*/
package jalview.io;
+import java.awt.Color;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.util.List;
+import java.util.Vector;
+
import jalview.analysis.AlignSeq;
import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentAnnotation.TFType;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureImportSettings;
-
-import java.awt.Color;
-import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.util.List;
-import java.util.Vector;
-
-import MCview.PDBChain;
+import mc_view.PDBChain;
public abstract class StructureFile extends AlignFile
{
private boolean pdbIdAvailable;
- public StructureFile(String inFile, DataSourceType sourceType)
+ public StructureFile(Object inFile, DataSourceType sourceType)
throws IOException
{
- super(inFile, sourceType);
+ this(inFile, sourceType, null);
+ }
+
+ public StructureFile(Object inFile, DataSourceType sourceType,
+ AlignmentAnnotation.TFType tempfacType) throws IOException
+ {
+ super(inFile, sourceType, tempfacType);
}
public StructureFile(FileParse fp) throws IOException
}
- public StructureFile(boolean parseImmediately, String dataObject,
+ public StructureFile(boolean parseImmediately, Object dataObject,
DataSourceType sourceType) throws IOException
{
super(parseImmediately, dataObject, sourceType);
pdbSequence.setName(getId() + "|" + pdbSequence.getName());
PDBEntry entry = new PDBEntry();
entry.setId(getId());
+ entry.setFakedPDBId(!isPPDBIdAvailable());
entry.setType(getStructureFileType());
if (chain.id != null)
{
StructureImportSettings.setShowSeqFeatures(true);
}
- public PDBChain findChain(String id) throws Exception
+ /**
+ * Answers the first PDBChain found matching the given id, or null if none is
+ * found
+ *
+ * @param id
+ * @return
+ */
+ public PDBChain findChain(String id)
{
for (PDBChain chain : getChains())
{
return chain;
}
}
- throw new Exception("PDB chain not Found!");
+ return null;
}
public void makeResidueList()