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jalviewX

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

File JalviewModelSequence.java

 

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Classes

Class Line # Actions
JalviewModelSequence 22 117 89 156
0.2571428725.7%
 

Contributing tests

This file is covered by 16 tests. .

Source view

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 JalviewModelSequence.
19    *
20    * @version $Revision$ $Date$
21    */
 
22    public class JalviewModelSequence implements java.io.Serializable
23    {
24   
25    // --------------------------/
26    // - Class/Member Variables -/
27    // --------------------------/
28   
29    /**
30    * Field _JSeqList.
31    */
32    private java.util.Vector _JSeqList;
33   
34    /**
35    * Field _JGroupList.
36    */
37    private java.util.Vector _JGroupList;
38   
39    /**
40    * Field _viewportList.
41    */
42    private java.util.Vector _viewportList;
43   
44    /**
45    * Field _userColoursList.
46    */
47    private java.util.Vector _userColoursList;
48   
49    /**
50    * Field _treeList.
51    */
52    private java.util.Vector _treeList;
53   
54    /**
55    * Field _featureSettings.
56    */
57    private jalview.schemabinding.version2.FeatureSettings _featureSettings;
58   
59    // ----------------/
60    // - Constructors -/
61    // ----------------/
62   
 
63  115 toggle public JalviewModelSequence()
64    {
65  115 super();
66  115 this._JSeqList = new java.util.Vector();
67  115 this._JGroupList = new java.util.Vector();
68  115 this._viewportList = new java.util.Vector();
69  115 this._userColoursList = new java.util.Vector();
70  115 this._treeList = new java.util.Vector();
71    }
72   
73    // -----------/
74    // - Methods -/
75    // -----------/
76   
77    /**
78    *
79    *
80    * @param vJGroup
81    * @throws java.lang.IndexOutOfBoundsException
82    * if the index given is outside the bounds of the collection
83    */
 
84  62 toggle public void addJGroup(final jalview.schemabinding.version2.JGroup vJGroup)
85    throws java.lang.IndexOutOfBoundsException
86    {
87  62 this._JGroupList.addElement(vJGroup);
88    }
89   
90    /**
91    *
92    *
93    * @param index
94    * @param vJGroup
95    * @throws java.lang.IndexOutOfBoundsException
96    * if the index given is outside the bounds of the collection
97    */
 
98  0 toggle public void addJGroup(final int index,
99    final jalview.schemabinding.version2.JGroup vJGroup)
100    throws java.lang.IndexOutOfBoundsException
101    {
102  0 this._JGroupList.add(index, vJGroup);
103    }
104   
105    /**
106    *
107    *
108    * @param vJSeq
109    * @throws java.lang.IndexOutOfBoundsException
110    * if the index given is outside the bounds of the collection
111    */
 
112  1825 toggle public void addJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
113    throws java.lang.IndexOutOfBoundsException
114    {
115  1825 this._JSeqList.addElement(vJSeq);
116    }
117   
118    /**
119    *
120    *
121    * @param index
122    * @param vJSeq
123    * @throws java.lang.IndexOutOfBoundsException
124    * if the index given is outside the bounds of the collection
125    */
 
126  0 toggle public void addJSeq(final int index,
127    final jalview.schemabinding.version2.JSeq vJSeq)
128    throws java.lang.IndexOutOfBoundsException
129    {
130  0 this._JSeqList.add(index, vJSeq);
131    }
132   
133    /**
134    *
135    *
136    * @param vTree
137    * @throws java.lang.IndexOutOfBoundsException
138    * if the index given is outside the bounds of the collection
139    */
 
140  14 toggle public void addTree(final jalview.schemabinding.version2.Tree vTree)
141    throws java.lang.IndexOutOfBoundsException
142    {
143  14 this._treeList.addElement(vTree);
144    }
145   
146    /**
147    *
148    *
149    * @param index
150    * @param vTree
151    * @throws java.lang.IndexOutOfBoundsException
152    * if the index given is outside the bounds of the collection
153    */
 
