/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
public class FormatAdapter extends AppletFormatAdapter
{
+ public FormatAdapter()
+ {
+ super();
+ if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+ {
+ annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+ true);
+ localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+ true);
+ serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+ true);
+ }
+ else
+ {
+ // disable all PDB annotation options
+ annotFromStructure = false;
+ localSecondaryStruct = false;
+ serviceSecondaryStruct = false;
+ }
+ }
public String formatSequences(String format, SequenceI[] seqs,
String[] omitHiddenColumns)
{
throws java.io.IOException
{
Alignment al;
- if (format.equals("HTML"))
+ if (format.equals(JSONFile.FILE_DESC))
{
- afile = new HtmlFile(inFile, type);
+ afile = new JSONFile(inFile, type);
al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(al);
+ for (SequenceGroup sg : afile.getSeqGroups())
+ {
+ al.addGroup(sg);
+ }
}
else
{
al = super.readFile(inFile, type, format);
}
-
return al;
}
throws java.io.IOException
{
Alignment al;
- if (format.equals("HTML"))
+ if (format.equals(JSONFile.FILE_DESC))
{
- afile = new HtmlFile(source);
+ afile = new JSONFile(source);
al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(al);
+ afile.addSeqGroups(al);
}
else
{
return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
}
+
}