Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AlignViewportI	49	0	0	0	-1.0 -	Show methods

Class AlignViewportI

Class AlignViewportI	Line # 49	Total Statements 0	Complexity 0	Uncovered Elements 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 jalview.analysis.Conservation;
24		import jalview.analysis.TreeModel;
25		import jalview.datamodel.AlignmentAnnotation;
26		import jalview.datamodel.AlignmentExportData;
27		import jalview.datamodel.AlignmentI;
28		import jalview.datamodel.AlignmentView;
29		import jalview.datamodel.ColumnSelection;
30		import jalview.datamodel.ProfilesI;
31		import jalview.datamodel.SearchResultsI;
32		import jalview.datamodel.SequenceCollectionI;
33		import jalview.datamodel.SequenceGroup;
34		import jalview.datamodel.SequenceI;
35		import jalview.renderer.ResidueShaderI;
36		import jalview.schemes.ColourSchemeI;
37		import jalview.viewmodel.ViewportRanges;
38
39		import java.awt.Color;
40		import java.awt.Font;
41		import java.util.Hashtable;
42		import java.util.List;
43		import java.util.Map;
44
45		/**
46		* @author jimp
47		*
48		*/
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
49		public interface AlignViewportI extends ViewStyleI
50		{
51
52		/**
53		* Get the ranges object containing details of the start and end sequences and
54		* residues
55		*
56		* @return
57		*/
58		public ViewportRanges getRanges();
59
60		/**
61		* calculate the height for visible annotation, revalidating bounds where
62		* necessary ABSTRACT GUI METHOD
63		*
64		* @return total height of annotation
65		*/
66		public int calcPanelHeight();
67
68		/**
69		* Answers true if the viewport has at least one column selected
70		*
71		* @return
72		*/
73		boolean hasSelectedColumns();
74
75		/**
76		* Answers true if the viewport has at least one hidden column
77		*
78		* @return
79		*/
80		boolean hasHiddenColumns();
81
82		boolean isValidCharWidth();
83
84		boolean isShowConsensusHistogram();
85
86		boolean isShowSequenceLogo();
87
88		boolean isNormaliseSequenceLogo();
89
90		ColourSchemeI getGlobalColourScheme();
91
92		/**
93		* Returns an object that describes colouring (including any thresholding or
94		* fading) of the alignment
95		*
96		* @return
97		*/
98		ResidueShaderI getResidueShading();
99
100		AlignmentI getAlignment();
101
102		ColumnSelection getColumnSelection();
103
104		ProfilesI getSequenceConsensusHash();
105
106		/**
107		* Get consensus data table for the cDNA complement of this alignment (if any)
108		*
109		* @return
110		*/
111		Hashtable[] getComplementConsensusHash();
112
113		Hashtable[] getRnaStructureConsensusHash();
114
115		boolean isIgnoreGapsConsensus();
116
117		boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
118
119		AlignmentAnnotation getAlignmentQualityAnnot();
120
121		AlignmentAnnotation getAlignmentConservationAnnotation();
122
123		/**
124		* get the container for alignment consensus annotation
125		*
126		* @return
127		*/
128		AlignmentAnnotation getAlignmentConsensusAnnotation();
129
130		/**
131		* get the container for alignment gap annotation
132		*
133		* @return
134		*/
135		AlignmentAnnotation getAlignmentGapAnnotation();
136
137		/**
138		* get the container for cDNA complement consensus annotation
139		*
140		* @return
141		*/
142		AlignmentAnnotation getComplementConsensusAnnotation();
143
144		/**
145		* Test to see if viewport is still open and active
146		*
147		* @return true indicates that all references to viewport should be dropped
148		*/
149		boolean isClosed();
150
151		/**
152		* Dispose of all references or resources held by the viewport
153		*/
154		void dispose();
155
156		/**
157		* get the associated calculation thread manager for the view
158		*
159		* @return
160		*/
161		AlignCalcManagerI getCalcManager();
162
163		/**
164		* get the percentage gaps allowed in a conservation calculation
165		*
166		*/
167		public int getConsPercGaps();
168
169		/**
170		* set the consensus result object for the viewport
171		*
172		* @param hconsensus
173		*/
174		void setSequenceConsensusHash(ProfilesI hconsensus);
175
176		/**
177		* Set the cDNA complement consensus for the viewport
178		*
179		* @param hconsensus
180		*/
181		void setComplementConsensusHash(Hashtable[] hconsensus);
182
183		/**
184		*
185		* @return the alignment annotation row for the structure consensus
186		* calculation
187		*/
188		AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
189
190		/**
191		* set the Rna structure consensus result object for the viewport
192		*
193		* @param hStrucConsensus
194		*/
195		void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
196
197		/**
198		* Sets the colour scheme for the background alignment (as distinct from
199		* sub-groups, which may have their own colour schemes). A null value is used
200		* for no residue colour (white).
