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jalviewX

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

File Colour.java

 

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35% of files have more coverage

Code metrics

10
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49
1
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281
57
0.78
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1.16

Classes

Class Line # Actions
Colour 22 73 57 60
0.5454545654.5%
 

Contributing tests

This file is covered by 1 test. .

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 Colour.
19    *
20    * @version $Revision$ $Date$
21    */
 
22    public class Colour implements java.io.Serializable
23    {
24   
25    // --------------------------/
26    // - Class/Member Variables -/
27    // --------------------------/
28   
29    /**
30    * Single letter residue code for an alignment colour scheme, or feature type
31    * for a feature colour scheme
32    */
33    private java.lang.String _name;
34   
35    /**
36    * Field _RGB.
37    */
38    private java.lang.String _RGB;
39   
40    /**
41    * Field _minRGB.
42    */
43    private java.lang.String _minRGB;
44   
45    /**
46    * Field _noValueColour.
47    */
48    private jalview.schemabinding.version2.types.NoValueColour _noValueColour = jalview.schemabinding.version2.types.NoValueColour
49    .valueOf("Min");
50   
51    /**
52    * Field _threshType.
53    */
54    private jalview.schemabinding.version2.types.ColourThreshTypeType _threshType;
55   
56    /**
57    * Field _threshold.
58    */
59    private float _threshold;
60   
61    /**
62    * keeps track of state for field: _threshold
63    */
64    private boolean _has_threshold;
65   
66    /**
67    * Field _max.
68    */
69    private float _max;
70   
71    /**
72    * keeps track of state for field: _max
73    */
74    private boolean _has_max;
75   
76    /**
77    * Field _min.
78    */
79    private float _min;
80   
81    /**
82    * keeps track of state for field: _min
83    */
84    private boolean _has_min;
85   
86    /**
87    * Field _colourByLabel.
88    */
89    private boolean _colourByLabel;
90   
91    /**
92    * keeps track of state for field: _colourByLabel
93    */
94    private boolean _has_colourByLabel;
95   
96    /**
97    * Field _autoScale.
98    */
99    private boolean _autoScale;
100   
101    /**
102    * keeps track of state for field: _autoScale
103    */
104    private boolean _has_autoScale;
105   
106    /**
107    * name of feature attribute to colour by, or attribute and sub-attribute
108    */
109    private java.util.Vector _attributeNameList;
110   
111    // ----------------/
112    // - Constructors -/
113    // ----------------/
114   
 
115  10 toggle public Colour()
116    {
117  10 super();
118  10 setNoValueColour(jalview.schemabinding.version2.types.NoValueColour
119    .valueOf("Min"));
120  10 this._attributeNameList = new java.util.Vector();
121    }
122   
123    // -----------/
124    // - Methods -/
125    // -----------/
126   
127    /**
128    *
129    *
130    * @param vAttributeName
131    * @throws java.lang.IndexOutOfBoundsException
132    * if the index given is outside the bounds of the collection
133    */
 
134  3 toggle public void addAttributeName(final java.lang.String vAttributeName)
135    throws java.lang.IndexOutOfBoundsException
136    {
137    // check for the maximum size
138  3 if (this._attributeNameList.size() >= 2)
139    {
140  0 throw new IndexOutOfBoundsException(
141    "addAttributeName has a maximum of 2");
142    }
143   
144  3 this._attributeNameList.addElement(vAttributeName);
145    }
146   
147    /**
148    *
149    *
150    * @param index
151    * @param vAttributeName
152    * @throws java.lang.IndexOutOfBoundsException
153    * if the index given is outside the bounds of the collection
154    */
 
155  0 toggle public void addAttributeName(final int index,
156    final java.lang.String vAttributeName)
157    throws java.lang.IndexOutOfBoundsException
158    {
159    // check for the maximum size
160  0 if (this._attributeNameList.size() >= 2)
161    {
162  0 throw new IndexOutOfBoundsException(
163    "addAttributeName has a maximum of 2");
164    }
165   
166  0 this._attributeNameList.add(index, vAttributeName);
167    }
168   
169    /**
170    */
 
171  0 toggle public void deleteAutoScale()
172    {
173  0 this._has_autoScale = false;
174    }
175   
176    /**
177    */
 
178  0 toggle public void deleteColourByLabel()
179    {
180  0 this._has_colourByLabel = false;
181    }
182   
183    /**
184    */
 
185  0 toggle public void deleteMax()
186    {
187  0 this._has_max = false;
188    }
189   
190    /**
191    */
 
192  0 toggle public void deleteMin()
193    {
194  0 this._has_min = false;
195    }
196   
197    /**
198    */
 
