Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
StructureMapping	31	104	53	0.00%	Show methods

Class StructureMapping

Class StructureMapping	Line # 31	Total Statements 104	Complexity 53	TOTAL Coverage 0.00%
StructureMapping(SequenceI,String,String,String,HashMap<Integer, int[]>,String)   StructureMapping(SequenceI,String,String,String,HashMap<Integer, int[]>,String)	6767	6.06	1.01	0.0 0.00%
StructureMapping(SequenceI,String,String,String,HashMap<Integer, int[]>,String,Mapping)   StructureMapping(SequenceI,String,String,String,HashMap<Integer, int[]>,String,Mapping)	7979	2.02	1.01	0.0 0.00%
getSequence() : SequenceI   getSequence() : SequenceI	8787	1.01	1.01	0.0 0.00%
getChain() : String   getChain() : String	9292	1.01	1.01	0.0 0.00%
getPdbId() : String   getPdbId() : String	9797	1.01	1.01	0.0 0.00%
getAtomNum(int) : int   getAtomNum(int) : int	107107	4.04	2.02	0.0 0.00%
getPDBResNum(int) : int   getPDBResNum(int) : int	126126	4.04	2.02	0.0 0.00%
getPDBResNumRanges(int,int) : List<int[]>   getPDBResNumRanges(int,int) : List<int[]>	147147	24.024	9.09	0.0 0.00%
getSeqPos(int) : int   getSeqPos(int) : int	208208	4.04	2.02	0.0 0.00%
transfer(AlignmentAnnotation) : AlignmentAnnotation   transfer(AlignmentAnnotation) : AlignmentAnnotation	230230	10.010	3.03	0.0 0.00%
getMappingDetailsOutput() : String   getMappingDetailsOutput() : String	253253	1.01	1.01	0.0 0.00%
getMapping() : HashMap<Integer, int[]>   getMapping() : HashMap<Integer, int[]>	258258	1.01	1.01	0.0 0.00%
getSeqToPdbMapping() : Mapping   getSeqToPdbMapping() : Mapping	263263	1.01	1.01	0.0 0.00%
hashCode() : int   hashCode() : int	272272	9.09	7.07	0.0 0.00%
equals(Object) : boolean   equals(Object) : boolean	290290	35.035	20.020	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.structure;
22
23		import jalview.datamodel.AlignmentAnnotation;
24		import jalview.datamodel.Mapping;
25		import jalview.datamodel.SequenceI;
26
27		import java.util.ArrayList;
28		import java.util.HashMap;
29		import java.util.List;
30
		0% Uncovered Elements: 193 (193) Complexity: 53 Complexity Density: 0.51
31		public class StructureMapping
32		{
33		public static final int UNASSIGNED_VALUE = Integer.MIN_VALUE;
34
35		private static final int PDB_RES_NUM_INDEX = 0;
36
37		private static final int PDB_ATOM_NUM_INDEX = 1;
38
39		String mappingDetails;
40
41		SequenceI sequence;
42
43		String pdbfile;
44
45		String pdbid;
46
47		String pdbchain;
48
49		// Mapping key is residue index while value is an array containing PDB resNum,
50		// and atomNo
51		HashMap<Integer, int[]> mapping;
52
53		jalview.datamodel.Mapping seqToPdbMapping = null;
54
55		/**
56		* Constructor
57		*
58		* @param seq
59		* @param pdbfile
60		* @param pdbid
61		* @param chain
62		* @param mapping
63		* a map from sequence to two values, { resNo, atomNo } in the
64		* structure
65		* @param mappingDetails
66		*/
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
67	0	public StructureMapping(SequenceI seq, String pdbfile, String pdbid,...
68		String chain, HashMap<Integer, int[]> mapping,
69		String mappingDetails)
70		{
71	0	sequence = seq;
72	0	this.pdbfile = pdbfile;
73	0	this.pdbid = pdbid;
74	0	this.pdbchain = chain;
75	0	this.mapping = mapping;
76	0	this.mappingDetails = mappingDetails;
77		}
78
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
79	0	public StructureMapping(SequenceI seq, String pdbFile2, String pdbId2,...
