import jalview.datamodel.*;
import jalview.io.FileParse;
+import jalview.io.RnamlFile;
+import jalview.ws.jws1.Annotate3D;
public class PDBfile extends jalview.io.AlignFile
{
*/
boolean VisibleChainAnnotation = false;
- public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+ public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
{
super(inFile, inType);
}
- public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+ public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
{
super(source);
}
return null;
}
- public void parse() throws IOException
+ public void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
{
// TODO set the filename sensibly - try using data source name.
id = safeName(getDataName());
if(isRNA(chainseq)==true)
{
System.out.println("this is a PDB format and RNA sequence");
+ Annotate3D an3d = new Annotate3D(id);
+ System.out.println(id);
+ //BufferedWriter r = an3d.getReader();
+
+ BufferedReader in = new BufferedReader(new FileReader("temp.rnaml"));
+
+ String str;
+ while ((str = in.readLine()) != null) {
+ System.out.println(str);
+ System.out.println("toto");
+
+ }
+ String type = "File";
+ RnamlFile rnaml =new RnamlFile("temp.rnaml",type);
+ System.out.println("Create rnamfile object");
+ //rnaml.parse("temp");
+ this.annotations =rnaml.getAnnot();
+
}
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();