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;
45 * additional identifier which properly disambiguates
46 * the structure view from any other view with the same
47 * attributes. This is not an ID,
48 * because it is possible to have many references to the same
49 * physical structure view
50 * from different sequences in an alignment. A structureState
51 * element citing the same
52 * viewId will appear for each instance.
54 private java.lang.String _viewId;
57 * Flag set if the alignment panel containing this JSeq should
58 * be included in those used to perform a structure
59 * superposition (since Jalview 2.7).
62 private boolean _alignwithAlignPanel = true;
65 * keeps track of state for field: _alignwithAlignPanel
67 private boolean _has_alignwithAlignPanel;
70 * Flag set if the alignment panel containing this JSeq should
71 * be included in those used to colour its associated sequences
72 * in this structureState(since Jalview 2.7).
75 private boolean _colourwithAlignPanel = false;
78 * keeps track of state for field: _colourwithAlignPanel
80 private boolean _has_colourwithAlignPanel;
83 * Flag set if the structure display is coloured by the Jmol
84 * state, rather than by one or more linked alignment views.
87 private boolean _colourByJmol = true;
90 * keeps track of state for field: _colourByJmol
92 private boolean _has_colourByJmol;
100 * keeps track of state for field: _width
102 private boolean _has_width;
110 * keeps track of state for field: _height
112 private boolean _has_height;
120 * keeps track of state for field: _xpos
122 private boolean _has_xpos;
130 * keeps track of state for field: _ypos
132 private boolean _has_ypos;
139 public StructureState() {
151 public void deleteAlignwithAlignPanel(
153 this._has_alignwithAlignPanel= false;
158 public void deleteColourByJmol(
160 this._has_colourByJmol= false;
165 public void deleteColourwithAlignPanel(
167 this._has_colourwithAlignPanel= false;
172 public void deleteHeight(
174 this._has_height= false;
179 public void deleteVisible(
181 this._has_visible= false;
186 public void deleteWidth(
188 this._has_width= false;
193 public void deleteXpos(
195 this._has_xpos= false;
200 public void deleteYpos(
202 this._has_ypos= false;
206 * Returns the value of field 'alignwithAlignPanel'. The field
207 * 'alignwithAlignPanel' has the following description: Flag
208 * set if the alignment panel containing this JSeq should be
209 * included in those used to perform a structure superposition
210 * (since Jalview 2.7).
213 * @return the value of field 'AlignwithAlignPanel'.
215 public boolean getAlignwithAlignPanel(
217 return this._alignwithAlignPanel;
221 * Returns the value of field 'colourByJmol'. The field
222 * 'colourByJmol' has the following description: Flag set if
223 * the structure display is coloured by the Jmol state, rather
224 * than by one or more linked alignment views.
227 * @return the value of field 'ColourByJmol'.
229 public boolean getColourByJmol(
231 return this._colourByJmol;
235 * Returns the value of field 'colourwithAlignPanel'. The field
236 * 'colourwithAlignPanel' has the following description: Flag
237 * set if the alignment panel containing this JSeq should be
238 * included in those used to colour its associated sequences in
239 * this structureState(since Jalview 2.7).
242 * @return the value of field 'ColourwithAlignPanel'.
244 public boolean getColourwithAlignPanel(
246 return this._colourwithAlignPanel;
250 * Returns the value of field 'content'. The field 'content'
251 * has the following description: internal content storage
253 * @return the value of field 'Content'.
255 public java.lang.String getContent(
257 return this._content;
261 * Returns the value of field 'height'.
263 * @return the value of field 'Height'.
265 public int getHeight(
271 * Returns the value of field 'viewId'. The field 'viewId' has
272 * the following description: additional identifier which
273 * properly disambiguates
274 * the structure view from any other view with the same
275 * attributes. This is not an ID,
276 * because it is possible to have many references to the same
277 * physical structure view
278 * from different sequences in an alignment. A structureState
279 * element citing the same
280 * viewId will appear for each instance.
282 * @return the value of field 'ViewId'.
284 public java.lang.String getViewId(
290 * Returns the value of field 'visible'.
292 * @return the value of field 'Visible'.
294 public boolean getVisible(
296 return this._visible;
300 * Returns the value of field 'width'.
302 * @return the value of field 'Width'.
310 * Returns the value of field 'xpos'.
312 * @return the value of field 'Xpos'.
320 * Returns the value of field 'ypos'.
322 * @return the value of field 'Ypos'.
330 * Method hasAlignwithAlignPanel.
332 * @return true if at least one AlignwithAlignPanel has been
335 public boolean hasAlignwithAlignPanel(
337 return this._has_alignwithAlignPanel;
341 * Method hasColourByJmol.
343 * @return true if at least one ColourByJmol has been added
345 public boolean hasColourByJmol(
347 return this._has_colourByJmol;
351 * Method hasColourwithAlignPanel.
353 * @return true if at least one ColourwithAlignPanel has been
356 public boolean hasColourwithAlignPanel(
358 return this._has_colourwithAlignPanel;
364 * @return true if at least one Height has been added
366 public boolean hasHeight(
368 return this._has_height;
374 * @return true if at least one Visible has been added
376 public boolean hasVisible(
378 return this._has_visible;
384 * @return true if at least one Width has been added
386 public boolean hasWidth(
388 return this._has_width;
394 * @return true if at least one Xpos has been added
396 public boolean hasXpos(
398 return this._has_xpos;
404 * @return true if at least one Ypos has been added
406 public boolean hasYpos(
408 return this._has_ypos;
412 * Returns the value of field 'alignwithAlignPanel'. The field
413 * 'alignwithAlignPanel' has the following description: Flag
414 * set if the alignment panel containing this JSeq should be
415 * included in those used to perform a structure superposition
416 * (since Jalview 2.7).
