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  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.schemabinding.version2

File JSeq.java

 

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Classes

Class Line # Actions
JSeq 22 127 96 146
0.3568281835.7%
 

Contributing tests

This file is covered by 16 tests. .

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1    /*
2    * This class was automatically generated with
3    * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
4    * Schema.
5    * $Id$
6    */
7   
8    package jalview.schemabinding.version2;
9   
10    //---------------------------------/
11    //- Imported classes and packages -/
12    //---------------------------------/
13   
14    import org.exolab.castor.xml.Marshaller;
15    import org.exolab.castor.xml.Unmarshaller;
16   
17    /**
18    * Class JSeq.
19    *
20    * @version $Revision$ $Date$
21    */
 
22    public class JSeq implements java.io.Serializable
23    {
24   
25    // --------------------------/
26    // - Class/Member Variables -/
27    // --------------------------/
28   
29    /**
30    * Field _colour.
31    */
32    private int _colour;
33   
34    /**
35    * keeps track of state for field: _colour
36    */
37    private boolean _has_colour;
38   
39    /**
40    * Field _start.
41    */
42    private int _start;
43   
44    /**
45    * keeps track of state for field: _start
46    */
47    private boolean _has_start;
48   
49    /**
50    * Field _end.
51    */
52    private int _end;
53   
54    /**
55    * keeps track of state for field: _end
56    */
57    private boolean _has_end;
58   
59    /**
60    * Field _id.
61    */
62    private java.lang.String _id;
63   
64    /**
65    * Field _hidden.
66    */
67    private boolean _hidden;
68   
69    /**
70    * keeps track of state for field: _hidden
71    */
72    private boolean _has_hidden;
73   
74    /**
75    * Field _viewreference.
76    */
77    private boolean _viewreference;
78   
79    /**
80    * keeps track of state for field: _viewreference
81    */
82    private boolean _has_viewreference;
83   
84    /**
85    * Field _featuresList.
86    */
87    private java.util.Vector _featuresList;
88   
89    /**
90    * Field _pdbidsList.
91    */
92    private java.util.Vector _pdbidsList;
93   
94    /**
95    * Field _hiddenSequencesList.
96    */
97    private java.util.Vector _hiddenSequencesList;
98   
99    /**
100    * Reference to a viewer showing RNA structure for this sequence. Schema
101    * supports one viewer showing multiple annotations for multiple sequences,
102    * though currently only one annotation for one sequence (gapped or trimmed)
103    * is used
104    *
105    */
106    private java.util.Vector _rnaViewerList;
107   
108    // ----------------/
109    // - Constructors -/
110    // ----------------/
111   
 
112  1825 toggle public JSeq()
113    {
114  1825 super();
115  1825 this._featuresList = new java.util.Vector();
116  1825 this._pdbidsList = new java.util.Vector();
117  1825 this._hiddenSequencesList = new java.util.Vector();
118  1825 this._rnaViewerList = new java.util.Vector();
119    }
120   
121    // -----------/
122    // - Methods -/
123    // -----------/
124   
125    /**
126    *
127    *
128    * @param vFeatures
129    * @throws java.lang.IndexOutOfBoundsException
130    * if the index given is outside the bounds of the collection
131    */
 
132  44398 toggle public void addFeatures(
133    final jalview.schemabinding.version2.Features vFeatures)
134    throws java.lang.IndexOutOfBoundsException
135    {
136  44398 this._featuresList.addElement(vFeatures);
137    }
138   
139    /**
140    *
141    *
142    * @param index
143    * @param vFeatures
144    * @throws java.lang.IndexOutOfBoundsException
145    * if the index given is outside the bounds of the collection
146    */
 
147  0 toggle public void addFeatures(final int index,
148    final jalview.schemabinding.version2.Features vFeatures)
149    throws java.lang.IndexOutOfBoundsException
150    {
151  0 this._featuresList.add(index, vFeatures);
152    }
153   
154    /**
155    *
156    *
157    * @param vHiddenSequences
158    * @throws java.lang.IndexOutOfBoundsException
159    * if the index given is outside the bounds of the collection
160    */
 
