2 * This class was automatically generated with
3 * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
8 package jalview.schemabinding.version2;
10 //---------------------------------/
11 //- Imported classes and packages -/
12 //---------------------------------/
14 import org.exolab.castor.xml.Marshaller;
15 import org.exolab.castor.xml.Unmarshaller;
18 * Class StructureState.
20 * @version $Revision$ $Date$
22 public class StructureState implements java.io.Serializable {
25 //--------------------------/
26 //- Class/Member Variables -/
27 //--------------------------/
30 * internal content storage
32 private java.lang.String _content = "";
37 private boolean _visible;
40 * keeps track of state for field: _visible
42 private boolean _has_visible;
50 * keeps track of state for field: _xpos
52 private boolean _has_xpos;
60 * keeps track of state for field: _ypos
62 private boolean _has_ypos;
70 * keeps track of state for field: _width
72 private boolean _has_width;
80 * keeps track of state for field: _height
82 private boolean _has_height;
85 * additional identifier which properly disambiguates
86 * the structure view from any other view with the same
87 * attributes. This is not an ID,
88 * because it is possible to have many references to the same
89 * physical structure view
90 * from different sequences in an alignment. A structureState
91 * element citing the same
92 * viewId will appear for each instance.
94 private java.lang.String _viewId;
97 * Flag set if the alignment panel containing this JSeq should
98 * be included in those used to perform a structure
99 * superposition (since Jalview 2.7).
102 private boolean _alignwithAlignPanel = true;
105 * keeps track of state for field: _alignwithAlignPanel
107 private boolean _has_alignwithAlignPanel;
110 * Flag set if the alignment panel containing this JSeq should
111 * be included in those used to colour its associated sequences
112 * in this structureState(since Jalview 2.7).
115 private boolean _colourwithAlignPanel = true;
118 * keeps track of state for field: _colourwithAlignPanel
120 private boolean _has_colourwithAlignPanel;
127 public StructureState() {
139 public void deleteAlignwithAlignPanel(
141 this._has_alignwithAlignPanel= false;
146 public void deleteColourwithAlignPanel(
148 this._has_colourwithAlignPanel= false;
153 public void deleteHeight(
155 this._has_height= false;
160 public void deleteVisible(
162 this._has_visible= false;
167 public void deleteWidth(
169 this._has_width= false;
174 public void deleteXpos(
176 this._has_xpos= false;
181 public void deleteYpos(
183 this._has_ypos= false;
187 * Returns the value of field 'alignwithAlignPanel'. The field
188 * 'alignwithAlignPanel' has the following description: Flag
189 * set if the alignment panel containing this JSeq should be
190 * included in those used to perform a structure superposition
191 * (since Jalview 2.7).
194 * @return the value of field 'AlignwithAlignPanel'.
196 public boolean getAlignwithAlignPanel(
198 return this._alignwithAlignPanel;
202 * Returns the value of field 'colourwithAlignPanel'. The field
203 * 'colourwithAlignPanel' has the following description: Flag
204 * set if the alignment panel containing this JSeq should be
205 * included in those used to colour its associated sequences in
206 * this structureState(since Jalview 2.7).
209 * @return the value of field 'ColourwithAlignPanel'.
211 public boolean getColourwithAlignPanel(
213 return this._colourwithAlignPanel;
217 * Returns the value of field 'content'. The field 'content'
218 * has the following description: internal content storage
220 * @return the value of field 'Content'.
222 public java.lang.String getContent(
224 return this._content;
228 * Returns the value of field 'height'.
230 * @return the value of field 'Height'.
232 public int getHeight(
238 * Returns the value of field 'viewId'. The field 'viewId' has
239 * the following description: additional identifier which
240 * properly disambiguates
241 * the structure view from any other view with the same
242 * attributes. This is not an ID,
243 * because it is possible to have many references to the same
244 * physical structure view
245 * from different sequences in an alignment. A structureState
246 * element citing the same
247 * viewId will appear for each instance.
249 * @return the value of field 'ViewId'.
251 public java.lang.String getViewId(
257 * Returns the value of field 'visible'.
259 * @return the value of field 'Visible'.
261 public boolean getVisible(
263 return this._visible;
267 * Returns the value of field 'width'.
269 * @return the value of field 'Width'.
277 * Returns the value of field 'xpos'.
279 * @return the value of field 'Xpos'.
287 * Returns the value of field 'ypos'.
289 * @return the value of field 'Ypos'.
297 * Method hasAlignwithAlignPanel.
299 * @return true if at least one AlignwithAlignPanel has been
302 public boolean hasAlignwithAlignPanel(
304 return this._has_alignwithAlignPanel;
308 * Method hasColourwithAlignPanel.
310 * @return true if at least one ColourwithAlignPanel has been
313 public boolean hasColourwithAlignPanel(
315 return this._has_colourwithAlignPanel;
321 * @return true if at least one Height has been added
323 public boolean hasHeight(
325 return this._has_height;
331 * @return true if at least one Visible has been added
333 public boolean hasVisible(
335 return this._has_visible;
341 * @return true if at least one Width has been added
343 public boolean hasWidth(
345 return this._has_width;
351 * @return true if at least one Xpos has been added
353 public boolean hasXpos(
355 return this._has_xpos;
361 * @return true if at least one Ypos has been added
363 public boolean hasYpos(
365 return this._has_ypos;
369 * Returns the value of field 'alignwithAlignPanel'. The field
370 * 'alignwithAlignPanel' has the following description: Flag
371 * set if the alignment panel containing this JSeq should be
372 * included in those used to perform a structure superposition
373 * (since Jalview 2.7).