199  0 toggle public void deleteThreshold()
200    {
201  0 this._has_threshold = false;
202    }
203   
204    /**
205    * Method enumerateAttributeName.
206    *
207    * @return an Enumeration over all java.lang.String elements
208    */
 
209  0 toggle public java.util.Enumeration enumerateAttributeName()
210    {
211  0 return this._attributeNameList.elements();
212    }
213   
214    /**
215    * Method getAttributeName.
216    *
217    * @param index
218    * @throws java.lang.IndexOutOfBoundsException
219    * if the index given is outside the bounds of the collection
220    * @return the value of the java.lang.String at the given index
221    */
 
222  0 toggle public java.lang.String getAttributeName(final int index)
223    throws java.lang.IndexOutOfBoundsException
224    {
225    // check bounds for index
226  0 if (index < 0 || index >= this._attributeNameList.size())
227    {
228  0 throw new IndexOutOfBoundsException("getAttributeName: Index value '"
229    + index + "' not in range [0.."
230    + (this._attributeNameList.size() - 1) + "]");
231    }
232   
233  0 return (java.lang.String) _attributeNameList.get(index);
234    }
235   
236    /**
237    * Method getAttributeName.Returns the contents of the collection in an Array.
238    * <p>
239    * Note: Just in case the collection contents are changing in another thread,
240    * we pass a 0-length Array of the correct type into the API call. This way we
241    * <i>know</i> that the Array returned is of exactly the correct length.
242    *
243    * @return this collection as an Array
244    */
 
245  19 toggle public java.lang.String[] getAttributeName()
246    {
247  19 java.lang.String[] array = new java.lang.String[0];
248  19 return (java.lang.String[]) this._attributeNameList.toArray(array);
249    }
250   
251    /**
252    * Method getAttributeNameCount.
253    *
254    * @return the size of this collection
255    */
 
256  0 toggle public int getAttributeNameCount()
257    {
258  0 return this._attributeNameList.size();
259    }
260   
261    /**
262    * Returns the value of field 'autoScale'.
263    *
264    * @return the value of field 'AutoScale'.
265    */
 
266  16 toggle public boolean getAutoScale()
267    {
268  16 return this._autoScale;
269    }
270   
271    /**
272    * Returns the value of field 'colourByLabel'.
273    *
274    * @return the value of field 'ColourByLabel'.
275    */
 
276  16 toggle public boolean getColourByLabel()
277    {
278  16 return this._colourByLabel;
279    }
280   
281    /**
282    * Returns the value of field 'max'.
283    *
284    * @return the value of field 'Max'.
285    */
 
286  16 toggle public float getMax()
287    {
288  16 return this._max;
289    }
290   
291    /**
292    * Returns the value of field 'min'.
293    *
294    * @return the value of field 'Min'.
295    */
 
296  16 toggle public float getMin()
297    {
298  16 return this._min;
299    }
300   
301    /**
302    * Returns the value of field 'minRGB'.
303    *
304    * @return the value of field 'MinRGB'.
305    */
 
306  19 toggle public java.lang.String getMinRGB()
307    {
308  19 return this._minRGB;
309    }
310   
311    /**
312    * Returns the value of field 'name'. The field 'name' has the following
313    * description: Single letter residue code for an alignment colour scheme, or
314    * feature type for a feature colour scheme
315    *
316    * @return the value of field 'Name'.
317    */
 
318  25 toggle public java.lang.String getName()
319    {
320  25 return this._name;
321    }
322   
323    /**
324    * Returns the value of field 'noValueColour'.
325    *
326    * @return the value of field 'NoValueColour'.
327    */
 
328  19 toggle public jalview.schemabinding.version2.types.NoValueColour getNoValueColour()
329    {
330  19 return this._noValueColour;
331    }
332   
333    /**
334    * Returns the value of field 'RGB'.
335    *
336    * @return the value of field 'RGB'.
337    */
 
338  20 toggle public java.lang.String getRGB()
339    {
340  20 return this._RGB;
341    }
342   
343    /**
344    * Returns the value of field 'threshType'.
345    *
346    * @return the value of field 'ThreshType'.
347    */
 
348  19 toggle public jalview.schemabinding.version2.types.ColourThreshTypeType getThreshType()
349    {
350  19 return this._threshType;
351    }
352   
353    /**
354    * Returns the value of field 'threshold'.
355    *
356    * @return the value of field 'Threshold'.
357    */
 
358  16 toggle public float getThreshold()
359    {
360  16 return this._threshold;
361    }
362   
363    /**
364    * Method hasAutoScale.
365    *
366    * @return true if at least one AutoScale has been added
367    */
 
