import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
- public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, String inFile, String type)
+ public JmolParser(String inFile, DataSourceType sourceType)
- public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, FileParse fp) throws IOException
+ public JmolParser(FileParse fp) throws IOException
viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
null, "-x -o -n", this);
// ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
null, "-x -o -n", this);
// ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
List<SequenceI> prot = new ArrayList<SequenceI>();
PDBChain tmpchain;
String pdbId = (String) ms.getInfo(0, "title");
List<SequenceI> prot = new ArrayList<SequenceI>();
PDBChain tmpchain;
String pdbId = (String) ms.getInfo(0, "title");
- setId(safeName(getDataName()));
+ // always use resource name, not the hardwired file
+ // Does the value of ID get used ? Behaviour needs to be
+ // documented and tested
+ setId(getDataName());
- asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
- secstrcode[p], Float.NaN);
- ssFound = true;
+ asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
+ secstrcode[p], Float.NaN);
+ ssFound = true;