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 CONTACT_MAP = 4;
+
+ /**
+ * property that when set to non-empty string disables display of column groups defined on the contact matrix
+ */
+ public static final String CONTACT_MAP_NOGROUPS = "CMNOGRPS";
+
public boolean belowAlignment = true;
public SequenceGroup groupRef = null;
: annotations[index + offset].displayCharacter == null
|| annotations[index
+ offset].displayCharacter
- .length() == 0
- ? annotations[index
- + offset].secondaryStructure
- : annotations[index
- + offset].displayCharacter
- .charAt(0));
+ .length() == 0
+ ? annotations[index
+ + offset].secondaryStructure
+ : annotations[index
+ + offset].displayCharacter
+ .charAt(0));
}
@Override
{
this.sequenceMapping = null;
}
+
}
// TODO: check if we need to do this: JAL-952
// if (this.isrna=annotation.isrna)
}
return aa;
}
+
+ /**
+ * convenience method to check for the 'CONTACT_MAP_NOGROUPS' property for this alignment annotation row
+ * @return true if no CONTACT_MAP_NOGROUPS property is found, or it is set to ""
+ */
+ public boolean isShowGroupsForContactMatrix()
+ {
+ return getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS)==null || "".equals(getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS));
+ }
+ /**
+ * set the 'CONTACT_MAP_NOGROUPS' property for this alignment annotation row
+ * @see isShowGroupsForContactMatrix
+ */
+ public void setShowGroupsForContactMatrix(boolean showGroups)
+ {
+ setProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS, showGroups ? "" : "nogroups");
+ }
+
}