Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ModellerDescription	31	123	67	0.00%	Show methods
ModellerDescription.resCode	80	4	2	0.00%	Show methods

Class ModellerDescription

Class ModellerDescription	Line # 31	Total Statements 123	Complexity 67	TOTAL Coverage 0.00%
ModellerDescription()   ModellerDescription()	7575	1.01	1.01	0.0 0.00%
validResidueCode(String) : resCode   validResidueCode(String) : resCode	9999	11.011	4.04	0.0 0.00%
parseDescription(String) : java.util.Hashtable   parseDescription(String) : java.util.Hashtable	125125	37.037	16.016	0.0 0.00%
ModellerDescription(String)   ModellerDescription(String)	212212	3.03	2.02	0.0 0.00%
setStartCode(int) : void   setStartCode(int) : void	221221	3.03	1.01	0.0 0.00%
setEndCode(int) : void   setEndCode(int) : void	228228	3.03	1.01	0.0 0.00%
ModellerDescription(SequenceI)   ModellerDescription(SequenceI)	241241	21.021	15.015	0.0 0.00%
isModellerFieldset() : boolean   isModellerFieldset() : boolean	308308	1.01	1.01	0.0 0.00%
getDescriptionLine() : String   getDescriptionLine() : String	313313	16.016	8.08	0.0 0.00%
getStartNum() : int   getStartNum() : int	358358	5.05	3.03	0.0 0.00%
getStartCode() : resCode   getStartCode() : resCode	369369	3.03	3.03	0.0 0.00%
getEndCode() : resCode   getEndCode() : resCode	378378	3.03	3.03	0.0 0.00%
getEndNum() : int   getEndNum() : int	387387	5.05	3.03	0.0 0.00%
updateSequenceI(SequenceI) : boolean   updateSequenceI(SequenceI) : boolean	405405	11.011	6.06	0.0 0.00%

 

Class ModellerDescription.resCode

Class ModellerDescription.resCode	Line # 80	Total Statements 4	Complexity 2	TOTAL Coverage 0.00%
resCode(String,Integer)   resCode(String,Integer)	8686	2.02	1.01	0.0 0.00%
resCode(int)   resCode(int)	9292	2.02	1.01	0.0 0.00%

 

