private boolean _has_aligned;
/**
- * Field _id
+ * Primary Key for vamsas object
+ * referencing
+ *
*/
private java.lang.String _id;
/**
- * Field _alignmentAnnotationsList
+ * objects with modifiable=false will
+ * not be modified by a vamsas client
+ * update
+ *
*/
- private java.util.Vector _alignmentAnnotationsList;
+ private boolean _modifiable = true;
+
+ /**
+ * keeps track of state for field: _modifiable
+ */
+ private boolean _has_modifiable;
+
+ /**
+ * This is annotation over the
+ * coordinate frame defined by all
+ * the columns in the alignment.
+ *
+ */
+ private java.util.Vector _alignmentAnnotationList;
/**
* Field _treeList
private java.util.Vector _alignmentSequenceList;
/**
+ * typical properties may be
+ * additional alignment score
+ * objects
+ *
+ */
+ private java.util.Vector _propertyList;
+
+ /**
* Field _provenance
*/
private org.vamsas.objects.core.Provenance _provenance;
public Alignment()
{
super();
- _alignmentAnnotationsList = new Vector();
+ _alignmentAnnotationList = new Vector();
_treeList = new Vector();
_alignmentSequenceList = new Vector();
+ _propertyList = new Vector();
} //-- org.vamsas.objects.core.Alignment()
//-----------/
/**
- * Method addAlignmentAnnotations
+ * Method addAlignmentAnnotation
*
*
*
- * @param vAlignmentAnnotations
+ * @param vAlignmentAnnotation
*/
- public void addAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations vAlignmentAnnotations)
+ public void addAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
throws java.lang.IndexOutOfBoundsException
{
- _alignmentAnnotationsList.addElement(vAlignmentAnnotations);
- } //-- void addAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations)
+ _alignmentAnnotationList.addElement(vAlignmentAnnotation);
+ } //-- void addAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation)
/**
- * Method addAlignmentAnnotations
+ * Method addAlignmentAnnotation
*
*
*
* @param index
- * @param vAlignmentAnnotations
+ * @param vAlignmentAnnotation
*/
- public void addAlignmentAnnotations(int index, org.vamsas.objects.core.AlignmentAnnotations vAlignmentAnnotations)
+ public void addAlignmentAnnotation(int index, org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
throws java.lang.IndexOutOfBoundsException
{
- _alignmentAnnotationsList.insertElementAt(vAlignmentAnnotations, index);
- } //-- void addAlignmentAnnotations(int, org.vamsas.objects.core.AlignmentAnnotations)
+ _alignmentAnnotationList.insertElementAt(vAlignmentAnnotation, index);
+ } //-- void addAlignmentAnnotation(int, org.vamsas.objects.core.AlignmentAnnotation)
/**
* Method addAlignmentSequence
} //-- void addAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence)
/**
+ * Method addProperty
+ *
+ *
+ *
+ * @param vProperty
+ */
+ public void addProperty(org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.addElement(vProperty);
+ } //-- void addProperty(org.vamsas.objects.core.Property)
+
+ /**
+ * Method addProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void addProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _propertyList.insertElementAt(vProperty, index);
+ } //-- void addProperty(int, org.vamsas.objects.core.Property)
+
+ /**
* Method addTree
*
*
} //-- void deleteAligned()
/**
- * Method enumerateAlignmentAnnotations
+ * Method deleteModifiable
+ *
+ */
+ public void deleteModifiable()
+ {
+ this._has_modifiable= false;
+ } //-- void deleteModifiable()
+
+ /**
+ * Method enumerateAlignmentAnnotation
*
*
*
* @return Enumeration
*/
- public java.util.Enumeration enumerateAlignmentAnnotations()
+ public java.util.Enumeration enumerateAlignmentAnnotation()
{
- return _alignmentAnnotationsList.elements();
- } //-- java.util.Enumeration enumerateAlignmentAnnotations()
+ return _alignmentAnnotationList.elements();
+ } //-- java.util.Enumeration enumerateAlignmentAnnotation()
/**
* Method enumerateAlignmentSequence
} //-- java.util.Enumeration enumerateAlignmentSequence()
/**
+ * Method enumerateProperty
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateProperty()
+ {
+ return _propertyList.elements();
+ } //-- java.util.Enumeration enumerateProperty()
+
+ /**
* Method enumerateTree
*
*
}
else if (temp._id != null)
return false;
- if (this._alignmentAnnotationsList != null) {
- if (temp._alignmentAnnotationsList == null) return false;
- else if (!(this._alignmentAnnotationsList.equals(temp._alignmentAnnotationsList)))
+ if (this._modifiable != temp._modifiable)
+ return false;
+ if (this._has_modifiable != temp._has_modifiable)
+ return false;
