- /**
- * set to true to add chain alignment annotation as visible annotation.
- */
- boolean VisibleChainAnnotation=false;
- public PDBfile(String inFile, String inType)
- throws IOException
+ public PDBfile(boolean addAlignmentAnnotations,
+ boolean predictSecondaryStructure, boolean externalSecStr)
+ {
+ super();
+ addSettings(addAlignmentAnnotations, predictSecondaryStructure,
+ externalSecStr);
+ }
+
+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, String file, String protocol)
+ throws IOException
+ {
+ super(false, file, protocol);
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+ doParse();
+ }
+
+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr,
+ FileParse source) throws IOException