419 * @return the value of field 'AlignwithAlignPanel'.
421 public boolean isAlignwithAlignPanel(
423 return this._alignwithAlignPanel;
427 * Returns the value of field 'colourByJmol'. The field
428 * 'colourByJmol' has the following description: Flag set if
429 * the structure display is coloured by the Jmol state, rather
430 * than by one or more linked alignment views.
433 * @return the value of field 'ColourByJmol'.
435 public boolean isColourByJmol(
437 return this._colourByJmol;
441 * Returns the value of field 'colourwithAlignPanel'. The field
442 * 'colourwithAlignPanel' has the following description: Flag
443 * set if the alignment panel containing this JSeq should be
444 * included in those used to colour its associated sequences in
445 * this structureState(since Jalview 2.7).
448 * @return the value of field 'ColourwithAlignPanel'.
450 public boolean isColourwithAlignPanel(
452 return this._colourwithAlignPanel;
458 * @return true if this object is valid according to the schema
460 public boolean isValid(
464 } catch (org.exolab.castor.xml.ValidationException vex) {
471 * Returns the value of field 'visible'.
473 * @return the value of field 'Visible'.
475 public boolean isVisible(
477 return this._visible;
484 * @throws org.exolab.castor.xml.MarshalException if object is
485 * null or if any SAXException is thrown during marshaling
486 * @throws org.exolab.castor.xml.ValidationException if this
487 * object is an invalid instance according to the schema
490 final java.io.Writer out)
491 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
492 Marshaller.marshal(this, out);
499 * @throws java.io.IOException if an IOException occurs during
501 * @throws org.exolab.castor.xml.ValidationException if this
502 * object is an invalid instance according to the schema
503 * @throws org.exolab.castor.xml.MarshalException if object is
504 * null or if any SAXException is thrown during marshaling
507 final org.xml.sax.ContentHandler handler)
508 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
509 Marshaller.marshal(this, handler);
513 * Sets the value of field 'alignwithAlignPanel'. The field
514 * 'alignwithAlignPanel' has the following description: Flag
515 * set if the alignment panel containing this JSeq should be
516 * included in those used to perform a structure superposition
517 * (since Jalview 2.7).
520 * @param alignwithAlignPanel the value of field
521 * 'alignwithAlignPanel'.
523 public void setAlignwithAlignPanel(
524 final boolean alignwithAlignPanel) {
525 this._alignwithAlignPanel = alignwithAlignPanel;
526 this._has_alignwithAlignPanel = true;
530 * Sets the value of field 'colourByJmol'. The field
531 * 'colourByJmol' has the following description: Flag set if
532 * the structure display is coloured by the Jmol state, rather
533 * than by one or more linked alignment views.
536 * @param colourByJmol the value of field 'colourByJmol'.
538 public void setColourByJmol(
539 final boolean colourByJmol) {
540 this._colourByJmol = colourByJmol;
541 this._has_colourByJmol = true;
545 * Sets the value of field 'colourwithAlignPanel'. The field
546 * 'colourwithAlignPanel' has the following description: Flag
547 * set if the alignment panel containing this JSeq should be
548 * included in those used to colour its associated sequences in
549 * this structureState(since Jalview 2.7).
552 * @param colourwithAlignPanel the value of field
553 * 'colourwithAlignPanel'.
555 public void setColourwithAlignPanel(
556 final boolean colourwithAlignPanel) {
557 this._colourwithAlignPanel = colourwithAlignPanel;
558 this._has_colourwithAlignPanel = true;
562 * Sets the value of field 'content'. The field 'content' has
563 * the following description: internal content storage
565 * @param content the value of field 'content'.
567 public void setContent(
568 final java.lang.String content) {
569 this._content = content;
573 * Sets the value of field 'height'.
575 * @param height the value of field 'height'.
577 public void setHeight(
579 this._height = height;
580 this._has_height = true;
584 * Sets the value of field 'viewId'. The field 'viewId' has the
585 * following description: additional identifier which properly
587 * the structure view from any other view with the same
588 * attributes. This is not an ID,
589 * because it is possible to have many references to the same
590 * physical structure view
591 * from different sequences in an alignment. A structureState
592 * element citing the same
593 * viewId will appear for each instance.
595 * @param viewId the value of field 'viewId'.
597 public void setViewId(
598 final java.lang.String viewId) {
599 this._viewId = viewId;
603 * Sets the value of field 'visible'.
605 * @param visible the value of field 'visible'.
607 public void setVisible(
608 final boolean visible) {
609 this._visible = visible;
610 this._has_visible = true;
614 * Sets the value of field 'width'.
616 * @param width the value of field 'width'.
618 public void setWidth(
621 this._has_width = true;
625 * Sets the value of field 'xpos'.
627 * @param xpos the value of field 'xpos'.
632 this._has_xpos = true;
636 * Sets the value of field 'ypos'.
638 * @param ypos the value of field 'ypos'.
643 this._has_ypos = true;
650 * @throws org.exolab.castor.xml.MarshalException if object is
651 * null or if any SAXException is thrown during marshaling
652 * @throws org.exolab.castor.xml.ValidationException if this
653 * object is an invalid instance according to the schema
654 * @return the unmarshaled
655 * jalview.schemabinding.version2.StructureState
657 public static jalview.schemabinding.version2.StructureState unmarshal(
658 final java.io.Reader reader)
659 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
660 return (jalview.schemabinding.version2.StructureState) Unmarshaller.unmarshal(jalview.schemabinding.version2.StructureState.class, reader);
666 * @throws org.exolab.castor.xml.ValidationException if this
667 * object is an invalid instance according to the schema
669 public void validate(
671 throws org.exolab.castor.xml.ValidationException {
672 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
673 validator.validate(this);