161  4 toggle public void addHiddenSequences(final int vHiddenSequences)
162    throws java.lang.IndexOutOfBoundsException
163    {
164  4 this._hiddenSequencesList.addElement(new java.lang.Integer(
165    vHiddenSequences));
166    }
167   
168    /**
169    *
170    *
171    * @param index
172    * @param vHiddenSequences
173    * @throws java.lang.IndexOutOfBoundsException
174    * if the index given is outside the bounds of the collection
175    */
 
176  0 toggle public void addHiddenSequences(final int index, final int vHiddenSequences)
177    throws java.lang.IndexOutOfBoundsException
178    {
179  0 this._hiddenSequencesList.add(index, new java.lang.Integer(
180    vHiddenSequences));
181    }
182   
183    /**
184    *
185    *
186    * @param vPdbids
187    * @throws java.lang.IndexOutOfBoundsException
188    * if the index given is outside the bounds of the collection
189    */
 
190  262 toggle public void addPdbids(final jalview.schemabinding.version2.Pdbids vPdbids)
191    throws java.lang.IndexOutOfBoundsException
192    {
193  262 this._pdbidsList.addElement(vPdbids);
194    }
195   
196    /**
197    *
198    *
199    * @param index
200    * @param vPdbids
201    * @throws java.lang.IndexOutOfBoundsException
202    * if the index given is outside the bounds of the collection
203    */
 
204  0 toggle public void addPdbids(final int index,
205    final jalview.schemabinding.version2.Pdbids vPdbids)
206    throws java.lang.IndexOutOfBoundsException
207    {
208  0 this._pdbidsList.add(index, vPdbids);
209    }
210   
211    /**
212    *
213    *
214    * @param vRnaViewer
215    * @throws java.lang.IndexOutOfBoundsException
216    * if the index given is outside the bounds of the collection
217    */
 
218  0 toggle public void addRnaViewer(
219    final jalview.schemabinding.version2.RnaViewer vRnaViewer)
220    throws java.lang.IndexOutOfBoundsException
221    {
222  0 this._rnaViewerList.addElement(vRnaViewer);
223    }
224   
225    /**
226    *
227    *
228    * @param index
229    * @param vRnaViewer
230    * @throws java.lang.IndexOutOfBoundsException
231    * if the index given is outside the bounds of the collection
232    */
 
233  0 toggle public void addRnaViewer(final int index,
234    final jalview.schemabinding.version2.RnaViewer vRnaViewer)
235    throws java.lang.IndexOutOfBoundsException
236    {
237  0 this._rnaViewerList.add(index, vRnaViewer);
238    }
239   
240    /**
241    */
 
242  0 toggle public void deleteColour()
243    {
244  0 this._has_colour = false;
245    }
246   
247    /**
248    */
 
249  0 toggle public void deleteEnd()
250    {
251  0 this._has_end = false;
252    }
253   
254    /**
255    */
 
256  0 toggle public void deleteHidden()
257    {
258  0 this._has_hidden = false;
259    }
260   
261    /**
262    */
 
263  0 toggle public void deleteStart()
264    {
265  0 this._has_start = false;
266    }
267   
268    /**
269    */
 
270  0 toggle public void deleteViewreference()
271    {
272  0 this._has_viewreference = false;
273    }
274   
275    /**
276    * Method enumerateFeatures.
277    *
278    * @return an Enumeration over all jalview.schemabinding.version2.Features
279    * elements
280    */
 
281  0 toggle public java.util.Enumeration enumerateFeatures()
282    {
283  0 return this._featuresList.elements();
284    }
285   
286    /**
287    * Method enumerateHiddenSequences.
288    *
289    * @return an Enumeration over all int elements
290    */
 
