import jalview.analysis.Rna;
import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.analysis.WUSSParseException;
+import jalview.structure.StructureImportSettings;
/**
* DOCUMENT ME!
*/
public class AlignmentAnnotation
{
+
private static final String ANNOTATION_ID_PREFIX = "ann";
/*
private long invalidrnastruc = -2;
/**
+ * the type of temperature factor plot (if it is one)
+ */
+ private StructureImportSettings.TFType tfType = StructureImportSettings.TFType.DEFAULT;
+
+ public void setTFType(StructureImportSettings.TFType t)
+ {
+ tfType = t;
+ }
+
+ public StructureImportSettings.TFType getTFType()
+ {
+ return tfType;
+ }
+
+ /**
* Updates the _rnasecstr field Determines the positions that base pair and
* the positions of helices based on secondary structure from a Stockholm file
*
public static final int LINE_GRAPH = 2;
- public static final int CUSTOMRENDERER = 4;
+ public static final int CONTACT_MAP = 4;
public boolean belowAlignment = true;
{
this.sequenceMapping = null;
}
+
}
// TODO: check if we need to do this: JAL-952
// if (this.isrna=annotation.isrna)