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  1. Project Clover database Mon Nov 11 2024 17:27:16 GMT
  2. Package jalview.datamodel

File AnnotatedCollectionI.java

 

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Classes

Class Line # Actions
AnnotatedCollectionI 23 0 0
-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   
 
23    public interface AnnotatedCollectionI
24    extends SequenceCollectionI, ContactMapHolderI
25    {
26   
27    /**
28    * TODO: decide if null is a valid response if there is no annotation on the
29    * object
30    *
31    * @return null
32    */
33    AlignmentAnnotation[] getAlignmentAnnotation();
34   
35    /**
36    * Returns a list of annotations matching the given calc id, or an empty list
37    * if calcId is null
38    *
39    * @param calcId
40    * @return
41    */
42    Iterable<AlignmentAnnotation> findAnnotation(String calcId);
43   
44    /**
45    * Returns an iterable collection of any annotations that match on given
46    * sequence ref, calcId and label (ignoring null values).
47    *
48    * @param seq
49    * null or reference sequence to select annotation for
50    * @param calcId
51    * null or the calcId to select annotation for
52    * @param label
53    * null or the label to select annotation for
54    */
55    Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
56    String calcId, String label);
57   
58    /**
59    * context for this annotated collection
60    *
61    * @return null or the collection upon which this collection is defined (e.g.
62    * alignment, parent group).
63    */
64    AnnotatedCollectionI getContext();
65    }