154  0 toggle public void addTree(final int index,
155    final jalview.schemabinding.version2.Tree vTree)
156    throws java.lang.IndexOutOfBoundsException
157    {
158  0 this._treeList.add(index, vTree);
159    }
160   
161    /**
162    *
163    *
164    * @param vUserColours
165    * @throws java.lang.IndexOutOfBoundsException
166    * if the index given is outside the bounds of the collection
167    */
 
168  0 toggle public void addUserColours(
169    final jalview.schemabinding.version2.UserColours vUserColours)
170    throws java.lang.IndexOutOfBoundsException
171    {
172  0 this._userColoursList.addElement(vUserColours);
173    }
174   
175    /**
176    *
177    *
178    * @param index
179    * @param vUserColours
180    * @throws java.lang.IndexOutOfBoundsException
181    * if the index given is outside the bounds of the collection
182    */
 
183  0 toggle public void addUserColours(final int index,
184    final jalview.schemabinding.version2.UserColours vUserColours)
185    throws java.lang.IndexOutOfBoundsException
186    {
187  0 this._userColoursList.add(index, vUserColours);
188    }
189   
190    /**
191    *
192    *
193    * @param vViewport
194    * @throws java.lang.IndexOutOfBoundsException
195    * if the index given is outside the bounds of the collection
196    */
 
197  91 toggle public void addViewport(
198    final jalview.schemabinding.version2.Viewport vViewport)
199    throws java.lang.IndexOutOfBoundsException
200    {
201  91 this._viewportList.addElement(vViewport);
202    }
203   
204    /**
205    *
206    *
207    * @param index
208    * @param vViewport
209    * @throws java.lang.IndexOutOfBoundsException
210    * if the index given is outside the bounds of the collection
211    */
 
212  0 toggle public void addViewport(final int index,
213    final jalview.schemabinding.version2.Viewport vViewport)
214    throws java.lang.IndexOutOfBoundsException
215    {
216  0 this._viewportList.add(index, vViewport);
217    }
218   
219    /**
220    * Method enumerateJGroup.
221    *
222    * @return an Enumeration over all jalview.schemabinding.version2.JGroup
223    * elements
224    */
 
225  0 toggle public java.util.Enumeration enumerateJGroup()
226    {
227  0 return this._JGroupList.elements();
228    }
229   
230    /**
231    * Method enumerateJSeq.
232    *
233    * @return an Enumeration over all jalview.schemabinding.version2.JSeq
234    * elements
235    */
 
236  0 toggle public java.util.Enumeration enumerateJSeq()
237    {
238  0 return this._JSeqList.elements();
239    }
240   
241    /**
242    * Method enumerateTree.
243    *
244    * @return an Enumeration over all jalview.schemabinding.version2.Tree
245    * elements
246    */
 
247  0 toggle public java.util.Enumeration enumerateTree()
248    {
249  0 return this._treeList.elements();
250    }
251   
252    /**
253    * Method enumerateUserColours.
254    *
255    * @return an Enumeration over all jalview.schemabinding.version2.UserColours
256    * elements
257    */
 
258  0 toggle public java.util.Enumeration enumerateUserColours()
259    {
260  0 return this._userColoursList.elements();
261    }
262   
263    /**
264    * Method enumerateViewport.
265    *
266    * @return an Enumeration over all jalview.schemabinding.version2.Viewport
267    * elements
268    */
 
269  0 toggle public java.util.Enumeration enumerateViewport()
270    {
271  0 return this._viewportList.elements();
272    }
273   
274    /**
275    * Returns the value of field 'featureSettings'.
276    *
277    * @return the value of field 'FeatureSettings'.
278    */
 
279  3186 toggle public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
280    {
281  3186 return this._featureSettings;
282    }
283   
284    /**
285    * Method getJGroup.
286    *
287    * @param index
288    * @throws java.lang.IndexOutOfBoundsException
289    * if the index given is outside the bounds of the collection
290    * @return the value of the jalview.schemabinding.version2.JGroup at the given
291    * index
292    */
 
