1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.datamodel

File ProfileI.java

 

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ProfileI 23 0 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   
 
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    }