Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ProfileI	23	0	0	-1.0 -	Show methods

Class ProfileI

Class ProfileI	Line # 23	Total Statements 0	Complexity 0	TOTAL Coverage -1.0 -

 

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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
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
23		public interface ProfileI
24		{
25
26		/**
27		* Set the full profile of counts
28		*
29		* @param residueCounts
30		*/
31		public abstract void setCounts(ResidueCount residueCounts);
32
33		/**
34		* Returns the percentage identity of the profile, i.e. the highest proportion
35		* of conserved (equal) symbols. The percentage is as a fraction of all
36		* sequences, or only ungapped sequences if flag ignoreGaps is set true.
37		*
38		* @param ignoreGaps
39		* @return
40		*/
41		public abstract float getPercentageIdentity(boolean ignoreGaps);
42
43		/**
44		* Returns the full symbol counts for this profile
45		*
46		* @return
47		*/
48		public abstract ResidueCount getCounts();
49
50		/**
51		* Returns the number of sequences in the profile
52		*
53		* @return
54		*/
55		public abstract int getHeight();
56
57		/**
58		* Returns the number of sequences in the profile which had a gap character
59		* (or were too short to be included in this column's profile)
60		*
61		* @return
62		*/
63		public abstract int getGapped();
64
65		/**
66		* Returns the highest count for any symbol(s) in the profile
67		*
68		* @return
69		*/
70		public abstract int getMaxCount();
71
72		/**
73		* Returns the symbol (or concatenated symbols) which have the highest count
74		* in the profile, or an empty string if there were no symbols counted
75		*
76		* @return
77		*/
78		public abstract String getModalResidue();
79
80		/**
81		* Answers the number of non-gapped sequences in the profile
82		*
83		* @return
84		*/
85		public abstract int getNonGapped();
86
87		}