- JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
- seqs = jsonFile.getSeqs();
- seqGroups = jsonFile.getSeqGroups();
- annotations = jsonFile.getAnnotations();
- showSeqFeatures = jsonFile.isShowSeqFeatures();
- colourScheme = jsonFile.getColourScheme();
+ if (content == null)
+ {
+ errormessage = "The html document is not embedded with BioJSON data";
+ throw new IOException(errormessage);
+ }
+ JSONFile jsonFile = new JSONFile().parse(new StringReader(
+ contentFromDiv ? content.text() : content.val()));
+ this.seqs = jsonFile.getSeqs();
+ this.seqGroups = jsonFile.getSeqGroups();
+ this.annotations = jsonFile.getAnnotations();
+ this.showSeqFeatures = jsonFile.isShowSeqFeatures();
+ this.globalColourScheme = jsonFile.getGlobalColourScheme();
+ this.hiddenSequences = jsonFile.getHiddenSequences();
+ this.columnSelection = jsonFile.getColumnSelection();
+ this.displayedFeatures = jsonFile.getDisplayedFeatures();