+ if (this._alignmentAnnotationList != null) {
+ if (temp._alignmentAnnotationList == null) return false;
+ else if (!(this._alignmentAnnotationList.equals(temp._alignmentAnnotationList)))
return false;
}
- else if (temp._alignmentAnnotationsList != null)
+ else if (temp._alignmentAnnotationList != null)
return false;
if (this._treeList != null) {
if (temp._treeList == null) return false;
}
else if (temp._alignmentSequenceList != null)
return false;
+ if (this._propertyList != null) {
+ if (temp._propertyList == null) return false;
+ else if (!(this._propertyList.equals(temp._propertyList)))
+ return false;
+ }
+ else if (temp._propertyList != null)
+ return false;
if (this._provenance != null) {
if (temp._provenance == null) return false;
else if (!(this._provenance.equals(temp._provenance)))
} //-- boolean getAligned()
/**
- * Method getAlignmentAnnotations
+ * Method getAlignmentAnnotation
*
*
*
* @param index
- * @return AlignmentAnnotations
+ * @return AlignmentAnnotation
*/
- public org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations(int index)
+ public org.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int index)
throws java.lang.IndexOutOfBoundsException
{
//-- check bounds for index
- if ((index < 0) || (index > _alignmentAnnotationsList.size())) {
- throw new IndexOutOfBoundsException("getAlignmentAnnotations: Index value '"+index+"' not in range [0.."+_alignmentAnnotationsList.size()+ "]");
+ if ((index < 0) || (index > _alignmentAnnotationList.size())) {
+ throw new IndexOutOfBoundsException("getAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]");
}
- return (org.vamsas.objects.core.AlignmentAnnotations) _alignmentAnnotationsList.elementAt(index);
- } //-- org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations(int)
+ return (org.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
+ } //-- org.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int)
/**
- * Method getAlignmentAnnotations
+ * Method getAlignmentAnnotation
*
*
*
- * @return AlignmentAnnotations
+ * @return AlignmentAnnotation
*/
- public org.vamsas.objects.core.AlignmentAnnotations[] getAlignmentAnnotations()
+ public org.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation()
{
- int size = _alignmentAnnotationsList.size();
- org.vamsas.objects.core.AlignmentAnnotations[] mArray = new org.vamsas.objects.core.AlignmentAnnotations[size];
+ int size = _alignmentAnnotationList.size();
+ org.vamsas.objects.core.AlignmentAnnotation[] mArray = new org.vamsas.objects.core.AlignmentAnnotation[size];
for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.AlignmentAnnotations) _alignmentAnnotationsList.elementAt(index);
+ mArray[index] = (org.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
}
return mArray;
- } //-- org.vamsas.objects.core.AlignmentAnnotations[] getAlignmentAnnotations()
+ } //-- org.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation()
/**
- * Method getAlignmentAnnotationsCount
+ * Method getAlignmentAnnotationCount
*
*
*
* @return int
*/
- public int getAlignmentAnnotationsCount()
+ public int getAlignmentAnnotationCount()
{
- return _alignmentAnnotationsList.size();
- } //-- int getAlignmentAnnotationsCount()
+ return _alignmentAnnotationList.size();
+ } //-- int getAlignmentAnnotationCount()
/**
* Method getAlignmentSequence
} //-- java.lang.String getGapChar()
/**
- * Returns the value of field 'id'.
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
*
* @return String
* @return the value of field 'id'.
} //-- java.lang.String getId()
/**
+ * Returns the value of field 'modifiable'. The field
+ * 'modifiable' has the following description: objects with
+ * modifiable=false will
+ * not be modified by a vamsas client
+ * update
+ *
+ *
+ * @return boolean
+ * @return the value of field 'modifiable'.
+ */
+ public boolean getModifiable()
+ {
+ return this._modifiable;
+ } //-- boolean getModifiable()
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property getProperty(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ } //-- org.vamsas.objects.core.Property getProperty(int)
+
+ /**
+ * Method getProperty
+ *
+ *
+ *
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property[] getProperty()
+ {
+ int size = _propertyList.size();
+ org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Property[] getProperty()
+
+ /**
+ * Method getPropertyCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getPropertyCount()
+ {
+ return _propertyList.size();
+ } //-- int getPropertyCount()
+
+ /**
* Returns the value of field 'provenance'.
