import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureImportSettings;
import jalview.util.Format;
import jalview.util.MessageManager;
{
Viewer viewer = null;
+ public JmolParser(boolean immediate, String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ super(immediate, inFile, sourceType);
+ }
+
public JmolParser(String inFile, DataSourceType sourceType)
throws IOException
{
}
lastID = tmpatom.resNumIns.trim();
}
- xferSettings();
+ if (isParseImmediately())
+ {
+ // configure parsing settings from the static singleton
+ xferSettings();
+ }
makeResidueList();
makeCaBondList();
prot.add(chainseq);
}
- if (StructureImportSettings.isProcessSecondaryStructure())
+ // look at local setting for adding secondary tructure
+ if (predictSecondaryStructure)
{
createAnnotation(chainseq, chain, ms.at);
}
SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
int firstResNum)
{
- char[] seq = sq.getSequence();
+ int length = sq.getLength();
boolean ssFound = false;
- Annotation asecstr[] = new Annotation[seq.length + firstResNum - 1];
- for (int p = 0; p < seq.length; p++)
+ Annotation asecstr[] = new Annotation[length + firstResNum - 1];
+ for (int p = 0; p < length; p++)
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')
{