293  0 toggle public jalview.schemabinding.version2.JGroup getJGroup(final int index)
294    throws java.lang.IndexOutOfBoundsException
295    {
296    // check bounds for index
297  0 if (index < 0 || index >= this._JGroupList.size())
298    {
299  0 throw new IndexOutOfBoundsException("getJGroup: Index value '"
300    + index + "' not in range [0.."
301    + (this._JGroupList.size() - 1) + "]");
302    }
303   
304  0 return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
305    }
306   
307    /**
308    * Method getJGroup.Returns the contents of the collection in an Array.
309    * <p>
310    * Note: Just in case the collection contents are changing in another thread,
311    * we pass a 0-length Array of the correct type into the API call. This way we
312    * <i>know</i> that the Array returned is of exactly the correct length.
313    *
314    * @return this collection as an Array
315    */
 
316  97 toggle public jalview.schemabinding.version2.JGroup[] getJGroup()
317    {
318  97 jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];
319  97 return (jalview.schemabinding.version2.JGroup[]) this._JGroupList
320    .toArray(array);
321    }
322   
323    /**
324    * Method getJGroupCount.
325    *
326    * @return the size of this collection
327    */
 
328  82 toggle public int getJGroupCount()
329    {
330  82 return this._JGroupList.size();
331    }
332   
333    /**
334    * Method getJSeq.
335    *
336    * @param index
337    * @throws java.lang.IndexOutOfBoundsException
338    * if the index given is outside the bounds of the collection
339    * @return the value of the jalview.schemabinding.version2.JSeq at the given
340    * index
341    */
 
342  0 toggle public jalview.schemabinding.version2.JSeq getJSeq(final int index)
343    throws java.lang.IndexOutOfBoundsException
344    {
345    // check bounds for index
346  0 if (index < 0 || index >= this._JSeqList.size())
347    {
348  0 throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
349    + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
350    }
351   
352  0 return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);
353    }
354   
355    /**
356    * Method getJSeq.Returns the contents of the collection in an Array.
357    * <p>
358    * Note: Just in case the collection contents are changing in another thread,
359    * we pass a 0-length Array of the correct type into the API call. This way we
360    * <i>know</i> that the Array returned is of exactly the correct length.
361    *
362    * @return this collection as an Array
363    */
 
364  140 toggle public jalview.schemabinding.version2.JSeq[] getJSeq()
365    {
366  140 jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];
367  140 return (jalview.schemabinding.version2.JSeq[]) this._JSeqList
368    .toArray(array);
369    }
370   
371    /**
372    * Method getJSeqCount.
373    *
374    * @return the size of this collection
375    */
 
376  0 toggle public int getJSeqCount()
377    {
378  0 return this._JSeqList.size();
379    }
380   
381    /**
382    * Method getTree.
383    *
384    * @param index
385    * @throws java.lang.IndexOutOfBoundsException
386    * if the index given is outside the bounds of the collection
387    * @return the value of the jalview.schemabinding.version2.Tree at the given
388    * index
389    */
 
390  12 toggle public jalview.schemabinding.version2.Tree getTree(final int index)
391    throws java.lang.IndexOutOfBoundsException
392    {
393    // check bounds for index
394  12 if (index < 0 || index >= this._treeList.size())
395    {
396  0 throw new IndexOutOfBoundsException("getTree: Index value '" + index
397    + "' not in range [0.." + (this._treeList.size() - 1) + "]");
398    }
399   
400  12 return (jalview.schemabinding.version2.Tree) _treeList.get(index);
401    }
402   
403    /**
404    * Method getTree.Returns the contents of the collection in an Array.
405    * <p>
406    * Note: Just in case the collection contents are changing in another thread,
407    * we pass a 0-length Array of the correct type into the API call. This way we
408    * <i>know</i> that the Array returned is of exactly the correct length.
409    *
410    * @return this collection as an Array
411    */
 
412  58 toggle public jalview.schemabinding.version2.Tree[] getTree()
413    {
414  58 jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];
415  58 return (jalview.schemabinding.version2.Tree[]) this._treeList
416    .toArray(array);
417    }
418   
419    /**
420    * Method getTreeCount.
421    *
422    * @return the size of this collection
423    */
 