201		*
202		* @param cs
203		*/
204		void setGlobalColourScheme(ColourSchemeI cs);
205
206		Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
207
208		void setHiddenRepSequences(
209		Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
210
211		/**
212		* hides or shows dynamic annotation rows based on groups and group and
213		* alignment associated auto-annotation state flags apply the current
214		* group/autoannotation settings to the alignment view. Usually you should
215		* call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to
216		* ensure the annotation panel bounds are set correctly.
217		*
218		* @param applyGlobalSettings
219		* - apply to all autoannotation rows or just the ones associated
220		* with the current visible region
221		* @param preserveNewGroupSettings
222		* - don't apply global settings to groups which don't already have
223		* group associated annotation
224		*/
225		void updateGroupAnnotationSettings(boolean applyGlobalSettings,
226		boolean preserveNewGroupSettings);
227
228		void setSequenceColour(SequenceI seq, Color col);
229
230		Color getSequenceColour(SequenceI seq);
231
232		void updateSequenceIdColours();
233
234		SequenceGroup getSelectionGroup();
235
236		/**
237		* get the currently selected sequence objects or all the sequences in the
238		* alignment. TODO: change to List<>
239		*
240		* @return array of references to sequence objects
241		*/
242		SequenceI[] getSequenceSelection();
243
244		void clearSequenceColours();
245
246		/**
247		* return a compact representation of the current alignment selection to pass
248		* to an analysis function
249		*
250		* @param selectedOnly
251		* boolean true to just return the selected view
252		* @return AlignmentView
253		*/
254		AlignmentView getAlignmentView(boolean selectedOnly);
255
256		/**
257		* return a compact representation of the current alignment selection to pass
258		* to an analysis function
259		*
260		* @param selectedOnly
261		* boolean true to just return the selected view
262		* @param markGroups
263		* boolean true to annotate the alignment view with groups on the
264		* alignment (and intersecting with selected region if selectedOnly
265		* is true)
266		* @return AlignmentView
267		*/
268		AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
269
270		/**
271		* This method returns the visible alignment as text, as seen on the GUI, ie
272		* if columns are hidden they will not be returned in the result. Use this for
273		* calculating trees, PCA, redundancy etc on views which contain hidden
274		* columns. This method doesn't exclude hidden sequences from the output.
275		*
276		* @param selectedRegionOnly
277		* - determines if only the selected region or entire alignment is
278		* exported
279		* @return String[]
280		*/
281		String[] getViewAsString(boolean selectedRegionOnly);
282
283		/**
284		* This method returns the visible alignment as text, as seen on the GUI, ie
285		* if columns are hidden they will not be returned in the result. Use this for
286		* calculating trees, PCA, redundancy etc on views which contain hidden
287		* columns.
288		*
289		* @param selectedRegionOnly
290		* - determines if only the selected region or entire alignment is
291		* exported
292		* @param isExportHiddenSeqs
293		* - determines if hidden sequences would be exported or not.
