Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
Rangetype	43	106	55	192	0.00%	Show methods

Class Rangetype

Class Rangetype	Line # 43	Total Statements 106	Complexity 55	Uncovered Elements 192	TOTAL Coverage 0.00%
Rangetype()   Rangetype()	4646	1.01	1.01	1.01	0.0 0.00%
Rangetype(VamsasAppDatastore)   Rangetype(VamsasAppDatastore)	5151	1.01	1.01	1.01	0.0 0.00%
Rangetype(VamsasAppDatastore,Vobject,Class)   Rangetype(VamsasAppDatastore,Vobject,Class)	5656	1.01	1.01	1.01	0.0 0.00%
Rangetype(VamsasAppDatastore,Object,Class)   Rangetype(VamsasAppDatastore,Object,Class)	6262	1.01	1.01	1.01	0.0 0.00%
getBounds(RangeType) : int[]   getBounds(RangeType) : int[]	7575	23.023	12.012	43.043	0.0 0.00%
getMapping(RangeType) : int[]   getMapping(RangeType) : int[]	132132	23.023	14.014	45.045	0.0 0.00%
getIntervals(RangeType) : int[]   getIntervals(RangeType) : int[]	179179	24.024	11.011	40.040	0.0 0.00%
initRangeType(RangeType,List<int[]>) : void   initRangeType(RangeType,List<int[]>) : void	231231	6.06	1.01	6.06	0.0 0.00%
parsemapType(MapType,int,int) : jalview.util.MapList   parsemapType(MapType,int,int) : jalview.util.MapList	254254	7.07	3.03	11.011	0.0 0.00%
parsemapType(MapType) : jalview.util.MapList   parsemapType(MapType) : jalview.util.MapList	270270	3.03	4.04	7.07	0.0 0.00%
initMapType(MapType,jalview.util.MapList,boolean) : void   initMapType(MapType,jalview.util.MapList,boolean) : void	289289	1.01	1.01	1.01	0.0 0.00%
initMapType(MapType,jalview.util.MapList,boolean,boolean) : void   initMapType(MapType,jalview.util.MapList,boolean,boolean) : void	303303	15.015	5.05	23.023	0.0 0.00%

 

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.io.vamsas;
22
23		import jalview.io.VamsasAppDatastore;
24		import jalview.util.MessageManager;
25
26		import java.util.List;
27		import java.util.Vector;
28
29		import uk.ac.vamsas.client.Vobject;
30		import uk.ac.vamsas.objects.core.Local;
31		import uk.ac.vamsas.objects.core.MapType;
32		import uk.ac.vamsas.objects.core.Mapped;
33		import uk.ac.vamsas.objects.core.RangeType;
34		import uk.ac.vamsas.objects.core.Seg;
35
36		/**
37		* Enhances DatastoreItem objects with additional functions to do with RangeType
38		* objects
39		*
40		* @author JimP
41		*
42		*/
		0% Uncovered Elements: 192 (192) Complexity: 55 Complexity Density: 0.52
43		public abstract class Rangetype extends DatastoreItem
44		{
45
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
46	0	public Rangetype()...
47		{
48	0	super();
49		}
50
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
51	0	public Rangetype(VamsasAppDatastore datastore)...
52		{
53	0	super(datastore);
54		}
55
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
56	0	public Rangetype(VamsasAppDatastore datastore, Vobject vobj,...
57		Class jvClass)
58		{
59	0	super(datastore, vobj, jvClass);
60		}
61
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
62	0	public Rangetype(VamsasAppDatastore datastore, Object jvobj, Class vClass)...
63		{
64	0	super(datastore, jvobj, vClass);
65		}
66
67		/**
68		* get real bounds of a RangeType's specification. start and end are an
69		* inclusive range within which all segments and positions lie. TODO: refactor
70		* to vamsas utils
71		*
72		* @param dseta
73		* @return int[] { start, end}
74		*/
		0% Uncovered Elements: 43 (43) Complexity: 12 Complexity Density: 0.52
75	0	protected int[] getBounds(RangeType dseta)...
