Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Profile	29	36	23	0.00%	Show methods

Class Profile

Class Profile	Line # 29	Total Statements 36	Complexity 23	TOTAL Coverage 0.00%
Profile(int,int,int,String)   Profile(int,int,int,String)	7878	4.04	1.01	0.0 0.00%
Profile(String,int,int,int,int)   Profile(String,int,int,int,int)	8686	5.05	1.01	0.0 0.00%
setCounts(ResidueCount) : void   setCounts(ResidueCount) : void	9999	1.01	1.01	0.0 0.00%
setSSCounts(SecondaryStructureCount) : void   setSSCounts(SecondaryStructureCount) : void	105105	1.01	1.01	0.0 0.00%
getPercentageIdentity(boolean) : float   getPercentageIdentity(boolean) : float	114114	7.07	4.04	0.0 0.00%
getSSPercentageIdentity(boolean) : float   getSSPercentageIdentity(boolean) : float	133133	7.07	4.04	0.0 0.00%
getCounts() : ResidueCount   getCounts() : ResidueCount	155155	1.01	1.01	0.0 0.00%
getSSCounts() : SecondaryStructureCount   getSSCounts() : SecondaryStructureCount	161161	1.01	1.01	0.0 0.00%
getHeight() : int   getHeight() : int	170170	1.01	1.01	0.0 0.00%
getGapped() : int   getGapped() : int	179179	1.01	1.01	0.0 0.00%
getMaxCount() : int   getMaxCount() : int	188188	1.01	1.01	0.0 0.00%
getMaxSSCount() : int   getMaxSSCount() : int	194194	1.01	1.01	0.0 0.00%
getModalResidue() : String   getModalResidue() : String	203203	1.01	1.01	0.0 0.00%
getModalSS() : String   getModalSS() : String	209209	1.01	1.01	0.0 0.00%
getNonGapped() : int   getNonGapped() : int	218218	1.01	1.01	0.0 0.00%
getSeqWithSSCount() : int   getSeqWithSSCount() : int	224224	1.01	1.01	0.0 0.00%
setSeqWithSSCount(int) : void   setSeqWithSSCount(int) : void	229229	1.01	1.01	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.datamodel;
22
23		/**
24		* A profile for one column of an alignment
25		*
26		* @author gmcarstairs
27		*
28		*/
		0% Uncovered Elements: 61 (61) Complexity: 23 Complexity Density: 0.64
29		public class Profile implements ProfileI
30		{
31		/*
32		* an object holding counts of symbols in the profile
33		*/
34		private ResidueCount counts;
35
36		private SecondaryStructureCount ssCounts;
37
38		private int seqWithSSCount = -1;
39
40		/*
41		* the number of sequences (gapped or not) in the profile
42		*/
43		private int height;
44
45		/*
46		* the number of non-gapped sequences in the profile
47		*/
48		private int gapped;
49
50		/*
51		* the highest count for any residue in the profile
52		*/
53		private int maxCount;
54
55		private int maxSSCount;
56
57		/*
58		* the residue (e.g. K) or residues (e.g. KQW) with the
59		* highest count in the profile
60		*/
61		private String modalResidue;
62
63		private String modalSS;
64
65		/**
66		* Constructor which allows derived data to be stored without having to store
67		* the full profile
68		*
69		* @param seqCount
70		* the number of sequences in the profile
71		* @param gaps
72		* the number of gapped sequences
73		* @param max
74		* the highest count for any residue
75		* @param modalres
76		* the residue (or concatenated residues) with the highest count
77		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
78	0	public Profile(int seqCount, int gaps, int max, String modalRes)...
79		{
80	0	this.height = seqCount;
81	0	this.gapped = gaps;
82	0	this.maxCount = max;
83	0	this.modalResidue = modalRes;
84		}
85
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
86	0	public Profile(String modalSS, int ssCount, int gaps, int maxSSCount,...
