Classes

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

Class JalviewJSApi

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

 

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1		package jalview.api;
2
3		import java.net.URL;
4
5		import jalview.datamodel.SequenceI;
6		import jalview.gui.AlignFrame;
7
8		/**
9		* JAL-3369 JalviewJS API BH 2019.07.17
10		*
11		* @author hansonr
12		*
13		*/
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
14		public interface JalviewJSApi
15		{
16
17		/**
18		* bind a pdb file to a sequence in the given AlignFrame.
19		*
20		* @param sequenceId
21		* - sequenceId within the dataset or null
22		* @param pdbId
23		* - the four-character PDB ID
24		* @param pdbFile
25		* - pdb file - either a URL or a valid PDB file or null.
26		* @param alFrame
27		* - null or specific AlignFrame. This specifies the dataset that
28		* will be searched for a seuqence called sequenceId
29		*
30		* @return true if binding was success
31		*/
32		public boolean addPdbFile(String sequenceId, String pdbId, String pdbFile,
33		AlignFrame alFrame);
34
35		/**
36		* Get alignment as format with or without the jalview start-end sequence
37		* suffix appended.
38		*
39		* @param format
40		* @param addSuffix
41		* (default false)
42		* @param alf
43		* (default current)
44		*
45		* @return
46		*/
47		public String getAlignment(String format, boolean addSuffix,
48		AlignFrame alf);
49
50		/**
51		* Get an array of sequence IDs reflecting the order of the alignment in the
52		* specified alignment frame
53		*
54		* @param alf
55		* (default current)
56		* @return array of sequence IDs
57		*/
58		public String[] getAlignmentOrder(AlignFrame alf);
59
60		/**
61		* Get alignment view alf's annotation as an annotation file
62		*
63		* @param alf
64		* (default current)
65		* @return annotation
66		*/
67		public String getAnnotation(AlignFrame alf);
68
69		/**
70		* Get the URL for the location where the code is found; typically ending in
71		* "swingjs/j2s".
72		*
73		* @return web page URL
74		*/
75		public URL getCodeBase();
76
77		AlignFrame getCurrentAlignFrame();
78
79		/**
80		* Get the URL for the hosting web page.
81		*
82		* @return web page URL
83		*/
84		public URL getDocumentBase();
85
86		/**
87		* Get the array of feature groups for an alignment frame.
88		*
89		* @param alf
90		* AlignFrame to get feature groups for (default current)
91		* @return
92		*/
93		public String[] getFeatureGroups(AlignFrame alf);
94
95		/**
96		* Get the array of feature groups for an alignment frame with a specific
97		* on/off state.
98		*
99		* @param visible
100		* (default off)
101		* @param alf
102		* align frame (default current)
103		*
104		* @return
105		*/
106		public String[] getFeatureGroupsOfState(boolean visible, AlignFrame alf);
107
108		/**
109		* Get the sequence features in the alignment frame in the given format
110		* (Jalview or GFF). Two additional options can be added to the format, each
111		* starting with a semicolon:
112		*
113		* ;includeNonpositional (default) or ;positionalOnly
114		*
115		* ;includeComplement
116		*
117		* @param format
118		* case-insensitive "Jalview" or "GFF" (default "GFF")
119		* @param alf
120		* (default current)
121		* @return formatted sequence features
122		*/
123		public String getFeatures(String format, AlignFrame alf);
124
125		/**
126		* Get an applet parameter as a string.
127		*
128		* @param name
129		* @return value or null
130		*/
131		public String getParameter(String name);
132
133		/**
134		* Get an applet parameter object value.
135		*
136		* @param name
137		* @return value or null
138		*/
139		public Object getParameterAsObject(String name);
140
141		/**
142		* @param alf
143		* AlignFrame containing selection
144		* @return String list of selected sequence IDs, each terminated by current
145		* default separator sequence
146		*
147		*/
148		public SequenceI[] getSelectedSequences(AlignFrame alf);
149
150		// BH incompatibility here -- JalviewLite created an AlignFrame; Jalview
151		// creates an AlignmentPanel
152		// /**
153		// * create a new view and return the AlignFrame instance
154		// *
155		// * @return
156		// */
157		//
158		// public AlignFrame newView();
159		//
160		// /**
161		// * create a new view named name and return the AlignFrame instance
162		// *
163		// * @param name
164		// * @return
165		// */
166		//
167		// public AlignFrame newView(String name);
168		//
169		// /**
170		// * create a new view on alf and return the AlignFrame instance
171		// *
172		// * @param alf
173		// * @return
174		// */
175		// public AlignFrame newViewFrom(AlignFrame alf);
176		//
177		// /**
178		// * create a new view named name on alf
179		// *
180		// * @param alf
181		// * @param name
182		// * @return
183		// */
184		// public AlignFrame newViewFrom(AlignFrame alf, String name);
185		//
186
187		/**
188		* get sequences selected in alf and return their alignment in format 'format'
189		* either with or without suffix
190		*
191		* @param format
192		* - format of alignment file
193		* @param alf
194		* - where selection is
195		* @param suffix
196		* - true to append /start-end string to each sequence ID
197		*
198		* @return selected sequences as flat file or empty string if there was no
199		* current selection
200		*/
201		public String getSelectedSequencesAsAlignment(String format,
202		boolean addSuffix, AlignFrame alf);
203
204		/**
205		*
206		* @param sequenceId
207		* id of sequence to highlight
208		* @param position
209		* integer position [ tobe implemented or range ] on sequence
210		* @param alignedPosition
211		* false, blank or something else - indicate if position is an
212		* alignment column or unaligned sequence position
