private boolean _has_showSequenceLogo;
/**
- * Field _ignoreGapsinConsensus.
- */
- private boolean _ignoreGapsinConsensus = true;
-
- /**
- * keeps track of state for field: _ignoreGapsinConsensus
- */
- private boolean _has_ignoreGapsinConsensus;
-
- /**
- * Field _xpos.
- */
- private int _xpos;
-
- /**
- * keeps track of state for field: _xpos
- */
- private boolean _has_xpos;
-
- /**
- * Field _ypos.
- */
- private int _ypos;
-
- /**
- * keeps track of state for field: _ypos
- */
- private boolean _has_ypos;
-
- /**
- * Field _width.
+ * Field _normaliseSequenceLogo.
*/
- private int _width;
+ private boolean _normaliseSequenceLogo = false;
/**
- * keeps track of state for field: _width
+ * keeps track of state for field: _normaliseSequenceLogo
*/
- private boolean _has_width;
+ private boolean _has_normaliseSequenceLogo;
/**
- * Field _height.
+ * Field _ignoreGapsinConsensus.
*/
- private int _height;
+ private boolean _ignoreGapsinConsensus = true;
/**
- * keeps track of state for field: _height
+ * keeps track of state for field: _ignoreGapsinConsensus
*/
- private boolean _has_height;
+ private boolean _has_ignoreGapsinConsensus;
/**
* Field _startRes.
private boolean _has_textColThreshold;
/**
- * unique id used by jalview to synchronize between stored and
- * instantiated views
+ * unique id used by jalview to
+ * synchronize between stored and
+ * instantiated views
*
*/
private java.lang.String _id;
/**
+ * The viewport id of this viewport's (cdna/protein) coding
+ * complement, if any
+ *
+ */
+ private java.lang.String _complementId;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
* Field _annotationColours.
*/
private jalview.schemabinding.version2.AnnotationColours _annotationColours;
*/
private java.util.Vector _hiddenColumnsList;
+ /**
+ * Field _calcIdParamList.
+ */
+ private java.util.Vector _calcIdParamList;
+
//----------------/
//- Constructors -/
public Viewport() {
super();
this._hiddenColumnsList = new java.util.Vector();
+ this._calcIdParamList = new java.util.Vector();
}
/**
*
*
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException {
+ this._calcIdParamList.addElement(vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addCalcIdParam(
+ final int index,
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException {
+ this._calcIdParamList.add(index, vCalcIdParam);
+ }
+
+ /**
+ *
+ *
* @param vHiddenColumns
* @throws java.lang.IndexOutOfBoundsException if the index
* given is outside the bounds of the collection
/**
*/
+ public void deleteNormaliseSequenceLogo(
+ ) {
+ this._has_normaliseSequenceLogo= false;
+ }
+
+ /**
+ */
public void deletePidSelected(
) {
this._has_pidSelected= false;
}
/**
+ * Method enumerateCalcIdParam.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.CalcIdParam elements
+ */
+ public java.util.Enumeration enumerateCalcIdParam(
+ ) {
+ return this._calcIdParamList.elements();
+ }
+
+ /**
* Method enumerateHiddenColumns.
*
* @return an Enumeration over all
}
/**
+ * Method getCalcIdParam.
+ *
+ * @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.CalcIdParam at the given index
+ */
+ public jalview.schemabinding.version2.CalcIdParam getCalcIdParam(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._calcIdParamList.size()) {
+ throw new IndexOutOfBoundsException("getCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.CalcIdParam) _calcIdParamList.get(index);
+ }
+
+ /**
+ * Method getCalcIdParam.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.CalcIdParam[] getCalcIdParam(
+ ) {
+ jalview.schemabinding.version2.CalcIdParam[] array = new jalview.schemabinding.version2.CalcIdParam[0];
+ return (jalview.schemabinding.version2.CalcIdParam[]) this._calcIdParamList.toArray(array);
+ }
+
+ /**
+ * Method getCalcIdParamCount.
+ *
+ * @return the size of this collection
+ */
+ public int getCalcIdParamCount(
+ ) {
+ return this._calcIdParamList.size();
+ }
+
+ /**
* Returns the value of field 'centreColumnLabels'.
*
* @return the value of field 'CentreColumnLabels'.
}
/**
+ * Returns the value of field 'complementId'. The field
+ * 'complementId' has the following description: The viewport
+ * id of this viewport's (cdna/protein) coding complement, if
+ * any
+ *
+ *
+ * @return the value of field 'ComplementId'.