424  81 toggle public int getTreeCount()
425    {
426  81 return this._treeList.size();
427    }
428   
429    /**
430    * Method getUserColours.
431    *
432    * @param index
433    * @throws java.lang.IndexOutOfBoundsException
434    * if the index given is outside the bounds of the collection
435    * @return the value of the jalview.schemabinding.version2.UserColours at the
436    * given index
437    */
 
438  0 toggle public jalview.schemabinding.version2.UserColours getUserColours(
439    final int index) throws java.lang.IndexOutOfBoundsException
440    {
441    // check bounds for index
442  0 if (index < 0 || index >= this._userColoursList.size())
443    {
444  0 throw new IndexOutOfBoundsException("getUserColours: Index value '"
445    + index + "' not in range [0.."
446    + (this._userColoursList.size() - 1) + "]");
447    }
448   
449  0 return (jalview.schemabinding.version2.UserColours) _userColoursList
450    .get(index);
451    }
452   
453    /**
454    * Method getUserColours.Returns the contents of the collection in an Array.
455    * <p>
456    * Note: Just in case the collection contents are changing in another thread,
457    * we pass a 0-length Array of the correct type into the API call. This way we
458    * <i>know</i> that the Array returned is of exactly the correct length.
459    *
460    * @return this collection as an Array
461    */
 
462  58 toggle public jalview.schemabinding.version2.UserColours[] getUserColours()
463    {
464  58 jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];
465  58 return (jalview.schemabinding.version2.UserColours[]) this._userColoursList
466    .toArray(array);
467    }
468   
469    /**
470    * Method getUserColoursCount.
471    *
472    * @return the size of this collection
473    */
 
474  0 toggle public int getUserColoursCount()
475    {
476  0 return this._userColoursList.size();
477    }
478   
479    /**
480    * Method getViewport.
481    *
482    * @param index
483    * @throws java.lang.IndexOutOfBoundsException
484    * if the index given is outside the bounds of the collection
485    * @return the value of the jalview.schemabinding.version2.Viewport at the
486    * given index
487    */
 
488  75 toggle public jalview.schemabinding.version2.Viewport getViewport(final int index)
489    throws java.lang.IndexOutOfBoundsException
490    {
491    // check bounds for index
492  75 if (index < 0 || index >= this._viewportList.size())
493    {
494  0 throw new IndexOutOfBoundsException("getViewport: Index value '"
495    + index + "' not in range [0.."
496    + (this._viewportList.size() - 1) + "]");
497    }
498   
499  75 return (jalview.schemabinding.version2.Viewport) _viewportList
500    .get(index);
501    }
502   
503    /**
504    * Method getViewport.Returns the contents of the collection in an Array.
505    * <p>
506    * Note: Just in case the collection contents are changing in another thread,
507    * we pass a 0-length Array of the correct type into the API call. This way we
508    * <i>know</i> that the Array returned is of exactly the correct length.
509    *
510    * @return this collection as an Array
511    */
 
512  58 toggle public jalview.schemabinding.version2.Viewport[] getViewport()
513    {
514  58 jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];
515  58 return (jalview.schemabinding.version2.Viewport[]) this._viewportList
516    .toArray(array);
517    }
518   
519    /**
520    * Method getViewportCount.
521    *
522    * @return the size of this collection
523    */
 
524  183 toggle public int getViewportCount()
525    {
526  183 return this._viewportList.size();
527    }
528   
529    /**
530    * Method isValid.
531    *
532    * @return true if this object is valid according to the schema
533    */
 
534  0 toggle public boolean isValid()
535    {
536  0 try
537    {
538  0 validate();
539    } catch (org.exolab.castor.xml.ValidationException vex)
540    {
541  0 return false;
542    }
543  0 return true;
544    }
545   
546    /**
547    *
548    *
549    * @param out
550    * @throws org.exolab.castor.xml.MarshalException
551    * if object is null or if any SAXException is thrown during
552    * marshaling
553    * @throws org.exolab.castor.xml.ValidationException
554    * if this object is an invalid instance according to the schema
555    */
 