76		{
77	0	if (dseta != null)
78		{
79	0	int[] se = null;
80	0	if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
81		{
82	0	throw new Error(MessageManager.getString(
83		"error.invalid_vamsas_rangetype_cannot_resolve_lists"));
84		}
85	0	if (dseta.getSegCount() > 0)
86		{
87	0	se = getSegRange(dseta.getSeg(0), true);
88	0	for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)
89		{
90	0	int nse[] = getSegRange(dseta.getSeg(s), true);
91	0	if (se[0] > nse[0])
92		{
93	0	se[0] = nse[0];
94		}
95	0	if (se[1] < nse[1])
96		{
97	0	se[1] = nse[1];
98		}
99		}
100		}
101	0	if (dseta.getPosCount() > 0)
102		{
103		// could do a polarity for pos range too. and pass back indication of
104		// discontinuities.
105	0	int pos = dseta.getPos(0).getI();
106	0	se = new int[] { pos, pos };
107	0	for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
108		{
109	0	pos = dseta.getPos(p).getI();
110	0	if (se[0] > pos)
111		{
112	0	se[0] = pos;
113		}
114	0	if (se[1] < pos)
115		{
116	0	se[1] = pos;
117		}
118		}
119		}
120	0	return se;
121		}
122	0	return null;
123		}
124
125		/**
126		* map from a rangeType's internal frame to the referenced object's coordinate
127		* frame.
128		*
129		* @param dseta
130		* @return int [] { ref(pos)...} for all pos in rangeType's frame.
131		*/
		0% Uncovered Elements: 45 (45) Complexity: 14 Complexity Density: 0.61
132	0	protected int[] getMapping(RangeType dseta)...
133		{
134	0	Vector posList = new Vector();
135	0	if (dseta != null)
136		{
137	0	int[] se = null;
138	0	if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
139		{
140	0	throw new Error(MessageManager.getString(
141		"error.invalid_vamsas_rangetype_cannot_resolve_lists"));
142		}
143	0	if (dseta.getSegCount() > 0)
144		{
145	0	for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)
146		{
147	0	se = getSegRange(dseta.getSeg(s), false);
148	0	int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
149	0	for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
150		{
151	0	posList.add(new Integer(p));
152		}
153		}
154		}
155	0	else if (dseta.getPosCount() > 0)
156		{
157	0	int pos = dseta.getPos(0).getI();
158
159	0	for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
160		{
161	0	pos = dseta.getPos(p).getI();
162	0	posList.add(new Integer(pos));
163		}
164		}
165		}
166	0	if (posList != null && posList.size() > 0)
167		{
168	0	int[] range = new int[posList.size()];
169	0	for (int i = 0; i < range.length; i++)
170		{
171	0	range[i] = ((Integer) posList.elementAt(i)).intValue();
172		}
173	0	posList.clear();
174	0	return range;
175		}
176	0	return null;
177		}
178
		0% Uncovered Elements: 40 (40) Complexity: 11 Complexity Density: 0.46
179	0	protected int[] getIntervals(RangeType range)...
180		{
181	0	int[] intervals = null;
182	0	Vector posList = new Vector();
183	0	if (range != null)
184		{
185	0	int[] se = null;
186	0	if (range.getSegCount() > 0 && range.getPosCount() > 0)
187		{
188	0	throw new Error(MessageManager.getString(
189		"error.invalid_vamsas_rangetype_cannot_resolve_lists"));
190		}
191	0	if (range.getSegCount() > 0)
192		{
193	0	for (int s = 0, sSize = range.getSegCount(); s < sSize; s++)
194		{
195	0	se = getSegRange(range.getSeg(s), false);
196	0	posList.addElement(new Integer(se[0]));
197	0	posList.addElement(new Integer(se[1]));
198		}
199		}
200	0	else if (range.getPosCount() > 0)
201		{
202	0	int pos = range.getPos(0).getI();
203
204	0	for (int p = 0, pSize = range.getPosCount(); p < pSize; p++)
205		{
206	0	pos = range.getPos(p).getI();
207	0	posList.add(new Integer(pos));
208	0	posList.add(new Integer(pos));
209		}
210		}
211		}
212	0	if (posList != null && posList.size() > 0)
213		{
214	0	intervals = new int[posList.size()];
215	0	java.util.Enumeration e = posList.elements();
216	0	int i = 0;
217	0	while (e.hasMoreElements())
218		{
219	0	intervals[i++] = ((Integer) e.nextElement()).intValue();
220		}
221		}
222	0	return intervals;
223		}
224
225		/**
226		* initialise a range type object from a set of start/end inclusive intervals
227		*
228		* @param mrt
229		* @param ranges
230		*/
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
231	0	protected void initRangeType(RangeType mrt, List<int[]> ranges)...
