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

File AlignViewControllerI.java

 

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Actions
AlignViewControllerI 40 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.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    */
 
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    }