291  0 toggle public java.util.Enumeration enumerateHiddenSequences()
292    {
293  0 return this._hiddenSequencesList.elements();
294    }
295   
296    /**
297    * Method enumeratePdbids.
298    *
299    * @return an Enumeration over all jalview.schemabinding.version2.Pdbids
300    * elements
301    */
 
302  0 toggle public java.util.Enumeration enumeratePdbids()
303    {
304  0 return this._pdbidsList.elements();
305    }
306   
307    /**
308    * Method enumerateRnaViewer.
309    *
310    * @return an Enumeration over all jalview.schemabinding.version2.RnaViewer
311    * elements
312    */
 
313  0 toggle public java.util.Enumeration enumerateRnaViewer()
314    {
315  0 return this._rnaViewerList.elements();
316    }
317   
318    /**
319    * Returns the value of field 'colour'.
320    *
321    * @return the value of field 'Colour'.
322    */
 
323  2065 toggle public int getColour()
324    {
325  2065 return this._colour;
326    }
327   
328    /**
329    * Returns the value of field 'end'.
330    *
331    * @return the value of field 'End'.
332    */
 
333  3201 toggle public int getEnd()
334    {
335  3201 return this._end;
336    }
337   
338    /**
339    * Method getFeatures.
340    *
341    * @param index
342    * @throws java.lang.IndexOutOfBoundsException
343    * if the index given is outside the bounds of the collection
344    * @return the value of the jalview.schemabinding.version2.Features at the
345    * given index
346    */
 
347  0 toggle public jalview.schemabinding.version2.Features getFeatures(final int index)
348    throws java.lang.IndexOutOfBoundsException
349    {
350    // check bounds for index
351  0 if (index < 0 || index >= this._featuresList.size())
352    {
353  0 throw new IndexOutOfBoundsException("getFeatures: Index value '"
354    + index + "' not in range [0.."
355    + (this._featuresList.size() - 1) + "]");
356    }
357   
358  0 return (jalview.schemabinding.version2.Features) _featuresList
359    .get(index);
360    }
361   
362    /**
363    * Method getFeatures.Returns the contents of the collection in an Array.
364    * <p>
365    * Note: Just in case the collection contents are changing in another thread,
366    * we pass a 0-length Array of the correct type into the API call. This way we
367    * <i>know</i> that the Array returned is of exactly the correct length.
368    *
369    * @return this collection as an Array
370    */
 
371  1170 toggle public jalview.schemabinding.version2.Features[] getFeatures()
372    {
373  1170 jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];
374  1170 return (jalview.schemabinding.version2.Features[]) this._featuresList
375    .toArray(array);
376    }
377   
378    /**
379    * Method getFeaturesCount.
380    *
381    * @return the size of this collection
382    */
 
383  513 toggle public int getFeaturesCount()
384    {
385  513 return this._featuresList.size();
386    }
387   
388    /**
389    * Returns the value of field 'hidden'.
390    *
391    * @return the value of field 'Hidden'.
392    */
 
393  1676 toggle public boolean getHidden()
394    {
395  1676 return this._hidden;
396    }
397   
398    /**
399    * Method getHiddenSequences.
400    *
401    * @param index
402    * @throws java.lang.IndexOutOfBoundsException
403    * if the index given is outside the bounds of the collection
404    * @return the value of the int at the given index
405    */
 
406  2 toggle public int getHiddenSequences(final int index)
407    throws java.lang.IndexOutOfBoundsException
408    {
409    // check bounds for index
410  2 if (index < 0 || index >= this._hiddenSequencesList.size())
411    {
412  0 throw new IndexOutOfBoundsException(
413    "getHiddenSequences: Index value '" + index
414    + "' not in range [0.."
415    + (this._hiddenSequencesList.size() - 1) + "]");
416    }
417   
418  2 return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();
419    }
420   
421    /**
422    * Method getHiddenSequences.Returns the contents of the collection in an
423    * Array.
424    *
425    * @return this collection as an Array
426    */
 
