alignAnnotPojo.setGraphType(annot.graph);
+
+ AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
+ annotSetting.setBelowAlignment(annot.belowAlignment);
+ annotSetting.setCentreColLabels(annot.centreColLabels);
+ annotSetting.setScaleColLabel(annot.scaleColLabel);
+ annotSetting.setShowAllColLabels(annot.showAllColLabels);
+ annotSetting.setVisible(annot.visible);
+ annotSetting.setHasIcon(annot.hasIcons);
+ alignAnnotPojo.setAnnotationSettings(annotSetting);
+ SequenceI refSeq = annot.sequenceRef;
+ if (refSeq != null)
+ {
+ alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
+ }
for (Annotation annotation : annot.annotations)
{
AnnotationPojo annotationPojo = new AnnotationPojo();
annotationPojo.setValue(annotation.value);
annotationPojo
.setSecondaryStructure(annotation.secondaryStructure);
- annotationPojo.setDisplayCharacter(annotation.displayCharacter);
+ String displayChar = annotation.displayCharacter == null ? null
+ : annotation.displayCharacter;
+ // System.out.println("--------------------->[" + displayChar + "]");
+ annotationPojo.setDisplayCharacter(displayChar);
+ if (annotation.colour != null)
+ {
+ annotationPojo.setColour(jalview.util.Format
+ .getHexString(annotation.colour));
+ }
alignAnnotPojo.getAnnotations().add(annotationPojo);
}
else
{
- alignAnnotPojo.getAnnotations().add(annotationPojo);
+ if (annot.getCalcId() != null
+ && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
+ {
+ // do nothing
+ }
+ else
+ {
+ alignAnnotPojo.getAnnotations().add(annotationPojo);
+ }
}
}
jsonAnnotations.add(alignAnnotPojo);
@SuppressWarnings("unchecked")
public JSONFile parse(Reader jsonAlignmentString)
{
- String jsColourScheme = null;
try
{
JSONParser jsonParser = new JSONParser();
if (jvSettingsJsonObj != null)
{
- jsColourScheme = (String) jvSettingsJsonObj
+ globalColourScheme = (String) jvSettingsJsonObj
.get("globalColorScheme");
Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
"showSeqFeatures").toString());
seqMap.put(seqUniqueId, seq);
}
- if (jsColourScheme != null)
- {
- setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
- jsColourScheme,
- new Alignment(seqs.toArray(new SequenceI[0]))));
- }
+
parseFeatures(jsonSeqArray);
for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
: annot.get("displayCharacter").toString();
annotations[count] = new Annotation(displayChar, desc, ss, val);
+ if (annot.get("colour") != null)
+ {
+ Color color = UserColourScheme.getColourFromString(annot.get(
+ "colour").toString());
+ annotations[count].colour = color;
+ }
}
++count;
}
AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
.get("label").toString(), alAnnot.get("description")
.toString(), annotations);
+ alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
+ .valueOf(alAnnot.get("graphType")
+ .toString());
+
+ JSONObject diplaySettings = (JSONObject) alAnnot
+ .get("annotationSettings");
+ if (diplaySettings != null)
+ {
+
+ alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
+ : Boolean.valueOf(diplaySettings.get("scaleColLabel")
+ .toString());
+ alignAnnot.showAllColLabels = (diplaySettings
+ .get("showAllColLabels") == null) ? true : Boolean
+ .valueOf(diplaySettings.get("showAllColLabels")
+ .toString());
+ alignAnnot.centreColLabels = (diplaySettings
+ .get("centreColLabels") == null) ? true
+ : Boolean.valueOf(diplaySettings.get("centreColLabels")
+ .toString());
+ alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
+ : Boolean.valueOf(diplaySettings.get("belowAlignment")
+ .toString());
+ alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
+ : Boolean.valueOf(diplaySettings.get("visible")
+ .toString());
+ alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
+ : Boolean.valueOf(diplaySettings.get("hasIcon")
+ .toString());
+
+ }
+ if (alAnnot.get("score") != null)
+ {
+ alignAnnot.score = Double
+ .valueOf(alAnnot.get("score").toString());
+ }
+
+ String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
+ "calcId").toString();
+ alignAnnot.setCalcId(calcId);
+ String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
+ .get("sequenceRef").toString() : null;
+
+ Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
+ if (sequence != null)
+ {
+ alignAnnot.sequenceRef = sequence;
+ sequence.addAlignmentAnnotation(alignAnnot);
+ if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
+ {
+ alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
+ false);
+ sequence.addAlignmentAnnotation(alignAnnot);
+ alignAnnot.adjustForAlignment();
+ }
+ }
+ alignAnnot.validateRangeAndDisplay();
this.annotations.add(alignAnnot);
- }
+ }
} catch (Exception e)
{
e.printStackTrace();
}
}
- public String getGlobalColorScheme()
- {
- return globalColorScheme;
- }
-
- public void setGlobalColorScheme(String globalColorScheme)
+ public String getGlobalColourScheme()
{
- this.globalColorScheme = globalColorScheme;
+ return globalColourScheme;
}
- public ColourSchemeI getColourScheme()
+ public void setGlobalColorScheme(String globalColourScheme)
{
- return colourScheme;
- }
-
- public void setColourScheme(ColourSchemeI colourScheme)
- {
- this.colourScheme = colourScheme;
+ this.globalColourScheme = globalColourScheme;
}
@Override
{
if (annot != null && !annot.autoCalculated)
{
- if (!annot.visible)
- {
- continue;
- }
annotations.add(annot);
}
}
- globalColorScheme = ColourSchemeProperty.getColourName(viewport
+ globalColourScheme = ColourSchemeProperty.getColourName(viewport
.getGlobalColourScheme());
setDisplayedFeatures(viewport.getFeaturesDisplayed());
showSeqFeatures = viewport.isShowSequenceFeatures();
git://source.jalview.org / jalview.git / blobdiff