232		{
233	0	for (int[] range : ranges)
234		{
235	0	Seg vSeg = new Seg();
236	0	vSeg.setStart(range[0]);
237	0	vSeg.setEnd(range[1]);
238	0	vSeg.setInclusive(true);
239	0	mrt.addSeg(vSeg);
240		}
241		}
242
243		/**
244		*
245		* @param maprange
246		* where the from range is the local mapped range, and the to range
247		* is the 'mapped' range in the MapRangeType
248		* @param default
249		* unit for local
250		* @param default
251		* unit for mapped
252		* @return MapList
253		*/
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
254	0	protected jalview.util.MapList parsemapType(MapType maprange, int localu,...
255		int mappedu)
256		{
257	0	jalview.util.MapList ml = null;
258	0	int[] localRange = getIntervals(maprange.getLocal());
259	0	int[] mappedRange = getIntervals(maprange.getMapped());
260	0	long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()
261		: localu;
262	0	long mu = maprange.getMapped().hasUnit()
263		? maprange.getMapped().getUnit()
264		: mappedu;
265	0	ml = new jalview.util.MapList(localRange, mappedRange, (int) lu,
266		(int) mu);
267	0	return ml;
268		}
269
		0% Uncovered Elements: 7 (7) Complexity: 4 Complexity Density: 1.33
270	0	protected jalview.util.MapList parsemapType(MapType map)...
271		{
272	0	if (!map.getLocal().hasUnit() || map.getMapped().hasUnit())
273		{
274	0	jalview.bin.Cache.log
275		.warn("using default mapping length of 1:1 for map "
276	0	+ (map.isRegistered() ? map.getVorbaId().toString()
277		: ("<no Id registered> " + map.toString())));
278		}
279	0	return parsemapType(map, 1, 1);
280		}
281
282		/**
283		* initialise a MapType object from a MapList object.
284		*
285		* @param maprange
286		* @param ml
287		* @param setUnits
288		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
289	0	protected void initMapType(MapType maprange, jalview.util.MapList ml,...
290		boolean setUnits)
291		{
292	0	initMapType(maprange, ml, setUnits, false);
293		}
294
295		/**
296		*
297		* @param maprange
298		* @param ml
299		* @param setUnits
300		* @param reverse
301		* - reverse MapList mapping for Local and Mapped ranges and units
302		*/
		0% Uncovered Elements: 23 (23) Complexity: 5 Complexity Density: 0.33
303	0	protected void initMapType(MapType maprange, jalview.util.MapList ml,...
304		boolean setUnits, boolean reverse)
305		{
306	0	if (ml == null)
307		{
308	0	throw new Error(MessageManager
309		.getString("error.implementation_error_maplist_is_null"));
310		}
311	0	maprange.setLocal(new Local());
312	0	maprange.setMapped(new Mapped());
313	0	if (!reverse)
314		{
315	0	initRangeType(maprange.getLocal(), ml.getFromRanges());
316	0	initRangeType(maprange.getMapped(), ml.getToRanges());
317		}
318		else
319		{
320	0	initRangeType(maprange.getLocal(), ml.getToRanges());
321	0	initRangeType(maprange.getMapped(), ml.getFromRanges());
322		}
323	0	if (setUnits)
324		{
325	0	if (!reverse)
326		{
327	0	maprange.getLocal().setUnit(ml.getFromRatio());
328	0	maprange.getMapped().setUnit(ml.getToRatio());
329		}
330		else
331		{
332	0	maprange.getLocal().setUnit(ml.getToRatio());
333	0	maprange.getMapped().setUnit(ml.getFromRatio());
334		}
335		// TODO: and verify - raise an implementation fault notice if local/mapped
336		// range % Local/Mapped Ratio != 0
337		// if (uk.ac.vamsas.objects.utils.Range.getIntervals(range))
338
339		}
340		}
341
342		}