427  930 toggle public int[] getHiddenSequences()
428    {
429  930 int size = this._hiddenSequencesList.size();
430  930 int[] array = new int[size];
431  930 java.util.Iterator iter = _hiddenSequencesList.iterator();
432  934 for (int index = 0; index < size; index++)
433    {
434  4 array[index] = ((java.lang.Integer) iter.next()).intValue();
435    }
436  930 return array;
437    }
438   
439    /**
440    * Method getHiddenSequencesCount.
441    *
442    * @return the size of this collection
443    */
 
444  992 toggle public int getHiddenSequencesCount()
445    {
446  992 return this._hiddenSequencesList.size();
447    }
448   
449    /**
450    * Returns the value of field 'id'.
451    *
452    * @return the value of field 'Id'.
453    */
 
454  2346 toggle public java.lang.String getId()
455    {
456  2346 return this._id;
457    }
458   
459    /**
460    * Method getPdbids.
461    *
462    * @param index
463    * @throws java.lang.IndexOutOfBoundsException
464    * if the index given is outside the bounds of the collection
465    * @return the value of the jalview.schemabinding.version2.Pdbids at the given
466    * index
467    */
 
468  0 toggle public jalview.schemabinding.version2.Pdbids getPdbids(final int index)
469    throws java.lang.IndexOutOfBoundsException
470    {
471    // check bounds for index
472  0 if (index < 0 || index >= this._pdbidsList.size())
473    {
474  0 throw new IndexOutOfBoundsException("getPdbids: Index value '"
475    + index + "' not in range [0.."
476    + (this._pdbidsList.size() - 1) + "]");
477    }
478   
479  0 return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);
480    }
481   
482    /**
483    * Method getPdbids.Returns the contents of the collection in an Array.
484    * <p>
485    * Note: Just in case the collection contents are changing in another thread,
486    * we pass a 0-length Array of the correct type into the API call. This way we
487    * <i>know</i> that the Array returned is of exactly the correct length.
488    *
489    * @return this collection as an Array
490    */
 
491  1173 toggle public jalview.schemabinding.version2.Pdbids[] getPdbids()
492    {
493  1173 jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];
494  1173 return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList
495    .toArray(array);
496    }
497   
498    /**
499    * Method getPdbidsCount.
500    *
501    * @return the size of this collection
502    */
 
503  1617 toggle public int getPdbidsCount()
504    {
505  1617 return this._pdbidsList.size();
506    }
507   
508    /**
509    * Method getRnaViewer.
510    *
511    * @param index
512    * @throws java.lang.IndexOutOfBoundsException
513    * if the index given is outside the bounds of the collection
514    * @return the value of the jalview.schemabinding.version2.RnaViewer at the
515    * given index
516    */
 
517  0 toggle public jalview.schemabinding.version2.RnaViewer getRnaViewer(
518    final int index) throws java.lang.IndexOutOfBoundsException
519    {
520    // check bounds for index
521  0 if (index < 0 || index >= this._rnaViewerList.size())
522    {
523  0 throw new IndexOutOfBoundsException("getRnaViewer: Index value '"
524    + index + "' not in range [0.."
525    + (this._rnaViewerList.size() - 1) + "]");
526    }
527   
528  0 return (jalview.schemabinding.version2.RnaViewer) _rnaViewerList
529    .get(index);
530    }
531   
532    /**
533    * Method getRnaViewer.Returns the contents of the collection in an Array.
534    * <p>
535    * Note: Just in case the collection contents are changing in another thread,
536    * we pass a 0-length Array of the correct type into the API call. This way we
537    * <i>know</i> that the Array returned is of exactly the correct length.
538    *
539    * @return this collection as an Array
540    */
 
541  930 toggle public jalview.schemabinding.version2.RnaViewer[] getRnaViewer()
542    {
543  930 jalview.schemabinding.version2.RnaViewer[] array = new jalview.schemabinding.version2.RnaViewer[0];
544  930 return (jalview.schemabinding.version2.RnaViewer[]) this._rnaViewerList
545    .toArray(array);
546    }
547   
548    /**
549    * Method getRnaViewerCount.
550    *
551    * @return the size of this collection
552    */
 