556  0 toggle public void marshal(final java.io.Writer out)
557    throws org.exolab.castor.xml.MarshalException,
558    org.exolab.castor.xml.ValidationException
559    {
560  0 Marshaller.marshal(this, out);
561    }
562   
563    /**
564    *
565    *
566    * @param handler
567    * @throws java.io.IOException
568    * if an IOException occurs during marshaling
569    * @throws org.exolab.castor.xml.ValidationException
570    * if this object is an invalid instance according to the schema
571    * @throws org.exolab.castor.xml.MarshalException
572    * if object is null or if any SAXException is thrown during
573    * marshaling
574    */
 
575  0 toggle public void marshal(final org.xml.sax.ContentHandler handler)
576    throws java.io.IOException,
577    org.exolab.castor.xml.MarshalException,
578    org.exolab.castor.xml.ValidationException
579    {
580  0 Marshaller.marshal(this, handler);
581    }
582   
583    /**
584    */
 
585  0 toggle public void removeAllJGroup()
586    {
587  0 this._JGroupList.clear();
588    }
589   
590    /**
591    */
 
592  0 toggle public void removeAllJSeq()
593    {
594  0 this._JSeqList.clear();
595    }
596   
597    /**
598    */
 
599  0 toggle public void removeAllTree()
600    {
601  0 this._treeList.clear();
602    }
603   
604    /**
605    */
 
606  0 toggle public void removeAllUserColours()
607    {
608  0 this._userColoursList.clear();
609    }
610   
611    /**
612    */
 
613  0 toggle public void removeAllViewport()
614    {
615  0 this._viewportList.clear();
616    }
617   
618    /**
619    * Method removeJGroup.
620    *
621    * @param vJGroup
622    * @return true if the object was removed from the collection.
623    */
 
624  0 toggle public boolean removeJGroup(
625    final jalview.schemabinding.version2.JGroup vJGroup)
626    {
627  0 boolean removed = _JGroupList.remove(vJGroup);
628  0 return removed;
629    }
630   
631    /**
632    * Method removeJGroupAt.
633    *
634    * @param index
635    * @return the element removed from the collection
636    */
 
637  0 toggle public jalview.schemabinding.version2.JGroup removeJGroupAt(
638    final int index)
639    {
640  0 java.lang.Object obj = this._JGroupList.remove(index);
641  0 return (jalview.schemabinding.version2.JGroup) obj;
642    }
643   
644    /**
645    * Method removeJSeq.
646    *
647    * @param vJSeq
648    * @return true if the object was removed from the collection.
649    */
 
650  0 toggle public boolean removeJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
651    {
652  0 boolean removed = _JSeqList.remove(vJSeq);
653  0 return removed;
654    }
655   
656    /**
657    * Method removeJSeqAt.
658    *
659    * @param index
660    * @return the element removed from the collection
661    */
 
662  0 toggle public jalview.schemabinding.version2.JSeq removeJSeqAt(final int index)
663    {
664  0 java.lang.Object obj = this._JSeqList.remove(index);
665  0 return (jalview.schemabinding.version2.JSeq) obj;
666    }
667   
668    /**
669    * Method removeTree.
670    *
671    * @param vTree
672    * @return true if the object was removed from the collection.
673    */
 
674  0 toggle public boolean removeTree(final jalview.schemabinding.version2.Tree vTree)
675    {
676  0 boolean removed = _treeList.remove(vTree);
677  0 return removed;
678    }
679   
680    /**
681    * Method removeTreeAt.
682    *
683    * @param index
684    * @return the element removed from the collection
685    */
 
686  0 toggle public jalview.schemabinding.version2.Tree removeTreeAt(final int index)
687    {
688  0 java.lang.Object obj = this._treeList.remove(index);
689  0 return (jalview.schemabinding.version2.Tree) obj;
690    }
691   
692    /**
693    * Method removeUserColours.
694    *
695    * @param vUserColours
696    * @return true if the object was removed from the collection.
697    */
 
698  0 toggle public boolean removeUserColours(
699    final jalview.schemabinding.version2.UserColours vUserColours)
700    {
701  0 boolean removed = _userColoursList.remove(vUserColours);
702  0 return removed;
703    }
704   
705    /**
706    * Method removeUserColoursAt.
707    *
708    * @param index
709    * @return the element removed from the collection
710    */
 