368  19 toggle public boolean hasAutoScale()
369    {
370  19 return this._has_autoScale;
371    }
372   
373    /**
374    * Method hasColourByLabel.
375    *
376    * @return true if at least one ColourByLabel has been added
377    */
 
378  19 toggle public boolean hasColourByLabel()
379    {
380  19 return this._has_colourByLabel;
381    }
382   
383    /**
384    * Method hasMax.
385    *
386    * @return true if at least one Max has been added
387    */
 
388  20 toggle public boolean hasMax()
389    {
390  20 return this._has_max;
391    }
392   
393    /**
394    * Method hasMin.
395    *
396    * @return true if at least one Min has been added
397    */
 
398  15 toggle public boolean hasMin()
399    {
400  15 return this._has_min;
401    }
402   
403    /**
404    * Method hasThreshold.
405    *
406    * @return true if at least one Threshold has been added
407    */
 
408  19 toggle public boolean hasThreshold()
409    {
410  19 return this._has_threshold;
411    }
412   
413    /**
414    * Returns the value of field 'autoScale'.
415    *
416    * @return the value of field 'AutoScale'.
417    */
 
418  0 toggle public boolean isAutoScale()
419    {
420  0 return this._autoScale;
421    }
422   
423    /**
424    * Returns the value of field 'colourByLabel'.
425    *
426    * @return the value of field 'ColourByLabel'.
427    */
 
428  0 toggle public boolean isColourByLabel()
429    {
430  0 return this._colourByLabel;
431    }
432   
433    /**
434    * Method isValid.
435    *
436    * @return true if this object is valid according to the schema
437    */
 
438  0 toggle public boolean isValid()
439    {
440  0 try
441    {
442  0 validate();
443    } catch (org.exolab.castor.xml.ValidationException vex)
444    {
445  0 return false;
446    }
447  0 return true;
448    }
449   
450    /**
451    *
452    *
453    * @param out
454    * @throws org.exolab.castor.xml.MarshalException
455    * if object is null or if any SAXException is thrown during
456    * marshaling
457    * @throws org.exolab.castor.xml.ValidationException
458    * if this object is an invalid instance according to the schema
459    */
 
460  0 toggle public void marshal(final java.io.Writer out)
461    throws org.exolab.castor.xml.MarshalException,
462    org.exolab.castor.xml.ValidationException
463    {
464  0 Marshaller.marshal(this, out);
465    }
466   
467    /**
468    *
469    *
470    * @param handler
471    * @throws java.io.IOException
472    * if an IOException occurs during marshaling
473    * @throws org.exolab.castor.xml.ValidationException
474    * if this object is an invalid instance according to the schema
475    * @throws org.exolab.castor.xml.MarshalException
476    * if object is null or if any SAXException is thrown during
477    * marshaling
478    */
 
479  0 toggle public void marshal(final org.xml.sax.ContentHandler handler)
480    throws java.io.IOException,
481    org.exolab.castor.xml.MarshalException,
482    org.exolab.castor.xml.ValidationException
483    {
484  0 Marshaller.marshal(this, handler);
485    }
486   
487    /**
488    */
 
489  0 toggle public void removeAllAttributeName()
490    {
491  0 this._attributeNameList.clear();
492    }
493   
494    /**
495    * Method removeAttributeName.
496    *
497    * @param vAttributeName
498    * @return true if the object was removed from the collection.
499    */
 
500  0 toggle public boolean removeAttributeName(final java.lang.String vAttributeName)
501    {
502  0 boolean removed = _attributeNameList.remove(vAttributeName);
503  0 return removed;
504    }
505   
506    /**
507    * Method removeAttributeNameAt.
508    *
509    * @param index
510    * @return the element removed from the collection
511    */
 
512  0 toggle public java.lang.String removeAttributeNameAt(final int index)
513    {
514  0 java.lang.Object obj = this._attributeNameList.remove(index);
515  0 return (java.lang.String) obj;
516    }
517   
518    /**
519    *
520    *
521    * @param index
522    * @param vAttributeName
523    * @throws java.lang.IndexOutOfBoundsException
524    * if the index given is outside the bounds of the collection
525    */
 
526  0 toggle public void setAttributeName(final int index,
527    final java.lang.String vAttributeName)
528    throws java.lang.IndexOutOfBoundsException
529    {
530    // check bounds for index
531  0 if (index < 0 || index >= this._attributeNameList.size())
532    {
533  0 throw new IndexOutOfBoundsException("setAttributeName: Index value '"
534    + index + "' not in range [0.."
535    + (this._attributeNameList.size() - 1) + "]");
536    }
537   
538  0 this._attributeNameList.set(index, vAttributeName);
539    }
540   
541    /**
542    *
543    *
544    * @param vAttributeNameArray
545    */
 
