+ private boolean processSecondaryStructure = false,
+ secStructServices = false, addTempFacAnnot = false;
+
+ /**
+ * @return true if will try to use external services for processing secondary
+ * structure
+ */
+ public boolean isSecStructServices()
+ {
+ return secStructServices;
+ }
+
+ /**
+ * control use of external services for processing secondary structure
+ *
+ * @param secStructServices
+ */
+ public void setSecStructServices(boolean secStructServices)
+ {
+ this.secStructServices = secStructServices;
+ }
+
+ /**
+ * flag controlling addition of any kind of structural annotation
+ *
+ * @return true if temperature factor annotation will be added
+ */
+ public boolean isAddTempFacAnnot()
+ {
+ return addTempFacAnnot;
+ }
+
+ /**
+ * set flag controlling addition of structural annotation
+ *
+ * @param addTempFacAnnot
+ */
+ public void setAddTempFacAnnot(boolean addTempFacAnnot)
+ {
+ this.addTempFacAnnot = addTempFacAnnot;
+ }
+
+ /**
+ *
+ * @return if true, the structure manager will attempt to add secondary
+ * structure lines for unannotated sequences
+ */
+
+ public boolean isProcessSecondaryStructure()
+ {
+ return processSecondaryStructure;
+ }
+
+ /**
+ * Control whether structure manager will try to annotate mapped sequences
+ * with secondary structure from PDB data.
+ *
+ * @param enable
+ */
+ public void setProcessSecondaryStructure(boolean enable)
+ {
+ processSecondaryStructure = enable;
+ }
+