711  0 toggle public jalview.schemabinding.version2.UserColours removeUserColoursAt(
712    final int index)
713    {
714  0 java.lang.Object obj = this._userColoursList.remove(index);
715  0 return (jalview.schemabinding.version2.UserColours) obj;
716    }
717   
718    /**
719    * Method removeViewport.
720    *
721    * @param vViewport
722    * @return true if the object was removed from the collection.
723    */
 
724  0 toggle public boolean removeViewport(
725    final jalview.schemabinding.version2.Viewport vViewport)
726    {
727  0 boolean removed = _viewportList.remove(vViewport);
728  0 return removed;
729    }
730   
731    /**
732    * Method removeViewportAt.
733    *
734    * @param index
735    * @return the element removed from the collection
736    */
 
737  0 toggle public jalview.schemabinding.version2.Viewport removeViewportAt(
738    final int index)
739    {
740  0 java.lang.Object obj = this._viewportList.remove(index);
741  0 return (jalview.schemabinding.version2.Viewport) obj;
742    }
743   
744    /**
745    * Sets the value of field 'featureSettings'.
746    *
747    * @param featureSettings
748    * the value of field 'featureSettings'.
749    */
 
750  62 toggle public void setFeatureSettings(
751    final jalview.schemabinding.version2.FeatureSettings featureSettings)
752    {
753  62 this._featureSettings = featureSettings;
754    }
755   
756    /**
757    *
758    *
759    * @param index
760    * @param vJGroup
761    * @throws java.lang.IndexOutOfBoundsException
762    * if the index given is outside the bounds of the collection
763    */
 
764  0 toggle public void setJGroup(final int index,
765    final jalview.schemabinding.version2.JGroup vJGroup)
766    throws java.lang.IndexOutOfBoundsException
767    {
768    // check bounds for index
769  0 if (index < 0 || index >= this._JGroupList.size())
770    {
771  0 throw new IndexOutOfBoundsException("setJGroup: Index value '"
772    + index + "' not in range [0.."
773    + (this._JGroupList.size() - 1) + "]");
774    }
775   
776  0 this._JGroupList.set(index, vJGroup);
777    }
778   
779    /**
780    *
781    *
782    * @param vJGroupArray
783    */
 
784  36 toggle public void setJGroup(
785    final jalview.schemabinding.version2.JGroup[] vJGroupArray)
786    {
787    // -- copy array
788  36 _JGroupList.clear();
789   
790  49 for (int i = 0; i < vJGroupArray.length; i++)
791    {
792  13 this._JGroupList.add(vJGroupArray[i]);
793    }
794    }
795   
796    /**
797    *
798    *
799    * @param index
800    * @param vJSeq
801    * @throws java.lang.IndexOutOfBoundsException
802    * if the index given is outside the bounds of the collection
803    */
 
804  0 toggle public void setJSeq(final int index,
805    final jalview.schemabinding.version2.JSeq vJSeq)
806    throws java.lang.IndexOutOfBoundsException
807    {
808    // check bounds for index
809  0 if (index < 0 || index >= this._JSeqList.size())
810    {
811  0 throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
812    + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
813    }
814   
815  0 this._JSeqList.set(index, vJSeq);
816    }
817   
818    /**
819    *
820    *
821    * @param vJSeqArray
822    */
 
823  0 toggle public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray)
824    {
825    // -- copy array
826  0 _JSeqList.clear();
827   
828  0 for (int i = 0; i < vJSeqArray.length; i++)
829    {
830  0 this._JSeqList.add(vJSeqArray[i]);
831    }
832    }
833   
834    /**
835    *
836    *
837    * @param index
838    * @param vTree
839    * @throws java.lang.IndexOutOfBoundsException
840    * if the index given is outside the bounds of the collection
841    */
 
