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		public abstract void setSSCounts(
34		SecondaryStructureCount secondaryStructureCount);
35
36		/**
37		* Returns the percentage identity of the profile, i.e. the highest proportion
38		* of conserved (equal) symbols. The percentage is as a fraction of all
39		* sequences, or only ungapped sequences if flag ignoreGaps is set true.
40		*
41		* @param ignoreGaps
42		* @return
43		*/
44		public abstract float getPercentageIdentity(boolean ignoreGaps);
45
46		public abstract float getSSPercentageIdentity(boolean ignoreGaps);
47
48		/**
49		* Returns the full symbol counts for this profile
50		*
51		* @return
52		*/
53		public abstract ResidueCount getCounts();
54
55		/**
56		* Returns the number of sequences in the profile
57		*
58		* @return
59		*/
60		public abstract int getHeight();
61
62		/**
63		* Returns the number of sequences in the profile which had a gap character
64		* (or were too short to be included in this column's profile)
65		*
66		* @return
67		*/
68		public abstract int getGapped();
69
70		/**
71		* Returns the highest count for any symbol(s) in the profile
72		*
73		* @return
74		*/
75		public abstract int getMaxCount();
76
77		public abstract int getMaxSSCount();
78
79		/**
80		* Returns the symbol (or concatenated symbols) which have the highest count
81		* in the profile, or an empty string if there were no symbols counted
82		*
83		* @return
84		*/
85		public abstract String getModalResidue();
86
87		public abstract String getModalSS();
88
89		/**
90		* Answers the number of non-gapped sequences in the profile
91		*
92		* @return
93		*/
94		public abstract int getNonGapped();
95
96		SecondaryStructureCount getSSCounts();
97
98		}