/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
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);
.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");