package jalview.io;
import jalview.analysis.AlignSeq;
+import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
this.predictSecondaryStructure = predictSecondaryStructure;
this.externalSecondaryStructure = externalSecStr;
}
+
+ public void xferSettings()
+ {
+ this.visibleChainAnnotation = StructureViewSettings
+ .isVisibleChainAnnotation();
+ this.predictSecondaryStructure = StructureViewSettings
+ .isPredictSecondaryStructure();
+ this.externalSecondaryStructure = StructureViewSettings
+ .isExternalSecondaryStructure();
+
+ }
+
public StructureFile(boolean parseImmediately, String inFile, String type)
throws IOException
{
final Constructor constructor = cl
.getConstructor(new Class[] {
boolean.class, boolean.class, boolean.class, FileParse.class });
- final Object[] args = new Object[] { true, true, true,
+ final Object[] args = new Object[] { visibleChainAnnotation,
+ predictSecondaryStructure, externalSecondaryStructure,
new FileParse(getDataName(),
type) };
StructureViewSettings.setShowSeqFeatures(false);
- StructureViewSettings.setPredictSecondaryStructure(true);
+ StructureViewSettings.setVisibleChainAnnotation(false);
+ StructureViewSettings
+ .setPredictSecondaryStructure(predictSecondaryStructure);
+ StructureViewSettings
+ .setExternalSecondaryStructure(externalSecondaryStructure);
Object jmf = constructor.newInstance(args);
AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
"getSeqsAsArray", new Class[] {}).invoke(jmf));
{
this.dbRefType = dbRefType;
}
+
+ /**
+ * Returns a descriptor for suitable feature display settings with
+ * <ul>
+ * <li>ResNums or insertions features visible</li>
+ * <li>insertions features coloured red</li>
+ * <li>ResNum features coloured by label</li>
+ * <li>Insertions displayed above (on top of) ResNums</li>
+ * </ul>
+ */
+ @Override
+ public FeatureSettingsModelI getFeatureColourScheme()
+ {
+ return new PDBFeatureSettings();
+ }
}