Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
StructureCommandsI	14	0	0	-1.0 -	Show methods

Class StructureCommandsI

Class StructureCommandsI	Line # 14	Total Statements 0	Complexity 0	TOTAL Coverage -1.0 -

 

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1		package jalview.structure;
2
3		import java.awt.Color;
4		import java.util.List;
5		import java.util.Map;
6
7		/**
8		* Methods that generate commands that can be sent to a molecular structure
9		* viewer program (e.g. Jmol, Chimera, ChimeraX)
10		*
11		* @author gmcarstairs
12		*
13		*/
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
14		public interface StructureCommandsI
15		{
16		/**
17		* Returns the command to colour by chain
18		*
19		* @return
20		*/
21		StructureCommandI colourByChain();
22
23		/**
24		* Returns the command to colour residues using a charge-based scheme:
25		* <ul>
26		* <li>Aspartic acid and Glutamic acid (negative charge) red</li>
27		* <li>Lysine and Arginine (positive charge) blue</li>
28		* <li>Cysteine - yellow</li>
29		* <li>all others - white</li>
30		* </ul>
31		*
32		* @return
33		*/
34		List<StructureCommandI> colourByCharge();
35
36		/**
37		* Returns the command to colour residues with the colours provided in the
38		* map, one per three letter residue code
39		*
40		* @param colours
41		* @return
42		*/
43		List<StructureCommandI> colourByResidues(Map<String, Color> colours);
44
45		/**
46		* Returns the command to set the background colour of the structure viewer
47		*
48		* @param col
49		* @return
50		*/
51		StructureCommandI setBackgroundColour(Color col);
52
53		/**
54		* Returns commands to colour mapped residues of structures according to
55		* Jalview's colouring (including feature colouring if applied). Parameter is
56		* a map from Color to a model of all residues assigned that colour.
57		*
58		* @param colourMap
59		* @return
60		*/
61
62		List<StructureCommandI> colourBySequence(
63		Map<Object, AtomSpecModel> colourMap);
64
65		/**
66		* Returns a command to centre the display in the structure viewer
67		*
68		* @return
69		*/
70		StructureCommandI focusView();
71
72		/**
73		* Returns a command to show only the selected chains. The items in the input
74		* list should be formatted as "modelid:chainid".
75		*
76		* @param toShow
77		* @return
78		*/
79		List<StructureCommandI> showChains(List<String> toShow);
80
81		/**
82		* Returns a command to superpose structures by closest positioning of
83		* residues in {@code atomSpec} to the corresponding residues in
84		* {@code refAtoms}. If wanted, this may include commands to visually
85		* highlight the residues that were used for the superposition.
86		*
87		* @param refAtoms
88		* @param atomSpec
89		* @return
90		*/
91		List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
92		AtomSpecModel atomSpec);
93
94		/**
95		* Returns a command to open a file of commands at the given path
96		*
97		* @param path
98		* @return
99		*/
100		StructureCommandI openCommandFile(String path);
101
102		/**
103		* Returns a command to save the current viewer session state to the given
104		* file
105		*
106		* @param filepath
107		* @return
108		*/
109		StructureCommandI saveSession(String filepath);
110
111		/**
112		* Returns a representation of the atom set represented by the model, in
113		* viewer syntax format. If {@code alphaOnly} is true, this is restricted to
114		* Alpha Carbon (peptide) or Phosphorous (rna) only
115		*
116		* @param model
117		* @param alphaOnly
118		* @return
119		*/
120		String getAtomSpec(AtomSpecModel model, boolean alphaOnly);
121
122		/**
123		* Returns the lowest model number used by the structure viewer (likely 0 or
124		* 1)
125		*
126		* @return
127		*/
128		// TODO remove by refactoring so command generation is purely driven by
129		// AtomSpecModel objects derived in the binding classes?
130		int getModelStartNo();
131
132		/**
133		* Returns command(s) to show only the backbone of the peptide (cartoons in
134		* Jmol, chain in Chimera)
135		*
136		* @return
137		*/
138		List<StructureCommandI> showBackbone();
139
140		/**
141		* Returns a command to open a file at the given path
142		*
143		* @param file
144		* @return
145		*/
146		// refactor if needed to distinguish loading data or session files
147		StructureCommandI loadFile(String file);
148
149		/**
150		* Returns commands to set atom attributes or properties, given a map of
151		* Jalview features as {featureType, {featureValue, AtomSpecModel}}. The
152		* assumption is that one command can be constructed for each feature type and
153		* value combination, to apply it to one or more residues.
154		*
155		* @param featureValues
156		* @return
157		*/
158		List<StructureCommandI> setAttributes(
159		Map<String, Map<Object, AtomSpecModel>> featureValues);
160
161		/**
162		* Returns command to open a saved structure viewer session file, or null if
163		* not supported
164		*
165		* @param filepath
166		* @return
167		*/
168		StructureCommandI openSession(String filepath);
169
170		/**
171		* Returns a command to ask the viewer to close down
172		*
173		* @return
174		*/
175		StructureCommandI closeViewer();
176
177		/**
178		* Returns one or more commands to ask the viewer to notify model or selection
179		* changes to the given uri. Returns null if this is not supported by the
180		* structure viewer.
181		*
182		* @param uri
183		* @return
184		*/
185		List<StructureCommandI> startNotifications(String uri);
186
187		/**
188		* Returns one or more commands to ask the viewer to stop notifying model or
189		* selection changes. Returns null if this is not supported by the structure
190		* viewer.
191		*
192		* @return
193		*/
194		List<StructureCommandI> stopNotifications();
195
196		/**
197		* Returns a command to ask the viewer for its current residue selection, or
198		* null if no such command is supported
199		*
200		* @return
201		*/
202		StructureCommandI getSelectedResidues();
203
204		/**
205		* Returns a command to list the unique names of residue attributes, or null
206		* if no such command is supported
207		*
208		* @return
209		*/
210		StructureCommandI listResidueAttributes();
211
212		/**
213		* Returns a command to list residues with an attribute of the given name,
214		* with attribute value, or null if no such command is supported
215		*
216		* @return
217		*/
218		StructureCommandI getResidueAttributes(String attName);
219		}