+ */
+ public java.lang.String getComplementId(
+ ) {
+ return this._complementId;
+ }
+
+ /**
* Returns the value of field 'consThreshold'.
*
* @return the value of field 'ConsThreshold'.
/**
* Returns the value of field 'id'. The field 'id' has the
* following description: unique id used by jalview to
- * synchronize between stored and instantiated views
+ * synchronize between stored and
+ * instantiated views
*
*
* @return the value of field 'Id'.
}
/**
+ * Returns the value of field 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean getNormaliseSequenceLogo(
+ ) {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
* Returns the value of field 'pidSelected'.
*
* @return the value of field 'PidSelected'.
}
/**
+ * Method hasNormaliseSequenceLogo.
+ *
+ * @return true if at least one NormaliseSequenceLogo has been
+ * added
+ */
+ public boolean hasNormaliseSequenceLogo(
+ ) {
+ return this._has_normaliseSequenceLogo;
+ }
+
+ /**
* Method hasPidSelected.
*
* @return true if at least one PidSelected has been added
}
/**
+ * Returns the value of field 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean isNormaliseSequenceLogo(
+ ) {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
* Returns the value of field 'pidSelected'.
*
* @return the value of field 'PidSelected'.
/**
*/
+ public void removeAllCalcIdParam(
+ ) {
+ this._calcIdParamList.clear();
+ }
+
+ /**
+ */
public void removeAllHiddenColumns(
) {
this._hiddenColumnsList.clear();
}
/**
+ * Method removeCalcIdParam.
+ *
+ * @param vCalcIdParam
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam) {
+ boolean removed = _calcIdParamList.remove(vCalcIdParam);
+ return removed;
+ }
+
+ /**
+ * Method removeCalcIdParamAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.CalcIdParam removeCalcIdParamAt(
+ final int index) {
+ java.lang.Object obj = this._calcIdParamList.remove(index);
+ return (jalview.schemabinding.version2.CalcIdParam) obj;
+ }
+
+ /**
* Method removeHiddenColumns.
*
* @param vHiddenColumns
}
/**
+ *
+ *
+ * @param index
+ * @param vCalcIdParam
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setCalcIdParam(
+ final int index,
+ final jalview.schemabinding.version2.CalcIdParam vCalcIdParam)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._calcIdParamList.size()) {
+ throw new IndexOutOfBoundsException("setCalcIdParam: Index value '" + index + "' not in range [0.." + (this._calcIdParamList.size() - 1) + "]");
+ }
+
+ this._calcIdParamList.set(index, vCalcIdParam);
+ }
+
+ /**
+ *
+ *
+ * @param vCalcIdParamArray
+ */
+ public void setCalcIdParam(
+ final jalview.schemabinding.version2.CalcIdParam[] vCalcIdParamArray) {
+ //-- copy array
+ _calcIdParamList.clear();
+
+ for (int i = 0; i < vCalcIdParamArray.length; i++) {
+ this._calcIdParamList.add(vCalcIdParamArray[i]);
+ }
+ }
+
+ /**
* Sets the value of field 'centreColumnLabels'.
*
* @param centreColumnLabels the value of field
}
/**
+ * Sets the value of field 'complementId'. The field
+ * 'complementId' has the following description: The viewport
+ * id of this viewport's (cdna/protein) coding complement, if
+ * any
+ *
+ *
+ * @param complementId the value of field 'complementId'.
+ */
+ public void setComplementId(
+ final java.lang.String complementId) {
+ this._complementId = complementId;
+ }
+
+ /**
* Sets the value of field 'consThreshold'.
*
* @param consThreshold the value of field 'consThreshold'.
/**
* Sets the value of field 'id'. The field 'id' has the
* following description: unique id used by jalview to
- * synchronize between stored and instantiated views
+ * synchronize between stored and
+ * instantiated views
*
*
* @param id the value of field 'id'.
}
/**
+ * Sets the value of field 'normaliseSequenceLogo'.
+ *
+ * @param normaliseSequenceLogo the value of field
+ * 'normaliseSequenceLogo'.
+ */
+ public void setNormaliseSequenceLogo(
+ final boolean normaliseSequenceLogo) {
+ this._normaliseSequenceLogo = normaliseSequenceLogo;
+ this._has_normaliseSequenceLogo = true;
+ }
+
+ /**
* Sets the value of field 'pidSelected'.
*
* @param pidSelected the value of field 'pidSelected'.
git://source.jalview.org / jalview.git / blobdiff