553  1104 toggle public int getRnaViewerCount()
554    {
555  1104 return this._rnaViewerList.size();
556    }
557   
558    /**
559    * Returns the value of field 'start'.
560    *
561    * @return the value of field 'Start'.
562    */
 
563  3201 toggle public int getStart()
564    {
565  3201 return this._start;
566    }
567   
568    /**
569    * Returns the value of field 'viewreference'.
570    *
571    * @return the value of field 'Viewreference'.
572    */
 
573  240 toggle public boolean getViewreference()
574    {
575  240 return this._viewreference;
576    }
577   
578    /**
579    * Method hasColour.
580    *
581    * @return true if at least one Colour has been added
582    */
 
583  930 toggle public boolean hasColour()
584    {
585  930 return this._has_colour;
586    }
587   
588    /**
589    * Method hasEnd.
590    *
591    * @return true if at least one End has been added
592    */
 
593  930 toggle public boolean hasEnd()
594    {
595  930 return this._has_end;
596    }
597   
598    /**
599    * Method hasHidden.
600    *
601    * @return true if at least one Hidden has been added
602    */
 
603  930 toggle public boolean hasHidden()
604    {
605  930 return this._has_hidden;
606    }
607   
608    /**
609    * Method hasStart.
610    *
611    * @return true if at least one Start has been added
612    */
 
613  930 toggle public boolean hasStart()
614    {
615  930 return this._has_start;
616    }
617   
618    /**
619    * Method hasViewreference.
620    *
621    * @return true if at least one Viewreference has been added
622    */
 
623  2226 toggle public boolean hasViewreference()
624    {
625  2226 return this._has_viewreference;
626    }
627   
628    /**
629    * Returns the value of field 'hidden'.
630    *
631    * @return the value of field 'Hidden'.
632    */
 
633  0 toggle public boolean isHidden()
634    {
635  0 return this._hidden;
636    }
637   
638    /**
639    * Method isValid.
640    *
641    * @return true if this object is valid according to the schema
642    */
 
643  0 toggle public boolean isValid()
644    {
645  0 try
646    {
647  0 validate();
648    } catch (org.exolab.castor.xml.ValidationException vex)
649    {
650  0 return false;
651    }
652  0 return true;
653    }
654   
655    /**
656    * Returns the value of field 'viewreference'.
657    *
658    * @return the value of field 'Viewreference'.
659    */
 
660  0 toggle public boolean isViewreference()
661    {
662  0 return this._viewreference;
663    }
664   
665    /**
666    *
667    *
668    * @param out
669    * @throws org.exolab.castor.xml.MarshalException
670    * if object is null or if any SAXException is thrown during
671    * marshaling
672    * @throws org.exolab.castor.xml.ValidationException
673    * if this object is an invalid instance according to the schema
674    */
 
675  0 toggle public void marshal(final java.io.Writer out)
676    throws org.exolab.castor.xml.MarshalException,
677    org.exolab.castor.xml.ValidationException
678    {
679  0 Marshaller.marshal(this, out);
680    }
681   
682    /**
683    *
684    *
685    * @param handler
686    * @throws java.io.IOException
687    * if an IOException occurs during marshaling
688    * @throws org.exolab.castor.xml.ValidationException
689    * if this object is an invalid instance according to the schema
690    * @throws org.exolab.castor.xml.MarshalException
691    * if object is null or if any SAXException is thrown during
692    * marshaling
693    */
 
694  0 toggle public void marshal(final org.xml.sax.ContentHandler handler)
695    throws java.io.IOException,
696    org.exolab.castor.xml.MarshalException,
697    org.exolab.castor.xml.ValidationException
698    {
699  0 Marshaller.marshal(this, handler);
700    }
701   
702    /**
703    */
 