376 * @return the value of field 'AlignwithAlignPanel'.
378 public boolean isAlignwithAlignPanel(
380 return this._alignwithAlignPanel;
384 * Returns the value of field 'colourwithAlignPanel'. The field
385 * 'colourwithAlignPanel' has the following description: Flag
386 * set if the alignment panel containing this JSeq should be
387 * included in those used to colour its associated sequences in
388 * this structureState(since Jalview 2.7).
391 * @return the value of field 'ColourwithAlignPanel'.
393 public boolean isColourwithAlignPanel(
395 return this._colourwithAlignPanel;
401 * @return true if this object is valid according to the schema
403 public boolean isValid(
407 } catch (org.exolab.castor.xml.ValidationException vex) {
414 * Returns the value of field 'visible'.
416 * @return the value of field 'Visible'.
418 public boolean isVisible(
420 return this._visible;
427 * @throws org.exolab.castor.xml.MarshalException if object is
428 * null or if any SAXException is thrown during marshaling
429 * @throws org.exolab.castor.xml.ValidationException if this
430 * object is an invalid instance according to the schema
433 final java.io.Writer out)
434 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
435 Marshaller.marshal(this, out);
442 * @throws java.io.IOException if an IOException occurs during
444 * @throws org.exolab.castor.xml.ValidationException if this
445 * object is an invalid instance according to the schema
446 * @throws org.exolab.castor.xml.MarshalException if object is
447 * null or if any SAXException is thrown during marshaling
450 final org.xml.sax.ContentHandler handler)
451 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
452 Marshaller.marshal(this, handler);
456 * Sets the value of field 'alignwithAlignPanel'. The field
457 * 'alignwithAlignPanel' has the following description: Flag
458 * set if the alignment panel containing this JSeq should be
459 * included in those used to perform a structure superposition
460 * (since Jalview 2.7).
463 * @param alignwithAlignPanel the value of field
464 * 'alignwithAlignPanel'.
466 public void setAlignwithAlignPanel(
467 final boolean alignwithAlignPanel) {
468 this._alignwithAlignPanel = alignwithAlignPanel;
469 this._has_alignwithAlignPanel = true;
473 * Sets the value of field 'colourwithAlignPanel'. The field
474 * 'colourwithAlignPanel' has the following description: Flag
475 * set if the alignment panel containing this JSeq should be
476 * included in those used to colour its associated sequences in
477 * this structureState(since Jalview 2.7).
480 * @param colourwithAlignPanel the value of field
481 * 'colourwithAlignPanel'.
483 public void setColourwithAlignPanel(
484 final boolean colourwithAlignPanel) {
485 this._colourwithAlignPanel = colourwithAlignPanel;
486 this._has_colourwithAlignPanel = true;
490 * Sets the value of field 'content'. The field 'content' has
491 * the following description: internal content storage
493 * @param content the value of field 'content'.
495 public void setContent(
496 final java.lang.String content) {
497 this._content = content;
501 * Sets the value of field 'height'.
503 * @param height the value of field 'height'.
505 public void setHeight(
507 this._height = height;
508 this._has_height = true;
512 * Sets the value of field 'viewId'. The field 'viewId' has the
513 * following description: additional identifier which properly
515 * the structure view from any other view with the same
516 * attributes. This is not an ID,
517 * because it is possible to have many references to the same
518 * physical structure view
519 * from different sequences in an alignment. A structureState
520 * element citing the same
521 * viewId will appear for each instance.
523 * @param viewId the value of field 'viewId'.
525 public void setViewId(
526 final java.lang.String viewId) {
527 this._viewId = viewId;
531 * Sets the value of field 'visible'.
533 * @param visible the value of field 'visible'.
535 public void setVisible(
536 final boolean visible) {
537 this._visible = visible;
538 this._has_visible = true;
542 * Sets the value of field 'width'.
544 * @param width the value of field 'width'.
546 public void setWidth(
549 this._has_width = true;
553 * Sets the value of field 'xpos'.
555 * @param xpos the value of field 'xpos'.
560 this._has_xpos = true;
564 * Sets the value of field 'ypos'.
566 * @param ypos the value of field 'ypos'.
571 this._has_ypos = true;
578 * @throws org.exolab.castor.xml.MarshalException if object is
579 * null or if any SAXException is thrown during marshaling
580 * @throws org.exolab.castor.xml.ValidationException if this
581 * object is an invalid instance according to the schema
582 * @return the unmarshaled
583 * jalview.schemabinding.version2.StructureState
585 public static jalview.schemabinding.version2.StructureState unmarshal(
586 final java.io.Reader reader)
587 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
588 return (jalview.schemabinding.version2.StructureState) Unmarshaller.unmarshal(jalview.schemabinding.version2.StructureState.class, reader);
594 * @throws org.exolab.castor.xml.ValidationException if this
595 * object is an invalid instance according to the schema
597 public void validate(
599 throws org.exolab.castor.xml.ValidationException {
600 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
601 validator.validate(this);