Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
MappableContactMatrixI	29	0	0	-1.0 -	Show methods

Class MappableContactMatrixI

Class MappableContactMatrixI	Line # 29	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.ws.datamodel;
22
23		import jalview.datamodel.ContactListI;
24		import jalview.datamodel.ContactMatrixI;
25		import jalview.datamodel.Mapping;
26		import jalview.datamodel.SequenceI;
27		import jalview.util.MapList;
28
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
29		public interface MappableContactMatrixI extends ContactMatrixI
30		{
31
32		boolean hasReferenceSeq();
33
34		SequenceI getReferenceSeq();
35
36		/**
37		* remaps the matrix to a new reference sequence
38		*
39		* @param dsq
40		* @param sqmpping
41		* - mapping from current reference to new reference - 1:1 only
42		* @return new ContactMatrixI instance with updated mapping
43		*/
44		MappableContactMatrixI liftOver(SequenceI dsq, Mapping sqmpping);
45
46		/**
47		* like ContactMatrixI.getContactList(int column) but
48		*
49		* @param localFrame
50		* - sequence or other object that this contact matrix is associated
51		* with
52		* @param column
53		* - position in localFrame
54		* @return ContactListI that returns contacts w.r.t. localFrame
55		*/
56
57		ContactListI getMappableContactList(SequenceI localFrame, int column);
58
59		/**
60		*
61		* Similar to AlignedCodonFrame.getMappingBetween
62		*
63		* @param sequenceRef
64		* - a reference sequence mappable to this contactMatrix - may be
65		* null
66		* @return null or the MapList mapping to the coordinates of the reference
67		* sequence (or if hasReferenceSeq() is false, and sequenceRef is
68		* null, any mapping present)
69		*
70		*/
71		MapList getMapFor(SequenceI sequenceRef);
72
73		/**
74		* Locate a position in the mapped sequence for a single column in the matrix.
75		* this to resolve positions corresponding to column clusters
76		*
77		* @param localFrame
78		* - sequence derivced from reference sequence
79		* @param column
80		* - matrix row/column
81		* @return sequence position(s) corresponding to column in contact matrix
82		*/
83		int[] getMappedPositionsFor(SequenceI localFrame, int column);
84
85		/**
86		* Locate a position in the mapped sequence for a contiguous range of columns
87		* in the matrix use this to resolve positions corresponding to column
88		* clusters
89		*
90		* @param localFrame
91		* - sequence derivced from reference sequence
92		* @param column
93		* - matrix row/column
94		* @return sequence position(s) corresponding to column in contact matrix
95		*/
96		int[] getMappedPositionsFor(SequenceI localFrame, int from, int to);
97
98		ContactMatrixI getMappedMatrix();
99		}