80		String chain, HashMap<Integer, int[]> mapping2,
81		String mappingOutput, Mapping seqToPdbMapping)
82		{
83	0	this(seq, pdbFile2, pdbId2, chain, mapping2, mappingOutput);
84	0	this.seqToPdbMapping = seqToPdbMapping;
85		}
86
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
87	0	public SequenceI getSequence()...
88		{
89	0	return sequence;
90		}
91
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
92	0	public String getChain()...
93		{
94	0	return pdbchain;
95		}
96
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
97	0	public String getPdbId()...
98		{
99	0	return pdbid;
100		}
101
102		/**
103		*
104		* @param seqpos
105		* @return 0 or corresponding atom number for the sequence position
106		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
107	0	public int getAtomNum(int seqpos)...
108		{
109	0	int[] resNumAtomMap = mapping.get(seqpos);
110	0	if (resNumAtomMap != null)
111		{
112	0	return resNumAtomMap[PDB_ATOM_NUM_INDEX];
113		}
114		else
115		{
116	0	return UNASSIGNED_VALUE;
117		}
118		}
119
120		/**
121		*
122		* @param seqpos
123		* @return UNASSIGNED_VALUE or the corresponding residue number for the
124		* sequence position
125		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
126	0	public int getPDBResNum(int seqpos)...
127		{
128	0	int[] resNumAtomMap = mapping.get(seqpos);
129	0	if (resNumAtomMap != null)
130		{
131	0	return resNumAtomMap[PDB_RES_NUM_INDEX];
132		}
133		else
134		{
135	0	return UNASSIGNED_VALUE;
136		}
137		}
138
139		/**
140		* Returns a (possibly empty) list of [start, end] residue positions in the
141		* mapped structure, corresponding to the given range of sequence positions
142		*
143		* @param fromSeqPos
144		* @param toSeqPos
145		* @return
146		*/
		0% Uncovered Elements: 38 (38) Complexity: 9 Complexity Density: 0.38
147	0	public List<int[]> getPDBResNumRanges(int fromSeqPos, int toSeqPos)...
148		{
149	0	List<int[]> result = new ArrayList<>();
150	0	int startRes = -1;
151	0	int endRes = -1;
152
153	0	for (int i = fromSeqPos; i <= toSeqPos; i++)
154		{
155	0	int resNo = getPDBResNum(i);
156	0	if (resNo == UNASSIGNED_VALUE)
157		{
158	0	continue; // no mapping from this sequence position
159		}
160	0	if (startRes == -1)
161		{
162	0	startRes = resNo;
163	0	endRes = resNo;
164		}
165	0	if (resNo >= startRes && resNo <= endRes)
166		{
167		// within the current range - no change
168	0	continue;
169		}
170	0	if (resNo == startRes - 1)
171		{
172		// extend beginning of current range
173	0	startRes--;
174	0	continue;
175		}
176	0	if (resNo == endRes + 1)
177		{
178		// extend end of current range
179	0	endRes++;
180	0	continue;
181		}
182
183		/*
184		* resNo is not within or contiguous with last range,
185		* so write out the last range
186		*/
187	0	result.add(new int[] { startRes, endRes });
188	0	startRes = resNo;
189	0	endRes = resNo;
190		}
191
192		/*
193		* and add the last range
194		*/
195	0	if (startRes != -1)
196		{
197	0	result.add(new int[] { startRes, endRes });
198		}
199
200	0	return result;
201		}
202
203		/**
204		*
205		* @param pdbResNum
206		* @return -1 or the corresponding sequence position for a pdb residue number
207		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
208	0	public int getSeqPos(int pdbResNum)...
209		{
210	0	for (Integer seqPos : mapping.keySet())
211		{
212	0	if (pdbResNum == getPDBResNum(seqPos))
213		{
214	0	return seqPos;
215		}
216		}
217	0	return UNASSIGNED_VALUE;
218		}
219
220		/**
221		* transfer a copy of an alignment annotation row in the PDB chain coordinate
222		* system onto the mapped sequence
223		*
224		* @param ana
225		* @return the copy that was remapped to the mapped sequence
226		* @note this method will create a copy and add it to the dataset sequence for
227		* the mapped sequence as well as the mapped sequence (if it is not a
228		* dataset sequence).