Contributing tests

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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;
22
23		import jalview.bin.Cache;
24		import jalview.datamodel.DBRefEntry;
25		import jalview.datamodel.SequenceI;
26
27		import java.util.List;
28
29		import com.stevesoft.pat.Regex;
30
		0% Uncovered Elements: 213 (213) Complexity: 67 Complexity Density: 0.54
31		public class ModellerDescription
32		{
33		/**
34		* Translates between a String containing a set of colon-separated values on a
35		* single line, and sequence start/end and other properties. See PIRFile IO
36		* for its use.
37		*/
38		final String[] seqTypes = { "sequence", "structure", "structureX",
39		"structureN" };
40
41		final String[] Fields = { "objectType", "objectId", "startField",
42		"startCode", "endField", "endCode", "description1", "description2",
43		"resolutionField", "tailField" };
44
45		final int TYPE = 0;
46
47		final int LOCALID = 1;
48
49		final int START = 2;
50
51		final int START_CHAIN = 3;
52
53		final int END = 4;
54
55		final int END_CHAIN = 5;
56
57		final int DESCRIPTION1 = 6;
58
59		final int DESCRIPTION2 = 7;
60
61		final int RESOLUTION = 8;
62
63		final int TAIL = 9;
64
65		/**
66		* 0 is free text or empty 1 is something that parses to an integer, or \@
67		*/
68		final int Types[] = { 0, 0, 1, 0, 1, 0, 0, 0, 0, 0 };
69
70		final char Padding[] = { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.',
71		'.' };
72
73		java.util.Hashtable fields = new java.util.Hashtable();
74
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
75	0	ModellerDescription()...
76		{
77	0	fields.put(Fields[TAIL], "");
78		}
79
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
80		class resCode
81		{
82		Integer val;
83
84		String field;
85
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
86	0	resCode(String f, Integer v)...
87		{
88	0	val = v;
89	0	field = f;
90		}
91
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
92	0	resCode(int v)...
93		{
94	0	val = Integer.valueOf(v);
95	0	field = val.toString();
96		}
97		};
98
		0% Uncovered Elements: 15 (15) Complexity: 4 Complexity Density: 0.36
99	0	private resCode validResidueCode(String field)...
100		{
101	0	Integer val = null;
102	0	Regex r = new Regex("\\s*((([-0-9]+).?)|FIRST|LAST|@)");
103
104	0	if (!r.search(field))
105		{
106	0	return null; // invalid
107		}
108	0	String value = r.stringMatched(3);
109	0	if (value == null)
110		{
111	0	value = r.stringMatched(1);
112		}
113		// Cache.debug("from '" + field + "' matched '" + value +
114		// "'");
115	0	try
116		{
117	0	val = Integer.valueOf(value);
118	0	return new resCode(field, val); // successful numeric extraction
119		} catch (Exception e)
120		{
121		}
122	0	return new resCode(field, null);
123		}
124
		0% Uncovered Elements: 65 (65) Complexity: 16 Complexity Density: 0.43
125	0	private java.util.Hashtable parseDescription(String desc)...
126		{
127	0	java.util.Hashtable fields = new java.util.Hashtable();
128	0	java.util.StringTokenizer st = new java.util.StringTokenizer(desc, ":",
129		true);
130
131	0	String field;
132	0	int type = -1;
133	0	if (st.countTokens() > 0)
134		{
135		// parse colon-fields
136	0	int i = 0;
137	0	field = st.nextToken(":");
138	0	do
139		{
140	0	if (seqTypes[i].equalsIgnoreCase(field))
141		{
142	0	break;
143		}
144	0	} while (++i < seqTypes.length);
145
146	0	if (i < seqTypes.length)
147		{
148	0	st.nextToken(); // skip ':'
149		// valid seqType for modeller
150	0	type = i;
151	0	i = 1; // continue parsing fields
152	0	while (i < TAIL && st.hasMoreTokens())
153		{
154	0	if ((field = st.nextToken(":")) != null)
155		{
156	0	if (!field.equals(":"))
157		{
158		// validate residue field value
159	0	if (Types[i] == 1)
160		{
161	0	resCode val = validResidueCode(field);
162	0	if (val != null)
163		{
164	0	fields.put(new String(Fields[i] + "num"), val);
165		}
166		else
167		{
168		// Cache.debug(
169		// "Ignoring non-Modeller description: invalid integer-like
170		// field '" + field + "'");
171	0	type = -1; /* invalid field! - throw the FieldSet away */
172		}
173	0	;
174		}
175	0	fields.put(Fields[i++], field);
176	0	if (st.hasMoreTokens())
177		{
178	0	st.nextToken(); // skip token sep.
179		}
180		}
181		else
182		{
183	0	i++;
184		}
185		}
186		}
187	0	if (i == TAIL)
188		{
189		// slurp remaining fields
190	0	while (st.hasMoreTokens())
191		{
192	0	String tl = st.nextToken(":");
193	0	field += tl.equals(":") ? tl : (":" + tl);
194		}
195	0	fields.put(Fields[TAIL], field);
196		}
197		}
198		}
199	0	if (type == -1)
200		{
201		// object is not a proper ModellerPIR object
202	0	fields = new java.util.Hashtable();
203	0	fields.put(Fields[TAIL], new String(desc));
204		}
205		else
206		{
207	0	fields.put(Fields[TYPE], seqTypes[type]);
208		}
209	0	return fields;
210		}
211
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
212	0	ModellerDescription(String desc)...
213		{
214	0	if (desc == null)
215		{
216	0	desc = "";
217		}
218	0	fields = parseDescription(desc);
219		}
220
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
221	0	void setStartCode(int v)...
222		{
223	0	resCode r;
224	0	fields.put(Fields[START] + "num", r = new resCode(v));
225	0	fields.put(Fields[START], r.field);
226		}
227
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
