import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.ext.jmol.JmolParser;
+import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
import java.io.File;
public static final String[] READABLE_FORMATS = new String[] { "BLC",
"CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
"JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
- IdentifyFile.GFF3File, "HTML", "mmCIF" };
+ IdentifyFile.FeaturesFile, "HTML", "mmCIF" };
/**
* List of readable format file extensions by application in order
*/
public static final String[] READABLE_FNAMES = new String[] { "Fasta",
"Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML",
- PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File,
+ PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.FeaturesFile,
"Jalview", HtmlFile.FILE_DESC, "mmCIF" };
/**
{
// TODO obtain config value from preference settings.
// Set value to 'true' to test PDB processing with Jmol: JAL-1213
- boolean isParseWithJMOL = false;
+ boolean isParseWithJMOL = StructureImportSettings
+ .getDefaultPDBFileParser().equalsIgnoreCase(
+ StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString());
if (isParseWithJMOL)
{
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
alignFile = new jalview.ext.jmol.JmolParser(inFile, type);
}
else
{
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ StructureImportSettings.setShowSeqFeatures(true);
alignFile = new MCview.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, inFile,
type);
}
+ ((StructureFile) alignFile).setDbRefType(format);
}
- else if (format.equals("mmCIF"))
+ else if (format.equalsIgnoreCase("mmCIF"))
{
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
alignFile = new jalview.ext.jmol.JmolParser(inFile, type);
+ ((StructureFile) alignFile).setDbRefType(format);
}
else if (format.equals("STH"))
{
{
alignFile = new RnamlFile(inFile, type);
}
- else if (format.equals(IdentifyFile.GFF3File))
+ else if (format.equals(IdentifyFile.FeaturesFile))
{
- alignFile = new Gff3File(inFile, type);
+ alignFile = new FeaturesFile(true, inFile, type);
}
return buildAlignmentFrom(alignFile);
} catch (Exception e)
boolean isParseWithJMOL = false;
if (isParseWithJMOL)
{
- alignFile = new jalview.ext.jmol.JmolParser(source);
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ alignFile = new JmolParser(source);
}
else
{
+ StructureImportSettings.setShowSeqFeatures(true);
alignFile = new MCview.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, source);
}
+ ((StructureFile) alignFile).setDbRefType(Type.PDB);
}
- else if (format.equals("mmCIF"))
+ else if (format.equalsIgnoreCase("mmCIF"))
{
- alignFile = new jalview.ext.jmol.JmolParser(source);
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ alignFile = new JmolParser(source);
+ ((StructureFile) alignFile).setDbRefType(Type.MMCIF);
}
else if (format.equals("STH"))
{
{
alignFile = new PhylipFile(source);
}
- else if (format.equals(IdentifyFile.GFF3File))
+ else if (format.equals(IdentifyFile.FeaturesFile))
{
- alignFile = new Gff3File(inFile, type);
+ alignFile = new FeaturesFile(inFile, type);
}
else if (format.equals(JSONFile.FILE_DESC))
{
long memf = -r.totalMemory() + r.freeMemory();
long t1 = -System.currentTimeMillis();
AlignmentI al = afa.readFile(args[i], FILE,
- new IdentifyFile().Identify(args[i], FILE));
+ new IdentifyFile().identify(args[i], FILE));
t1 += System.currentTimeMillis();
System.gc();
memf += r.totalMemory() - r.freeMemory();
{
try
{
- String idformat = new jalview.io.IdentifyFile().Identify(file,
+ String idformat = new jalview.io.IdentifyFile().identify(file,
protocol);
if (idformat == null)
{