546  2 toggle public void setAttributeName(final java.lang.String[] vAttributeNameArray)
547    {
548    // -- copy array
549  2 _attributeNameList.clear();
550   
551  5 for (int i = 0; i < vAttributeNameArray.length; i++)
552    {
553  3 this._attributeNameList.add(vAttributeNameArray[i]);
554    }
555    }
556   
557    /**
558    * Sets the value of field 'autoScale'.
559    *
560    * @param autoScale
561    * the value of field 'autoScale'.
562    */
 
563  8 toggle public void setAutoScale(final boolean autoScale)
564    {
565  8 this._autoScale = autoScale;
566  8 this._has_autoScale = true;
567    }
568   
569    /**
570    * Sets the value of field 'colourByLabel'.
571    *
572    * @param colourByLabel
573    * the value of field 'colourByLabel'.
574    */
 
575  8 toggle public void setColourByLabel(final boolean colourByLabel)
576    {
577  8 this._colourByLabel = colourByLabel;
578  8 this._has_colourByLabel = true;
579    }
580   
581    /**
582    * Sets the value of field 'max'.
583    *
584    * @param max
585    * the value of field 'max'.
586    */
 
587  8 toggle public void setMax(final float max)
588    {
589  8 this._max = max;
590  8 this._has_max = true;
591    }
592   
593    /**
594    * Sets the value of field 'min'.
595    *
596    * @param min
597    * the value of field 'min'.
598    */
 
599  8 toggle public void setMin(final float min)
600    {
601  8 this._min = min;
602  8 this._has_min = true;
603    }
604   
605    /**
606    * Sets the value of field 'minRGB'.
607    *
608    * @param minRGB
609    * the value of field 'minRGB'.
610    */
 
611  8 toggle public void setMinRGB(final java.lang.String minRGB)
612    {
613  8 this._minRGB = minRGB;
614    }
615   
616    /**
617    * Sets the value of field 'name'. The field 'name' has the following
618    * description: Single letter residue code for an alignment colour scheme, or
619    * feature type for a feature colour scheme
620    *
621    * @param name
622    * the value of field 'name'.
623    */
 
624  10 toggle public void setName(final java.lang.String name)
625    {
626  10 this._name = name;
627    }
628   
629    /**
630    * Sets the value of field 'noValueColour'.
631    *
632    * @param noValueColour
633    * the value of field 'noValueColour'.
634    */
 
635  19 toggle public void setNoValueColour(
636    final jalview.schemabinding.version2.types.NoValueColour noValueColour)
637    {
638  19 this._noValueColour = noValueColour;
639    }
640   
641    /**
642    * Sets the value of field 'RGB'.
643    *
644    * @param RGB
645    * the value of field 'RGB'.
646    */
 
647  10 toggle public void setRGB(final java.lang.String RGB)
648    {
649  10 this._RGB = RGB;
650    }
651   
652    /**
653    * Sets the value of field 'threshType'.
654    *
655    * @param threshType
656    * the value of field 'threshType'.
657    */
 
658  8 toggle public void setThreshType(
659    final jalview.schemabinding.version2.types.ColourThreshTypeType threshType)
660    {
661  8 this._threshType = threshType;
662    }
663   
664    /**
665    * Sets the value of field 'threshold'.
666    *
667    * @param threshold
668    * the value of field 'threshold'.
669    */
 
670  8 toggle public void setThreshold(final float threshold)
671    {
672  8 this._threshold = threshold;
673  8 this._has_threshold = true;
674    }
675   
676    /**
677    * Method unmarshal.
678    *
679    * @param reader
680    * @throws org.exolab.castor.xml.MarshalException
681    * if object is null or if any SAXException is thrown during
682    * marshaling
683    * @throws org.exolab.castor.xml.ValidationException
684    * if this object is an invalid instance according to the schema
685    * @return the unmarshaled jalview.schemabinding.version2.Colour
686    */
 
687  0 toggle public static jalview.schemabinding.version2.Colour unmarshal(
688    final java.io.Reader reader)
689    throws org.exolab.castor.xml.MarshalException,
690    org.exolab.castor.xml.ValidationException
691    {
692  0 return (jalview.schemabinding.version2.Colour) Unmarshaller
693    .unmarshal(jalview.schemabinding.version2.Colour.class, reader);
694    }
695   
696    /**
697    *
698    *
699    * @throws org.exolab.castor.xml.ValidationException
700    * if this object is an invalid instance according to the schema
701    */
 
702  0 toggle public void validate() throws org.exolab.castor.xml.ValidationException
703    {
704  0 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
705  0 validator.validate(this);
706    }
707   
708    }
  • 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.