Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignViewControllerI	40	0	0	-1.0 -	Show methods

Class AlignViewControllerI

Class AlignViewControllerI	Line # 40	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.api;
22
23		import java.util.List;
24
25		import jalview.io.DataSourceType;
26
27		/**
28		* prototype abstract controller for a Jalview alignment view
29		*
30		* @author jimp
31		*
32		* All operations should return true if the view has changed as a result
33		* of the operation
34		*
35		* The controller holds methods that operate on an alignment view,
36		* modifying its state in some way that may result in side effects
37		* reflected in an associated GUI
38		*
39		*/
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
40		public interface AlignViewControllerI
41		{
42
43		public boolean makeGroupsFromSelection();
44
45		public boolean createGroup();
46
47		public boolean unGroup();
48
49		public boolean deleteGroups();
50
51		public void setViewportAndAlignmentPanel(AlignViewportI viewport,
52		AlignmentViewPanel alignPanel);
53
54		/**
55		* Mark columns in the current column selection according to positions of
56		* sequence features
57		*
58		* @param invert
59		* - when set, mark all but columns containing given type
60		* @param extendCurrent
61		* - when set, do not clear existing column selection
62		* @param toggle
63		* - rather than explicitly set, toggle selection state
64		* @param featureType
65		* - feature type string
66		* @return true if operation affected state
67		*/
68		boolean markColumnsContainingFeatures(boolean invert,
69		boolean extendCurrent, boolean toggle, String featureType);
70
71		/**
72		* sort the alignment or current selection by average score over the given set
73		* of features
74		*
75		* @param typ
76		* list of feature names or null to use currently displayed features
77		*/
78		void sortAlignmentByFeatureScore(List<String> typ);
79
80		/**
81		* sort the alignment or current selection by distribution of the given set of
82		* features
83		*
84		* @param typ
85		* list of feature names or null to use currently displayed features
86		*/
87		void sortAlignmentByFeatureDensity(List<String> typ);
88
89		/**
90		* add a features file of some kind to the current view
91		*
92		* @param file
93		* @param sourceType
94		* @param relaxedIdMatching
95		* if true, try harder to match up IDs with local sequence data
96		* @return true if parsing resulted in something being imported to the view or
97		* dataset
98		*/
99		public boolean parseFeaturesFile(Object file, DataSourceType sourceType,
100		boolean relaxedIdMatching);
101
102		/**
103		* mark columns containing highlighted regions (e.g. from search, structure
104		* highlight, or a mouse over event in another viewer)
105		*
106		* @param invert
107		* @param extendCurrent
108		* @param toggle
109		* @return
110		*/
111		boolean markHighlightedColumns(boolean invert, boolean extendCurrent,
112		boolean toggle);
113
114		/**
115		* copies each distinct highlighted region on the current view as a new
116		* sequence on the clipboard
117		*
118		* @return
119		*/
120		boolean copyHighlightedRegionsToClipboard();
121
122		/**
123		* Justify alignment or currently selected region left or right
124		*
125		* @param left
126		* - true - means justify left
127		* @return
128		*/
129		boolean justify_Region(boolean left);
130		}