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ProfileI | 23 | 0 | 0 |
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 | 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 | public abstract int getSeqWithSSCount(); | |
63 | ||
64 | /** | |
65 | * Returns the number of sequences in the profile which had a gap character | |
66 | * (or were too short to be included in this column's profile) | |
67 | * | |
68 | * @return | |
69 | */ | |
70 | public abstract int getGapped(); | |
71 | ||
72 | /** | |
73 | * Returns the highest count for any symbol(s) in the profile | |
74 | * | |
75 | * @return | |
76 | */ | |
77 | public abstract int getMaxCount(); | |
78 | ||
79 | public abstract int getMaxSSCount(); | |
80 | ||
81 | /** | |
82 | * Returns the symbol (or concatenated symbols) which have the highest count | |
83 | * in the profile, or an empty string if there were no symbols counted | |
84 | * | |
85 | * @return | |
86 | */ | |
87 | public abstract String getModalResidue(); | |
88 | ||
89 | public abstract String getModalSS(); | |
90 | ||
91 | /** | |
92 | * Answers the number of non-gapped sequences in the profile | |
93 | * | |
94 | * @return | |
95 | */ | |
96 | public abstract int getNonGapped(); | |
97 | ||
98 | SecondaryStructureCount getSSCounts(); | |
99 | ||
100 | } |