+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, String dataObject,
+ DataSourceType sourceType) throws IOException
+ {
+ super(false, dataObject, sourceType);
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+ doParse();
+ }
+
+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, FileParse source) throws IOException
+ {
+ super(false, source);
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+ doParse();
+ }
+
+ @Override
+ public String print(SequenceI[] seqs, boolean jvSuffix)