private boolean _has_autoCalculated;
/**
+ * is to be shown below the alignment - introduced in Jalview
+ * 2.8 for visualizing T-COFFEE alignment scores
+ */
+ private boolean _belowAlignment = true;
+
+ /**
+ * keeps track of state for field: _belowAlignment
+ */
+ private boolean _has_belowAlignment;
+
+ /**
+ * Optional string identifier used to group sets of annotation
+ * produced by a particular calculation. Values are opaque
+ * strings but have semantic meaning to Jalview's renderer,
+ * data importer and calculation system.
+ */
+ private java.lang.String _calcId;
+
+ /**
* Field _annotationElementList.
*/
private java.util.Vector _annotationElementList;
*/
private jalview.schemabinding.version2.ThresholdLine _thresholdLine;
+ /**
+ * Field _propertyList.
+ */
+ private java.util.Vector _propertyList;
+
//----------------/
//- Constructors -/
public Annotation() {
super();
this._annotationElementList = new java.util.Vector();
+ this._propertyList = new java.util.Vector();
}
}
/**
+ *
+ *
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addProperty(
+ final jalview.schemabinding.version2.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.addElement(vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addProperty(
+ final int index,
+ final jalview.schemabinding.version2.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.add(index, vProperty);
+ }
+
+ /**
*/
public void deleteAutoCalculated(
) {
/**
*/
+ public void deleteBelowAlignment(
+ ) {
+ this._has_belowAlignment= false;
+ }
+
+ /**
+ */
public void deleteCentreColLabels(
) {
this._has_centreColLabels= false;
}
/**
+ * Method enumerateProperty.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.Property elements
+ */
+ public java.util.Enumeration enumerateProperty(
+ ) {
+ return this._propertyList.elements();
+ }
+
+ /**
* Method getAnnotationElement.
*
* @param index
}
/**
+ * Returns the value of field 'belowAlignment'. The field
+ * 'belowAlignment' has the following description: is to be
+ * shown below the alignment - introduced in Jalview 2.8 for
+ * visualizing T-COFFEE alignment scores
+ *
+ * @return the value of field 'BelowAlignment'.
+ */
+ public boolean getBelowAlignment(
+ ) {
+ return this._belowAlignment;
+ }
+
+ /**
+ * Returns the value of field 'calcId'. The field 'calcId' has
+ * the following description: Optional string identifier used
+ * to group sets of annotation produced by a particular
+ * calculation. Values are opaque strings but have semantic
+ * meaning to Jalview's renderer, data importer and calculation
+ * system.
+ *
+ * @return the value of field 'CalcId'.
+ */
+ public java.lang.String getCalcId(
+ ) {
+ return this._calcId;
+ }
+
+ /**
* Returns the value of field 'centreColLabels'.
*
* @return the value of field 'CentreColLabels'.
}
/**
+ * Method getProperty.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the
+ * jalview.schemabinding.version2.Property at the given index
+ */
+ public jalview.schemabinding.version2.Property getProperty(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Property) _propertyList.get(index);
+ }
+
+ /**
+ * Method getProperty.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Property[] getProperty(
+ ) {
+ jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0];
+ return (jalview.schemabinding.version2.Property[]) this._propertyList.toArray(array);
+ }
+
+ /**
+ * Method getPropertyCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPropertyCount(
+ ) {
+ return this._propertyList.size();
+ }
+
+ /**
* Returns the value of field 'scaleColLabels'.
*
* @return the value of field 'ScaleColLabels'.
}
/**
+ * Method hasBelowAlignment.
+ *
+ * @return true if at least one BelowAlignment has been added
+ */
+ public boolean hasBelowAlignment(
+ ) {
+ return this._has_belowAlignment;
+ }
+
+ /**
* Method hasCentreColLabels.
*
* @return true if at least one CentreColLabels has been added
}
/**
+ * Returns the value of field 'belowAlignment'. The field
+ * 'belowAlignment' has the following description: is to be
+ * shown below the alignment - introduced in Jalview 2.8 for
+ * visualizing T-COFFEE alignment scores
+ *
+ * @return the value of field 'BelowAlignment'.
+ */
+ public boolean isBelowAlignment(
+ ) {
+ return this._belowAlignment;
+ }
+
+ /**
* Returns the value of field 'centreColLabels'.
*
* @return the value of field 'CentreColLabels'.
}
/**
+ */
+ public void removeAllProperty(
+ ) {
+ this._propertyList.clear();
+ }
+
+ /**
* Method removeAnnotationElement.
*
* @param vAnnotationElement
}
/**
+ * Method removeProperty.
+ *
+ * @param vProperty
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeProperty(
+ final jalview.schemabinding.version2.Property vProperty) {
+ boolean removed = _propertyList.remove(vProperty);
+ return removed;
+ }
+
+ /**
+ * Method removePropertyAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Property removePropertyAt(
+ final int index) {
+ java.lang.Object obj = this._propertyList.remove(index);
+ return (jalview.schemabinding.version2.Property) obj;
+ }
+
+ /**
*
*
* @param index
}
/**
+ * Sets the value of field 'belowAlignment'. The field
+ * 'belowAlignment' has the following description: is to be
+ * shown below the alignment - introduced in Jalview 2.8 for
+ * visualizing T-COFFEE alignment scores
+ *
+ * @param belowAlignment the value of field 'belowAlignment'.
+ */
+ public void setBelowAlignment(
+ final boolean belowAlignment) {
+ this._belowAlignment = belowAlignment;
+ this._has_belowAlignment = true;
+ }
+
+ /**
+ * Sets the value of field 'calcId'. The field 'calcId' has the
+ * following description: Optional string identifier used to
+ * group sets of annotation produced by a particular
+ * calculation. Values are opaque strings but have semantic
+ * meaning to Jalview's renderer, data importer and calculation
+ * system.
+ *
+ * @param calcId the value of field 'calcId'.
+ */
+ public void setCalcId(
+ final java.lang.String calcId) {
+ this._calcId = calcId;
+ }
+
+ /**
* Sets the value of field 'centreColLabels'.
*
* @param centreColLabels the value of field 'centreColLabels'.
}
/**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setProperty(
+ final int index,
+ final jalview.schemabinding.version2.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+ }
+
+ this._propertyList.set(index, vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param vPropertyArray
+ */
+ public void setProperty(
+ final jalview.schemabinding.version2.Property[] vPropertyArray) {
+ //-- copy array
+ _propertyList.clear();
+
+ for (int i = 0; i < vPropertyArray.length; i++) {
+ this._propertyList.add(vPropertyArray[i]);
+ }
+ }
+
+ /**
* Sets the value of field 'scaleColLabels'.
*
* @param scaleColLabels the value of field 'scaleColLabels'.
git://source.jalview.org / jalview.git / blobdiff