import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
import java.awt.Color;
import java.io.IOException;
private String id;
private String dbRefType;
+
/**
* set to true to add derived sequence annotations (temp factor read from
* file, or computed secondary structure) to the alignment
public void xferSettings()
{
- this.visibleChainAnnotation = StructureViewSettings
+ this.visibleChainAnnotation = StructureImportSettings
.isVisibleChainAnnotation();
- this.predictSecondaryStructure = StructureViewSettings
+ this.predictSecondaryStructure = StructureImportSettings
.isPredictSecondaryStructure();
- this.externalSecondaryStructure = StructureViewSettings
+ this.externalSecondaryStructure = StructureImportSettings
.isExternalSecondaryStructure();
}
- public StructureFile(boolean parseImmediately, String inFile, String type)
+ public StructureFile(boolean parseImmediately, String dataObject, String type)
throws IOException
{
- super(parseImmediately, inFile, type);
+ super(parseImmediately, dataObject, type);
}
public StructureFile(boolean a, FileParse fp) throws IOException
sourceDBRef.setSource(DBRefSource.PDB);
sourceDBRef.setStartRes(pdbSequence.getStart());
sourceDBRef.setEndRes(pdbSequence.getEnd());
-
- SequenceI chainseq = pdbSequence.deriveSequence();
- chainseq.setSourceDBRef(sourceDBRef);
- chainseq.addPDBId(entry);
- chainseq.addDBRef(sourceDBRef);
-
+ pdbSequence.setSourceDBRef(sourceDBRef);
+ pdbSequence.addPDBId(entry);
+ pdbSequence.addDBRef(sourceDBRef);
+ SequenceI chainseq = pdbSequence;
seqs.addElement(chainseq);
-
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
if (chainannot != null && visibleChainAnnotation)
@SuppressWarnings("unchecked")
protected void replaceAndUpdateChains(List<SequenceI> prot,
- AlignmentI al,
- String pep, boolean b)
+ AlignmentI al, String pep, boolean b)
{
List<List<? extends Object>> replaced = AlignSeq
.replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
}
@SuppressWarnings({ "unchecked", "rawtypes" })
- private void processWithJmolParser(List<SequenceI> prot)
- throws Exception
+ private void processWithJmolParser(List<SequenceI> prot) throws Exception
{
try
{
Class cl = Class.forName("jalview.ext.jmol.JmolParser");
if (cl != null)
{
- final Constructor constructor = cl
-.getConstructor(new Class[] {
+ final Constructor constructor = cl.getConstructor(new Class[] {
boolean.class, boolean.class, boolean.class, FileParse.class });
final Object[] args = new Object[] { visibleChainAnnotation,
predictSecondaryStructure, externalSecondaryStructure,
- new FileParse(getDataName(),
- type) };
+ new FileParse(getDataName(), type) };
- StructureViewSettings.setShowSeqFeatures(false);
- StructureViewSettings.setVisibleChainAnnotation(false);
- StructureViewSettings
+ StructureImportSettings.setShowSeqFeatures(false);
+ StructureImportSettings.setVisibleChainAnnotation(false);
+ StructureImportSettings
.setPredictSecondaryStructure(predictSecondaryStructure);
- StructureViewSettings
+ StructureImportSettings
.setExternalSecondaryStructure(externalSecondaryStructure);
Object jmf = constructor.newInstance(args);
AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
} catch (ClassNotFoundException q)
{
}
+ StructureImportSettings.setShowSeqFeatures(true);
}
public PDBChain findChain(String id) throws Exception
{
for (PDBChain chain : getChains())
{
- if (chain.id.equalsIgnoreCase(id))
+ if (chain.id.equals(id))
{
return chain;
}