87		int seqWithSSCount)
88		{
89	0	this.height = ssCount;
90	0	this.gapped = gaps;
91	0	this.maxSSCount = maxSSCount;
92	0	this.modalSS = modalSS;
93	0	this.setSeqWithSSCount(seqWithSSCount);
94		}
95
96		/* (non-Javadoc)
97		* @see jalview.datamodel.ProfileI#setCounts(jalview.datamodel.ResidueCount)
98		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
99	0	@Override...
100		public void setCounts(ResidueCount residueCounts)
101		{
102	0	this.counts = residueCounts;
103		}
104
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
105	0	@Override...
106		public void setSSCounts(SecondaryStructureCount secondaryStructureCount)
107		{
108	0	this.ssCounts = secondaryStructureCount;
109		}
110
111		/* (non-Javadoc)
112		* @see jalview.datamodel.ProfileI#getPercentageIdentity(boolean)
113		*/
		0% Uncovered Elements: 11 (11) Complexity: 4 Complexity Density: 0.57
114	0	@Override...
115		public float getPercentageIdentity(boolean ignoreGaps)
116		{
117	0	if (height == 0)
118		{
119	0	return 0f;
120		}
121	0	float pid = 0f;
122	0	if (ignoreGaps && gapped < height)
123		{
124	0	pid = (maxCount * 100f) / (height - gapped);
125		}
126		else
127		{
128	0	pid = (maxCount * 100f) / height;
129		}
130	0	return pid;
131		}
132
		0% Uncovered Elements: 11 (11) Complexity: 4 Complexity Density: 0.57
133	0	@Override...
134		public float getSSPercentageIdentity(boolean ignoreGaps)
135		{
136	0	if (height == 0)
137		{
138	0	return 0f;
139		}
140	0	float ssPid = 0f;
141	0	if (ignoreGaps && gapped < height)
142		{
143	0	ssPid = (maxSSCount * 100f) / (height - gapped);
144		}
145		else
146		{
147	0	ssPid = (maxSSCount * 100f) / height;
148		}
149	0	return ssPid;
150		}
151
152		/* (non-Javadoc)
153		* @see jalview.datamodel.ProfileI#getCounts()
154		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
155	0	@Override...
156		public ResidueCount getCounts()
157		{
158	0	return counts;
159		}
160
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
161	0	@Override...
162		public SecondaryStructureCount getSSCounts()
163		{
164	0	return ssCounts;
165		}
166
167		/* (non-Javadoc)
168		* @see jalview.datamodel.ProfileI#getHeight()
169		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
170	0	@Override...
171		public int getHeight()
172		{
173	0	return height;
174		}
175
176		/* (non-Javadoc)
177		* @see jalview.datamodel.ProfileI#getGapped()
178		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
179	0	@Override...
180		public int getGapped()
181		{
182	0	return gapped;
183		}
184
185		/* (non-Javadoc)
186		* @see jalview.datamodel.ProfileI#getMaxCount()
187		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
188	0	@Override...
189		public int getMaxCount()
190		{
191	0	return maxCount;
192		}
193
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
194	0	@Override...
195		public int getMaxSSCount()
196		{
197	0	return maxSSCount;
198		}
199
200		/* (non-Javadoc)
201		* @see jalview.datamodel.ProfileI#getModalResidue()
202		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
203	0	@Override...
204		public String getModalResidue()
205		{
206	0	return modalResidue;
207		}
208
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
209	0	@Override...
210		public String getModalSS()
211		{
212	0	return modalSS;
213		}
214
215		/* (non-Javadoc)
216		* @see jalview.datamodel.ProfileI#getNonGapped()
217		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
218	0	@Override...
219		public int getNonGapped()
220		{
221	0	return height - gapped;
222		}
223
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
224	0	public int getSeqWithSSCount()...
225		{
226	0	return seqWithSSCount;
227		}
228
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
229	0	public void setSeqWithSSCount(int seqWithSSCount)...
230		{
231	0	this.seqWithSSCount = seqWithSSCount;
232		}
233		}