- 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());
- 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.score = alAnnot.get("score") == null ? null : Double
- .valueOf(alAnnot.get("score").toString());
+ 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());
+
+ Map<String, Object> diplaySettings = (Map<String, Object>) 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();