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javadoc
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentAnnotation.java
diff --git
a/src/jalview/datamodel/AlignmentAnnotation.java
b/src/jalview/datamodel/AlignmentAnnotation.java
index
78f64ac
..
936ba42
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentAnnotation.java
+++ b/
src/jalview/datamodel/AlignmentAnnotation.java
@@
-45,17
+45,24
@@
public class AlignmentAnnotation
*/
public boolean autoCalculated = false;
*/
public boolean autoCalculated = false;
+ /**
+ * unique ID for this annotation, used to match up the same annotation row
+ * shown in multiple views and alignments
+ */
public String annotationId;
public String annotationId;
+ /**
+ * the sequence this annotation is associated with (or null)
+ */
public SequenceI sequenceRef;
public SequenceI sequenceRef;
- /** DOCUMENT ME!! */
+ /** label shown in dropdown menus and in the annotation label area */
public String label;
public String label;
- /** DOCUMENT ME!! */
+ /** longer description text shown as a tooltip */
public String description;
public String description;
- /** DOCUMENT ME!! */
+ /** Array of annotations placed in the current coordinate system */
public Annotation[] annotations;
public ArrayList<SimpleBP> bps = null;
public Annotation[] annotations;
public ArrayList<SimpleBP> bps = null;
@@
-105,6
+112,9
@@
public class AlignmentAnnotation
// System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
}
// System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
}
+ /**
+ * map of positions in the associated annotation
+ */
public java.util.Hashtable<Integer, Annotation> sequenceMapping;
/** DOCUMENT ME!! */
public java.util.Hashtable<Integer, Annotation> sequenceMapping;
/** DOCUMENT ME!! */