704  0 toggle public void removeAllFeatures()
705    {
706  0 this._featuresList.clear();
707    }
708   
709    /**
710    */
 
711  0 toggle public void removeAllHiddenSequences()
712    {
713  0 this._hiddenSequencesList.clear();
714    }
715   
716    /**
717    */
 
718  0 toggle public void removeAllPdbids()
719    {
720  0 this._pdbidsList.clear();
721    }
722   
723    /**
724    */
 
725  0 toggle public void removeAllRnaViewer()
726    {
727  0 this._rnaViewerList.clear();
728    }
729   
730    /**
731    * Method removeFeatures.
732    *
733    * @param vFeatures
734    * @return true if the object was removed from the collection.
735    */
 
736  0 toggle public boolean removeFeatures(
737    final jalview.schemabinding.version2.Features vFeatures)
738    {
739  0 boolean removed = _featuresList.remove(vFeatures);
740  0 return removed;
741    }
742   
743    /**
744    * Method removeFeaturesAt.
745    *
746    * @param index
747    * @return the element removed from the collection
748    */
 
749  0 toggle public jalview.schemabinding.version2.Features removeFeaturesAt(
750    final int index)
751    {
752  0 java.lang.Object obj = this._featuresList.remove(index);
753  0 return (jalview.schemabinding.version2.Features) obj;
754    }
755   
756    /**
757    * Method removeHiddenSequences.
758    *
759    * @param vHiddenSequences
760    * @return true if the object was removed from the collection.
761    */
 
762  0 toggle public boolean removeHiddenSequences(final int vHiddenSequences)
763    {
764  0 boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(
765    vHiddenSequences));
766  0 return removed;
767    }
768   
769    /**
770    * Method removeHiddenSequencesAt.
771    *
772    * @param index
773    * @return the element removed from the collection
774    */
 
775  0 toggle public int removeHiddenSequencesAt(final int index)
776    {
777  0 java.lang.Object obj = this._hiddenSequencesList.remove(index);
778  0 return ((java.lang.Integer) obj).intValue();
779    }
780   
781    /**
782    * Method removePdbids.
783    *
784    * @param vPdbids
785    * @return true if the object was removed from the collection.
786    */
 
787  0 toggle public boolean removePdbids(
788    final jalview.schemabinding.version2.Pdbids vPdbids)
789    {
790  0 boolean removed = _pdbidsList.remove(vPdbids);
791  0 return removed;
792    }
793   
794    /**
795    * Method removePdbidsAt.
796    *
797    * @param index
798    * @return the element removed from the collection
799    */
 
800  0 toggle public jalview.schemabinding.version2.Pdbids removePdbidsAt(
801    final int index)
802    {
803  0 java.lang.Object obj = this._pdbidsList.remove(index);
804  0 return (jalview.schemabinding.version2.Pdbids) obj;
805    }
806   
807    /**
808    * Method removeRnaViewer.
809    *
810    * @param vRnaViewer
811    * @return true if the object was removed from the collection.
812    */
 
813  0 toggle public boolean removeRnaViewer(
814    final jalview.schemabinding.version2.RnaViewer vRnaViewer)
815    {
816  0 boolean removed = _rnaViewerList.remove(vRnaViewer);
817  0 return removed;
818    }
819   
820    /**
821    * Method removeRnaViewerAt.
822    *
823    * @param index
824    * @return the element removed from the collection
825    */
 
826  0 toggle public jalview.schemabinding.version2.RnaViewer removeRnaViewerAt(
827    final int index)
828    {
829  0 java.lang.Object obj = this._rnaViewerList.remove(index);
830  0 return (jalview.schemabinding.version2.RnaViewer) obj;
831    }
832   
833    /**
834    * Sets the value of field 'colour'.
835    *
836    * @param colour
837    * the value of field 'colour'.
838    */
 