*
* @return Provenance
} //-- boolean hasAligned()
/**
+ * Method hasModifiable
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasModifiable()
+ {
+ return this._has_modifiable;
+ } //-- boolean hasModifiable()
+
+ /**
* Method isValid
*
*
} //-- void marshal(org.xml.sax.ContentHandler)
/**
- * Method removeAlignmentAnnotations
+ * Method removeAlignmentAnnotation
*
*
*
* @param index
- * @return AlignmentAnnotations
+ * @return AlignmentAnnotation
*/
- public org.vamsas.objects.core.AlignmentAnnotations removeAlignmentAnnotations(int index)
+ public org.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int index)
{
- java.lang.Object obj = _alignmentAnnotationsList.elementAt(index);
- _alignmentAnnotationsList.removeElementAt(index);
- return (org.vamsas.objects.core.AlignmentAnnotations) obj;
- } //-- org.vamsas.objects.core.AlignmentAnnotations removeAlignmentAnnotations(int)
+ java.lang.Object obj = _alignmentAnnotationList.elementAt(index);
+ _alignmentAnnotationList.removeElementAt(index);
+ return (org.vamsas.objects.core.AlignmentAnnotation) obj;
+ } //-- org.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int)
/**
* Method removeAlignmentSequence
} //-- org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int)
/**
- * Method removeAllAlignmentAnnotations
+ * Method removeAllAlignmentAnnotation
*
*/
- public void removeAllAlignmentAnnotations()
+ public void removeAllAlignmentAnnotation()
{
- _alignmentAnnotationsList.removeAllElements();
- } //-- void removeAllAlignmentAnnotations()
+ _alignmentAnnotationList.removeAllElements();
+ } //-- void removeAllAlignmentAnnotation()
/**
* Method removeAllAlignmentSequence
} //-- void removeAllAlignmentSequence()
/**
+ * Method removeAllProperty
+ *
+ */
+ public void removeAllProperty()
+ {
+ _propertyList.removeAllElements();
+ } //-- void removeAllProperty()
+
+ /**
* Method removeAllTree
*
*/
} //-- void removeAllTree()
/**
+ * Method removeProperty
+ *
+ *
+ *
+ * @param index
+ * @return Property
+ */
+ public org.vamsas.objects.core.Property removeProperty(int index)
+ {
+ java.lang.Object obj = _propertyList.elementAt(index);
+ _propertyList.removeElementAt(index);
+ return (org.vamsas.objects.core.Property) obj;
+ } //-- org.vamsas.objects.core.Property removeProperty(int)
+
+ /**
* Method removeTree
*
*
} //-- void setAligned(boolean)
/**
- * Method setAlignmentAnnotations
+ * Method setAlignmentAnnotation
*
*
*
* @param index
- * @param vAlignmentAnnotations
+ * @param vAlignmentAnnotation
*/
- public void setAlignmentAnnotations(int index, org.vamsas.objects.core.AlignmentAnnotations vAlignmentAnnotations)
+ public void setAlignmentAnnotation(int index, org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
throws java.lang.IndexOutOfBoundsException
{
//-- check bounds for index
- if ((index < 0) || (index > _alignmentAnnotationsList.size())) {
- throw new IndexOutOfBoundsException("setAlignmentAnnotations: Index value '"+index+"' not in range [0.."+_alignmentAnnotationsList.size()+ "]");
+ if ((index < 0) || (index > _alignmentAnnotationList.size())) {
+ throw new IndexOutOfBoundsException("setAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]");
}
- _alignmentAnnotationsList.setElementAt(vAlignmentAnnotations, index);
- } //-- void setAlignmentAnnotations(int, org.vamsas.objects.core.AlignmentAnnotations)
+ _alignmentAnnotationList.setElementAt(vAlignmentAnnotation, index);
+ } //-- void setAlignmentAnnotation(int, org.vamsas.objects.core.AlignmentAnnotation)
/**
- * Method setAlignmentAnnotations
+ * Method setAlignmentAnnotation
*
*
*
- * @param alignmentAnnotationsArray
+ * @param alignmentAnnotationArray
*/
- public void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations[] alignmentAnnotationsArray)
+ public void setAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation[] alignmentAnnotationArray)
{
//-- copy array
- _alignmentAnnotationsList.removeAllElements();
- for (int i = 0; i < alignmentAnnotationsArray.length; i++) {
- _alignmentAnnotationsList.addElement(alignmentAnnotationsArray[i]);
+ _alignmentAnnotationList.removeAllElements();
+ for (int i = 0; i < alignmentAnnotationArray.length; i++) {
+ _alignmentAnnotationList.addElement(alignmentAnnotationArray[i]);
}
- } //-- void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations)
+ } //-- void setAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation)
/**
* Method setAlignmentSequence
} //-- void setGapChar(java.lang.String)
/**
- * Sets the value of field 'id'.
+ * Sets the value of field 'id'. The field 'id' has the
+ * following description: Primary Key for vamsas object
+ * referencing
+ *
*
* @param id the value of field 'id'.
*/
} //-- void setId(java.lang.String)
/**
+ * Sets the value of field 'modifiable'. The field 'modifiable'
+ * has the following description: objects with modifiable=false
+ * will
+ * not be modified by a vamsas client
+ * update
+ *
+ *
+ * @param modifiable the value of field 'modifiable'.
+ */
+ public void setModifiable(boolean modifiable)
+ {
+ this._modifiable = modifiable;
+ this._has_modifiable = true;
+ } //-- void setModifiable(boolean)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param index
+ * @param vProperty
+ */
+ public void setProperty(int index, org.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _propertyList.size())) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
+ }
+ _propertyList.setElementAt(vProperty, index);
+ } //-- void setProperty(int, org.vamsas.objects.core.Property)
+
+ /**
+ * Method setProperty
+ *
+ *
+ *
+ * @param propertyArray
+ */
+ public void setProperty(org.vamsas.objects.core.Property[] propertyArray)
+ {
+ //-- copy array
+ _propertyList.removeAllElements();
+ for (int i = 0; i < propertyArray.length; i++) {
+ _propertyList.addElement(propertyArray[i]);
+ }
+ } //-- void setProperty(org.vamsas.objects.core.Property)
+
+ /**
* Sets the value of field 'provenance'.
*
* @param provenance the value of field 'provenance'.
git://source.jalview.org / vamsas.git / blobdiff