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

File SequenceCollectionI.java

 

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Classes

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SequenceCollectionI 26 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    import java.util.List;
24    import java.util.Map;
25   
 
26    public interface SequenceCollectionI
27    {
28    /**
29    *
30    * @return (visible) sequences in this collection. This may be a direct
31    * reference to the collection so not thread safe
32    */
33    List<SequenceI> getSequences();
34   
35    /**
36    * FIXME: AlignmentI.getSequences(hiddenReps) doesn't actually obey this
37    * contract!
38    *
39    * @param hiddenReps
40    * @return the full set of sequences in this collection, including any
41    * sequences represented by sequences in the collection.
42    */
43    List<SequenceI> getSequences(
44    Map<SequenceI, SequenceCollectionI> hiddenReps);
45   
46    int getWidth();
47   
48    /**
49    *
50    * @return true if getSeqrep doesn't return null
51    */
52    boolean hasSeqrep();
53   
54    /**
55    * get the reference or representative sequence within this collection
56    *
57    * @return null or the current reference sequence
58    */
59    SequenceI getSeqrep();
60   
61    /**
62    * set the reference or representative sequence for this collection. Reference
63    * is assumed to be present within the collection.
64    *
65    * @return
66    */
67    void setSeqrep(SequenceI refseq);
68   
69    /**
70    * @return the first column included in this collection. Runs from 0<=i<N_cols
71    */
72    int getStartRes();
73   
74    /**
75    *
76    * @return the last column in this collection. Runs from 0<=i<N_cols
77    */
78    int getEndRes();
79   
80    /**
81    * Answers true if sequence data is nucleotide (according to some heuristic)
82    *
83    * @return
84    */
85    boolean isNucleotide();
86    }