839  1825 toggle public void setColour(final int colour)
840    {
841  1825 this._colour = colour;
842  1825 this._has_colour = true;
843    }
844   
845    /**
846    * Sets the value of field 'end'.
847    *
848    * @param end
849    * the value of field 'end'.
850    */
 
851  1825 toggle public void setEnd(final int end)
852    {
853  1825 this._end = end;
854  1825 this._has_end = true;
855    }
856   
857    /**
858    *
859    *
860    * @param index
861    * @param vFeatures
862    * @throws java.lang.IndexOutOfBoundsException
863    * if the index given is outside the bounds of the collection
864    */
 
865  0 toggle public void setFeatures(final int index,
866    final jalview.schemabinding.version2.Features vFeatures)
867    throws java.lang.IndexOutOfBoundsException
868    {
869    // check bounds for index
870  0 if (index < 0 || index >= this._featuresList.size())
871    {
872  0 throw new IndexOutOfBoundsException("setFeatures: Index value '"
873    + index + "' not in range [0.."
874    + (this._featuresList.size() - 1) + "]");
875    }
876   
877  0 this._featuresList.set(index, vFeatures);
878    }
879   
880    /**
881    *
882    *
883    * @param vFeaturesArray
884    */
 
885  0 toggle public void setFeatures(
886    final jalview.schemabinding.version2.Features[] vFeaturesArray)
887    {
888    // -- copy array
889  0 _featuresList.clear();
890   
891  0 for (int i = 0; i < vFeaturesArray.length; i++)
892    {
893  0 this._featuresList.add(vFeaturesArray[i]);
894    }
895    }
896   
897    /**
898    * Sets the value of field 'hidden'.
899    *
900    * @param hidden
901    * the value of field 'hidden'.
902    */
 
903  1180 toggle public void setHidden(final boolean hidden)
904    {
905  1180 this._hidden = hidden;
906  1180 this._has_hidden = true;
907    }
908   
909    /**
910    *
911    *
912    * @param index
913    * @param vHiddenSequences
914    * @throws java.lang.IndexOutOfBoundsException
915    * if the index given is outside the bounds of the collection
916    */
 
917  0 toggle public void setHiddenSequences(final int index, final int vHiddenSequences)
918    throws java.lang.IndexOutOfBoundsException
919    {
920    // check bounds for index
921  0 if (index < 0 || index >= this._hiddenSequencesList.size())
922    {
923  0 throw new IndexOutOfBoundsException(
924    "setHiddenSequences: Index value '" + index
925    + "' not in range [0.."
926    + (this._hiddenSequencesList.size() - 1) + "]");
927    }
928   
929  0 this._hiddenSequencesList.set(index, new java.lang.Integer(
930    vHiddenSequences));
931    }
932   
933    /**
934    *
935    *
936    * @param vHiddenSequencesArray
937    */
 
938  0 toggle public void setHiddenSequences(final int[] vHiddenSequencesArray)
939    {
940    // -- copy array
941  0 _hiddenSequencesList.clear();
942   
943  0 for (int i = 0; i < vHiddenSequencesArray.length; i++)
944    {
945  0 this._hiddenSequencesList.add(new java.lang.Integer(
946    vHiddenSequencesArray[i]));
947    }
948    }
949   
950    /**
951    * Sets the value of field 'id'.
952    *
953    * @param id
954    * the value of field 'id'.
955    */
 
956  1825 toggle public void setId(final java.lang.String id)
957    {
958  1825 this._id = id;
959    }
960   
961    /**
962    *
963    *
964    * @param index
965    * @param vPdbids
966    * @throws java.lang.IndexOutOfBoundsException
967    * if the index given is outside the bounds of the collection
968    */
 