213		* @param alf
214		* alignment frame (default current)
215		*/
216		public void highlight(String sequenceId, String position,
217		String alignedPosition, AlignFrame alf);
218
219		/**
220		*
221		* @param data
222		* alignment data as a string
223		* @param title
224		* window title
225		* @param width
226		* desired width or 0 for default width
227		* @param height
228		* desired height or 0 for default height
229		* @return null or new alignment frame
230		*/
231
232		public AlignFrame loadAlignment(String data, String title, int width,
233		int height);
234
235		/**
236		* add the given features or annotation to the given alignment view
237		*
238		* @param annotation
239		* @param alf
240		* alignment frame (default current)
241		*/
242		public void loadAnnotation(String annotation, AlignFrame alf);
243
244		/**
245		* Parse the given string as a jalview feature or GFF annotation file and
246		* optionally enable feature display on the given AlignFrame.
247		*
248		* @param features
249		* - gff or features file
250		* @param autoenabledisplay
251		* - when true, feature display will be enabled if any features can
252		* be parsed from the string.
253		* @param alf
254		* alignment frame (default current)
255		*
256		* @return true if data parsed as features
257		*/
258		public boolean loadFeatures(String features, boolean autoenabledisplay,
259		AlignFrame alf);
260
261		/**
262		* Load a score file.
263		*
264		* @param sScoreFile
265		* @param alf
266		* alignment frame (default current)
267		*
268		* @return
269		*/
270		public boolean loadScoreFile(String sScoreFile, AlignFrame alf);
271
272		/**
273		* public static method for JalviewJS API to open a PCAPanel without
274		* necessarily using a dialog.
275		*
276		* @param modelName
277		* @param alf
278		* may be null
279		*
280		* @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
281		* if number of sequences selected is inappropriate
282		*/
283		public Object openPcaPanel(String modelName, AlignFrame alf);
284
285		/**
286		* Open a new Tree panel on the desktop statically. Params are standard (not
287		* set by Groovy). No dialog is opened.
288		*
289		* @param treeType
290		* @param modelName
291		* @param alf
292		* align frame (default current)
293		*
294		* @return null, or the string "label.you_need_at_least_n_sequences" if number
295		* of sequences selected is inappropriate
296		*/
297		public Object openTreePanel(String treeType, String modelName,
298		AlignFrame alf);
299
300		/**
301		* re-order the given alignment using the given array of sequence IDs
302		*
303		* @param ids
304		* array of sequence IDs
305		* @param undoName
306		* - string to use when referring to ordering action in undo buffer
307		* @param alf
308		* alignment frame (default current)
309		*
310		* @return 'true' if alignment was actually reordered. empty string if
311		* alignment did not contain sequences.
312		*/
313		public boolean orderAlignment(String[] ids, String undoName,
314		AlignFrame alf);
315
316		/**
317		* process commandline arguments after the JavaScript application has started
318		*
319		* @param args
320		* @return
321		*/
322		public Object parseArguments(String[] args);
323
324		boolean parseFeaturesFile(String filename, AlignFrame alf);
325
326		// Bob's additions:
327
328		/**
329		* remove any callback using the given listener function and associated with
330		* the given AlignFrame (or null for all callbacks);
331		*
332		* @param listener
333		* (may be null);
334		* @param alf
335		* alignment frame (default current)
336		*/
337		public void removeSelectionListener(String listener, AlignFrame af);
338
339		/**
340		* adjust horizontal/vertical scroll to make the given location the top left
341		* hand corner for the given view
342		*
343		* @param topRow
344		* -1 for current top row
345		* @param leftHandColumn
346		* -1 for current left-hand column
347		* @param alf
348		* alignment frame (default current)
349		*/
350		public void scrollViewTo(int topRow, int leftHandColumn, AlignFrame alf);
351		/**
352		* select regions of the given alignment frame
353		*
354		* @param alf
355		* alignment frame (default current)
356		* @param toselect
357		* String separated list { column range, seq1...seqn sequence ids }
358		* @param sep
359		* separator between toselect fields
360		*/
361		public void select(String[] sequenceIds, String[] columns,
362		AlignFrame alf);
363
364		/**
365		* Set the state (visible or not) of the selected feature groups.
366		*
367		* @param groups
368		* @param state
369		* @param alf
370		* (default current)
371		*/
372		public void setFeatureGroupState(String[] groups, boolean state,
373		AlignFrame alf);
374
375		/**
376		* Register a JavaScript function to handle alignment selection events. Events
377		* are generated when the user completes a selection event, or when the user
378		* deselects all selected regions. The method is called back with the
379		* following arguments:
380		*
381		* the appletID (such as "Jalview1")
382		*
383		* the source alignment frame
384		*
385		* the SelectionSource object (for example, an AlignViewport)
386		*
387		* the sequence set ID
388		*
389		* an array of sequence IDs
390		*
391		* an array of columns (single number or hyphenated range)
392		*
393		* @param listener
394		* name of JavaScript function to be called
395		*
396		* @param alf
397		* alignment frame (default ALL)
398		*/
399		public void setSelectionListener(String listener, AlignFrame alf);
400
401		public void showOverview();
402
403		/**
404		*
405		* @param pdbID
406		* @param fileType
407		* @param alf
408		* align frame (default current)
409		*/
410		public void showStructure(String pdbID, String fileType, AlignFrame alf);
411
412		}