229		*/
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
230	0	public AlignmentAnnotation transfer(AlignmentAnnotation ana)...
231		{
232	0	AlignmentAnnotation ala_copy = new AlignmentAnnotation(ana);
233	0	SequenceI ds = sequence;
234	0	while (ds.getDatasetSequence() != null)
235		{
236	0	ds = ds.getDatasetSequence();
237		}
238		// need to relocate annotation from pdb coordinates to local sequence
239		// -1,-1 doesn't look at pdbresnum but fails to remap sequence positions...
240
241	0	ala_copy.remap(ds, mapping, -1, -1, 0);
242	0	ds.addAlignmentAnnotation(ala_copy);
243	0	if (ds != sequence)
244		{
245		// mapping wasn't to an original dataset sequence, so we make a copy on
246		// the mapped sequence too
247	0	ala_copy = new AlignmentAnnotation(ala_copy);
248	0	sequence.addAlignmentAnnotation(ala_copy);
249		}
250	0	return ala_copy;
251		}
252
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
253	0	public String getMappingDetailsOutput()...
254		{
255	0	return mappingDetails;
256		}
257
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
258	0	public HashMap<Integer, int[]> getMapping()...
259		{
260	0	return mapping;
261		}
262
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
263	0	public Mapping getSeqToPdbMapping()...
264		{
265	0	return seqToPdbMapping;
266		}
267
268		/**
269		* A hash function that satisfies the contract that if two mappings are
270		* equal(), they have the same hashCode
271		*/
		0% Uncovered Elements: 21 (21) Complexity: 7 Complexity Density: 0.78
272	0	@Override...
273		public int hashCode()
274		{
275	0	final int prime = 31;
276	0	int result = 1;
277	0	result = prime * result
278	0	+ ((mappingDetails == null) ? 0 : mappingDetails.hashCode());
279	0	result = prime * result
280	0	+ ((pdbchain == null) ? 0 : pdbchain.hashCode());
281	0	result = prime * result + ((pdbfile == null) ? 0 : pdbfile.hashCode());
282	0	result = prime * result + ((pdbid == null) ? 0 : pdbid.hashCode());
283	0	result = prime * result
284	0	+ ((seqToPdbMapping == null) ? 0 : seqToPdbMapping.hashCode());
285	0	result = prime * result
286	0	+ ((sequence == null) ? 0 : sequence.hashCode());
287	0	return result;
288		}
289
		0% Uncovered Elements: 73 (73) Complexity: 20 Complexity Density: 0.57
290	0	@Override...
291		public boolean equals(Object obj)
292		{
293	0	if (this == obj)
294		{
295	0	return true;
296		}
297	0	if (obj == null)
298		{
299	0	return false;
300		}
301	0	if (getClass() != obj.getClass())
302		{
303	0	return false;
304		}
305	0	StructureMapping other = (StructureMapping) obj;
306	0	if (mappingDetails == null)
307		{
308	0	if (other.mappingDetails != null)
309		{
310	0	return false;
311		}
312		}
313	0	else if (!mappingDetails.equals(other.mappingDetails))
314		{
315	0	return false;
316		}
317	0	if (pdbchain == null)
318		{
319	0	if (other.pdbchain != null)
320		{
321	0	return false;
322		}
323		}
324	0	else if (!pdbchain.equals(other.pdbchain))
325		{
326	0	return false;
327		}
328	0	if (pdbfile == null)
329		{
330	0	if (other.pdbfile != null)
331		{
332	0	return false;
333		}
334		}
335	0	else if (!pdbfile.equals(other.pdbfile))
336		{
337	0	return false;
338		}
339	0	if (pdbid == null)
340		{
341	0	if (other.pdbid != null)
342		{
343	0	return false;
344		}
345		}
346	0	else if (!pdbid.equals(other.pdbid))
347		{
348	0	return false;
349		}
350	0	if (seqToPdbMapping == null)
351		{
352	0	if (other.seqToPdbMapping != null)
353		{
354	0	return false;
355		}
356		}
357	0	else if (!seqToPdbMapping.equals(other.seqToPdbMapping))
358		{
359	0	return false;
360		}
361	0	if (sequence != other.sequence)
362		{
363	0	return false;
364		}
365
366	0	return true;
367		}
368		}