969  0 toggle public void setPdbids(final int index,
970    final jalview.schemabinding.version2.Pdbids vPdbids)
971    throws java.lang.IndexOutOfBoundsException
972    {
973    // check bounds for index
974  0 if (index < 0 || index >= this._pdbidsList.size())
975    {
976  0 throw new IndexOutOfBoundsException("setPdbids: Index value '"
977    + index + "' not in range [0.."
978    + (this._pdbidsList.size() - 1) + "]");
979    }
980   
981  0 this._pdbidsList.set(index, vPdbids);
982    }
983   
984    /**
985    *
986    *
987    * @param vPdbidsArray
988    */
 
989  0 toggle public void setPdbids(
990    final jalview.schemabinding.version2.Pdbids[] vPdbidsArray)
991    {
992    // -- copy array
993  0 _pdbidsList.clear();
994   
995  0 for (int i = 0; i < vPdbidsArray.length; i++)
996    {
997  0 this._pdbidsList.add(vPdbidsArray[i]);
998    }
999    }
1000   
1001    /**
1002    *
1003    *
1004    * @param index
1005    * @param vRnaViewer
1006    * @throws java.lang.IndexOutOfBoundsException
1007    * if the index given is outside the bounds of the collection
1008    */
 
1009  0 toggle public void setRnaViewer(final int index,
1010    final jalview.schemabinding.version2.RnaViewer vRnaViewer)
1011    throws java.lang.IndexOutOfBoundsException
1012    {
1013    // check bounds for index
1014  0 if (index < 0 || index >= this._rnaViewerList.size())
1015    {
1016  0 throw new IndexOutOfBoundsException("setRnaViewer: Index value '"
1017    + index + "' not in range [0.."
1018    + (this._rnaViewerList.size() - 1) + "]");
1019    }
1020   
1021  0 this._rnaViewerList.set(index, vRnaViewer);
1022    }
1023   
1024    /**
1025    *
1026    *
1027    * @param vRnaViewerArray
1028    */
 
1029  0 toggle public void setRnaViewer(
1030    final jalview.schemabinding.version2.RnaViewer[] vRnaViewerArray)
1031    {
1032    // -- copy array
1033  0 _rnaViewerList.clear();
1034   
1035  0 for (int i = 0; i < vRnaViewerArray.length; i++)
1036    {
1037  0 this._rnaViewerList.add(vRnaViewerArray[i]);
1038    }
1039    }
1040   
1041    /**
1042    * Sets the value of field 'start'.
1043    *
1044    * @param start
1045    * the value of field 'start'.
1046    */
 
1047  1825 toggle public void setStart(final int start)
1048    {
1049  1825 this._start = start;
1050  1825 this._has_start = true;
1051    }
1052   
1053    /**
1054    * Sets the value of field 'viewreference'.
1055    *
1056    * @param viewreference
1057    * the value of field 'viewreference'.
1058    */
 
1059  160 toggle public void setViewreference(final boolean viewreference)
1060    {
1061  160 this._viewreference = viewreference;
1062  160 this._has_viewreference = true;
1063    }
1064   
1065    /**
1066    * Method unmarshal.
1067    *
1068    * @param reader
1069    * @throws org.exolab.castor.xml.MarshalException
1070    * if object is null or if any SAXException is thrown during
1071    * marshaling
1072    * @throws org.exolab.castor.xml.ValidationException
1073    * if this object is an invalid instance according to the schema
1074    * @return the unmarshaled jalview.schemabinding.version2.JSeq
1075    */
 
1076  0 toggle public static jalview.schemabinding.version2.JSeq unmarshal(
1077    final java.io.Reader reader)
1078    throws org.exolab.castor.xml.MarshalException,
1079    org.exolab.castor.xml.ValidationException
1080    {
1081  0 return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(
1082    jalview.schemabinding.version2.JSeq.class, reader);
1083    }
1084   
1085    /**
1086    *
1087    *
1088    * @throws org.exolab.castor.xml.ValidationException
1089    * if this object is an invalid instance according to the schema
1090    */
 
1091  0 toggle public void validate() throws org.exolab.castor.xml.ValidationException
1092    {
1093  0 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
1094  0 validator.validate(this);
1095    }
1096   
1097    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.