228	0	void setEndCode(int v)...
229		{
230	0	resCode r;
231	0	fields.put(Fields[END] + "num", r = new resCode(v));
232	0	fields.put(Fields[END], r.field);
233		}
234
235		/**
236		* make a possibly updated modeller field line for the sequence object
237		*
238		* @param seq
239		* SequenceI
240		*/
		0% Uncovered Elements: 37 (37) Complexity: 15 Complexity Density: 0.71
241	0	ModellerDescription(SequenceI seq)...
242		{
243
244	0	if (seq.getDescription() != null)
245		{
246	0	fields = parseDescription(seq.getDescription());
247		}
248
249	0	if (isModellerFieldset())
250		{
251		// Set start and end before we update the type (in the case of a
252		// synthesized field set)
253	0	if (getStartCode() == null || (getStartNum() != seq.getStart()
254		&& getStartCode().val != null))
255		{
256		// unset or user updated sequence start position
257	0	setStartCode(seq.getStart());
258		}
259
260	0	if (getEndCode() == null || (getEndNum() != seq.getEnd()
261		&& getStartCode() != null && getStartCode().val != null))
262		{
263	0	setEndCode(seq.getEnd());
264		}
265		}
266		else
267		{
268		// synthesize fields
269	0	setStartCode(seq.getStart());
270	0	setEndCode(seq.getEnd());
271	0	fields.put(Fields[LOCALID], seq.getName()); // this may be overwritten
272		// below...
273		// type - decide based on evidence of PDB database references - this also
274		// sets the local reference field
275	0	int t = 0; // sequence
276	0	if (seq.getDatasetSequence() != null
277		&& seq.getDatasetSequence().getDBRefs() != null)
278		{
279	0	List<DBRefEntry> dbr = seq.getDatasetSequence().getDBRefs();
280	0	for (int i = 0, ni = dbr.size(); i < ni; i++)
281		{
282	0	DBRefEntry dbri = dbr.get(i);
283	0	if (dbri != null)
284		{
285		// JBPNote PDB dbRefEntry needs properties to propagate onto
286		// ModellerField
287		// JBPNote Need to get info from the user about whether the sequence
288		// is the one being modelled, or if it is a template.
289	0	if (dbri.getSource().equals(jalview.datamodel.DBRefSource.PDB))
290		{
291	0	fields.put(Fields[LOCALID], dbri.getAccessionId());
292	0	t = 2;
293	0	break;
294		}
295		}
296		}
297		}
298	0	fields.put(Fields[TYPE], seqTypes[t]);
299		}
300
301		}
302
303		/**
304		* Indicate if fields parsed to a modeller-like colon-separated value line
305		*
306		* @return boolean
307		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
308	0	boolean isModellerFieldset()...
309		{
310	0	return (fields.containsKey(Fields[TYPE]));
311		}
312
		0% Uncovered Elements: 28 (28) Complexity: 8 Complexity Density: 0.5
313	0	String getDescriptionLine()...
314		{
315	0	String desc = "";
316	0	int lastfield = Fields.length - 1;
317
318	0	if (isModellerFieldset())
319		{
320	0	String value;
321		// try to write a minimal modeller field set, so..
322
323		// find the last valid field in the entry
324
325	0	for (; lastfield > 6; lastfield--)
326		{
327	0	if (fields.containsKey(Fields[lastfield]))
328		{
329	0	break;
330		}
331		}
332
333	0	for (int i = 0; i < lastfield; i++)
334		{
335	0	value = (String) fields.get(Fields[i]);
336	0	if (value != null && value.length() > 0)
337		{
338	0	desc += ((String) fields.get(Fields[i])) + ":";
339		}
340		else
341		{
342	0	desc += Padding[i] + ":";
343		}
344		}
345		}
346		// just return the last field if no others were defined.
347	0	if (fields.containsKey(Fields[lastfield]))
348		{
349	0	desc += (String) fields.get(Fields[lastfield]);
350		}
351		else
352		{
353	0	desc += ".";
354		}
355	0	return desc;
356		}
357
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.6
358	0	int getStartNum()...
359		{
360	0	int start = 0;
361	0	resCode val = getStartCode();
362	0	if (val != null && val.val != null)
363		{
364	0	return val.val.intValue();
365		}
366	0	return start;
367		}
368
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
369	0	resCode getStartCode()...
370		{
371	0	if (isModellerFieldset() && fields.containsKey(Fields[START] + "num"))
372		{
373	0	return (resCode) fields.get(Fields[START] + "num");
374		}
375	0	return null;
376		}
377
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
378	0	resCode getEndCode()...
379		{
380	0	if (isModellerFieldset() && fields.containsKey(Fields[END] + "num"))
381		{
382	0	return (resCode) fields.get(Fields[END] + "num");
383		}
384	0	return null;
385		}
386
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.6
387	0	int getEndNum()...
388		{
389	0	int end = 0;
390	0	resCode val = getEndCode();
391	0	if (val != null && val.val != null)
392		{
393	0	return val.val.intValue();
394		}
395	0	return end;
396		}
397
398		/**
399		* returns true if sequence object was modifed with a valid modellerField set
400		*
401		* @param newSeq
402		* SequenceI
403		* @return boolean
404		*/
		0% Uncovered Elements: 17 (17) Complexity: 6 Complexity Density: 0.55
405	0	boolean updateSequenceI(SequenceI newSeq)...
406		{
407	0	if (isModellerFieldset())
408		{
409	0	resCode rc = getStartCode();
410	0	if (rc != null && rc.val != null)
411		{
412	0	newSeq.setStart(getStartNum());
413		}
414		else
415		{
416	0	newSeq.setStart(1);
417		}
418	0	rc = getEndCode();
419	0	if (rc != null && rc.val != null)
420		{
421	0	newSeq.setEnd(getEndNum());
422		}
423		else
424		{
425	0	newSeq.setEnd(newSeq.getStart() + newSeq.getLength());
426		}
427	0	return true;
428		}
429	0	return false;
430		}
431		}