294		*
295		* @return String[]
296		*/
297		String[] getViewAsString(boolean selectedRegionOnly,
298		boolean isExportHiddenSeqs);
299
300		void setSelectionGroup(SequenceGroup sg);
301
302		char getGapCharacter();
303
304		void setColumnSelection(ColumnSelection cs);
305
306		void setConservation(Conservation cons);
307
308		/**
309		* get a copy of the currently visible alignment annotation
310		*
311		* @param selectedOnly
312		* if true - trim to selected regions on the alignment
313		* @return an empty list or new alignment annotation objects shown only
314		* visible columns trimmed to selected region only
315		*/
316		List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
317		boolean selectedOnly);
318
319		FeaturesDisplayedI getFeaturesDisplayed();
320
321		String getSequenceSetId();
322
323		boolean areFeaturesDisplayed();
324
325		void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI);
326
327		void alignmentChanged(AlignmentViewPanel ap);
328
329		/**
330		* @return the padGaps
331		*/
332		boolean isPadGaps();
333
334		/**
335		* @param padGaps
336		* the padGaps to set
337		*/
338		void setPadGaps(boolean padGaps);
339
340		/**
341		* return visible region boundaries within given column range
342		*
343		* @param min
344		* first column (inclusive, from 0)
345		* @param max
346		* last column (exclusive)
347		* @return int[][] range of {start,end} visible positions
348		*/
349		List<int[]> getVisibleRegionBoundaries(int min, int max);
350
351		/**
352		* This method returns an array of new SequenceI objects derived from the
353		* whole alignment or just the current selection with start and end points
354		* adjusted
355		*
356		* @note if you need references to the actual SequenceI objects in the
357		* alignment or currently selected then use getSequenceSelection()
358		* @return selection as new sequenceI objects
359		*/
360		SequenceI[] getSelectionAsNewSequence();
361
362		void invertColumnSelection();
363
364		/**
365		* broadcast selection to any interested parties
366		*/
367		void sendSelection();
368
369		/**
370		* calculate the row position for alignmentIndex if all hidden sequences were
371		* shown
372		*
373		* @param alignmentIndex
374		* @return adjusted row position
375		*/
376		int adjustForHiddenSeqs(int alignmentIndex);
377
378		boolean hasHiddenRows();
379
380		/**
381		*
382		* @return a copy of this view's current display settings
383		*/
384		public ViewStyleI getViewStyle();
385
386		/**
387		* update the view's display settings with the given style set
388		*
389		* @param settingsForView
390		*/
391		public void setViewStyle(ViewStyleI settingsForView);
392
393		/**
394		* Returns a viewport which holds the cDna for this (protein), or vice versa,
395		* or null if none is set.
396		*
397		* @return
398		*/
399		AlignViewportI getCodingComplement();
400
401		/**
402		* Sets the viewport which holds the cDna for this (protein), or vice versa.
403		* Implementation should guarantee that the reciprocal relationship is always
404		* set, i.e. each viewport is the complement of the other.
405		*/
406		void setCodingComplement(AlignViewportI sl);
407
408		/**
409		* Answers true if viewport hosts DNA/RNA, else false.
410		*
411		* @return
412		*/
413		boolean isNucleotide();
414
415		/**
416		* Returns an id guaranteed to be unique for this viewport.
417		*
418		* @return
419		*/
420		String getViewId();
421
422		/**
423		* Return true if view should scroll to show the highlighted region of a
424		* sequence
425		*
426		* @return
427		*/
428		boolean isFollowHighlight();
429
430		/**
431		* Set whether view should scroll to show the highlighted region of a sequence
432		*/
433		void setFollowHighlight(boolean b);
434
435		public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
436
437		/**
438		* check if current selection group is defined on the view, or is simply a
439		* temporary group.
440		*
441		* @return true if group is defined on the alignment
442		*/
443		boolean isSelectionDefinedGroup();
444
445		/**
446		*
447		* @return true if there are search results on the view
448		*/
449		boolean hasSearchResults();
450
451		/**
452		* set the search results for the view
453		*
454		* @param results
455		* - or null to clear current results
456		*/
457		void setSearchResults(SearchResultsI results);
458
459		/**
460		* get search results for this view (if any)
461		*
462		* @return search results or null
463		*/
464		SearchResultsI getSearchResults();
465
466		/**
467		* Updates view settings with the given font. You may need to call
468		* AlignmentPanel.fontChanged to update the layout geometry.
469		*
470		* @param setGrid
471		* when true, charWidth/height is set according to font metrics
472		*/
473		void setFont(Font newFont, boolean b);
474
475		/**
476		* Answers true if split screen protein and cDNA use the same font
477		*
478		* @return
479		*/
480		@Override
481		boolean isProteinFontAsCdna();
482
483		/**
484		* Set the flag for whether split screen protein and cDNA use the same font
485		*
486		* @return
487		*/
488		@Override
489		void setProteinFontAsCdna(boolean b);
490
491		TreeModel getCurrentTree();
492
493		void setCurrentTree(TreeModel tree);
494
495		/**
496		* Answers a data bean containing data for export as configured by the
497		* supplied options
498		*
499		* @param options
500		* @return
501		*/
502		AlignmentExportData getAlignExportData(AlignExportSettingsI options);
503		}