842  0 toggle public void setTree(final int index,
843    final jalview.schemabinding.version2.Tree vTree)
844    throws java.lang.IndexOutOfBoundsException
845    {
846    // check bounds for index
847  0 if (index < 0 || index >= this._treeList.size())
848    {
849  0 throw new IndexOutOfBoundsException("setTree: Index value '" + index
850    + "' not in range [0.." + (this._treeList.size() - 1) + "]");
851    }
852   
853  0 this._treeList.set(index, vTree);
854    }
855   
856    /**
857    *
858    *
859    * @param vTreeArray
860    */
 
861  0 toggle public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray)
862    {
863    // -- copy array
864  0 _treeList.clear();
865   
866  0 for (int i = 0; i < vTreeArray.length; i++)
867    {
868  0 this._treeList.add(vTreeArray[i]);
869    }
870    }
871   
872    /**
873    *
874    *
875    * @param index
876    * @param vUserColours
877    * @throws java.lang.IndexOutOfBoundsException
878    * if the index given is outside the bounds of the collection
879    */
 
880  0 toggle public void setUserColours(final int index,
881    final jalview.schemabinding.version2.UserColours vUserColours)
882    throws java.lang.IndexOutOfBoundsException
883    {
884    // check bounds for index
885  0 if (index < 0 || index >= this._userColoursList.size())
886    {
887  0 throw new IndexOutOfBoundsException("setUserColours: Index value '"
888    + index + "' not in range [0.."
889    + (this._userColoursList.size() - 1) + "]");
890    }
891   
892  0 this._userColoursList.set(index, vUserColours);
893    }
894   
895    /**
896    *
897    *
898    * @param vUserColoursArray
899    */
 
900  0 toggle public void setUserColours(
901    final jalview.schemabinding.version2.UserColours[] vUserColoursArray)
902    {
903    // -- copy array
904  0 _userColoursList.clear();
905   
906  0 for (int i = 0; i < vUserColoursArray.length; i++)
907    {
908  0 this._userColoursList.add(vUserColoursArray[i]);
909    }
910    }
911   
912    /**
913    *
914    *
915    * @param index
916    * @param vViewport
917    * @throws java.lang.IndexOutOfBoundsException
918    * if the index given is outside the bounds of the collection
919    */
 
920  0 toggle public void setViewport(final int index,
921    final jalview.schemabinding.version2.Viewport vViewport)
922    throws java.lang.IndexOutOfBoundsException
923    {
924    // check bounds for index
925  0 if (index < 0 || index >= this._viewportList.size())
926    {
927  0 throw new IndexOutOfBoundsException("setViewport: Index value '"
928    + index + "' not in range [0.."
929    + (this._viewportList.size() - 1) + "]");
930    }
931   
932  0 this._viewportList.set(index, vViewport);
933    }
934   
935    /**
936    *
937    *
938    * @param vViewportArray
939    */
 
940  0 toggle public void setViewport(
941    final jalview.schemabinding.version2.Viewport[] vViewportArray)
942    {
943    // -- copy array
944  0 _viewportList.clear();
945   
946  0 for (int i = 0; i < vViewportArray.length; i++)
947    {
948  0 this._viewportList.add(vViewportArray[i]);
949    }
950    }
951   
952    /**
953    * Method unmarshal.
954    *
955    * @param reader
956    * @throws org.exolab.castor.xml.MarshalException
957    * if object is null or if any SAXException is thrown during
958    * marshaling
959    * @throws org.exolab.castor.xml.ValidationException
960    * if this object is an invalid instance according to the schema
961    * @return the unmarshaled jalview.schemabinding.version2.JalviewModelSequence
962    */
 
963  0 toggle public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(
964    final java.io.Reader reader)
965    throws org.exolab.castor.xml.MarshalException,
966    org.exolab.castor.xml.ValidationException
967    {
968  0 return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller
969    .unmarshal(
970    jalview.schemabinding.version2.JalviewModelSequence.class,
971    reader);
972    }
973   
974    /**
975    *
976    *
977    * @throws org.exolab.castor.xml.ValidationException
978    * if this object is an invalid instance according to the schema
979    */
 
980  0 toggle public void validate() throws org.exolab.castor.xml.ValidationException
981    {
982  0 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
983  0 validator.validate(this);
984    }
985   
986    }
  • 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.