AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
alignAnnotPojo.setDescription(annot.description);
alignAnnotPojo.setLabel(annot.label);
- alignAnnotPojo.setScore(annot.score);
+ 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.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)
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
seqMap.put(seqUniqueId, seq);
}
-
parseFeatures(jsonSeqArray);
for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
}
}
SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
- displayBoxes, displayText, colourText,
- startRes, endRes);
+ displayBoxes, displayText, colourText, startRes, endRes);
seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
seqGrp);
seqGrp.setShowNonconserved(showNonconserved);
.hasNext();)
{
JSONObject alAnnot = alAnnotIter.next();
- if (alAnnot == null)
- {
- continue;
- }
-
JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
Annotation[] annotations = new Annotation[annotJsonArray.size()];
int count = 0;
.get("secondaryStructure").toString().charAt(0);
String displayChar = annot.get("displayCharacter") == null ? ""
: annot.get("displayCharacter").toString();
- Color color = annot.get("colour") == null ? Color.white
- : UserColourScheme.getColourFromString(annot.get(
- "colour").toString());
- annotations[count] = new Annotation(displayChar, desc, ss, val,
- color);
+
+ 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;
}
.get("label").toString(), alAnnot.get("description")
.toString(), annotations);
alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
- .valueOf(alAnnot.get("graphType")
- .toString());
+ .valueOf(alAnnot.get("graphType").toString());
JSONObject diplaySettings = (JSONObject) alAnnot
.get("annotationSettings");
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.adjustForAlignment();
}
}
+ alignAnnot.validateRangeAndDisplay();
this.annotations.add(alignAnnot);
+
}
} catch (Exception e)
{