2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
23 import jalview.analysis.Conservation;
24 import jalview.datamodel.AlignmentAnnotation;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.AlignmentView;
27 import jalview.datamodel.CigarArray;
28 import jalview.datamodel.ColumnSelection;
29 import jalview.datamodel.ProfilesI;
30 import jalview.datamodel.SearchResultsI;
31 import jalview.datamodel.SequenceCollectionI;
32 import jalview.datamodel.SequenceGroup;
33 import jalview.datamodel.SequenceI;
34 import jalview.renderer.ResidueShaderI;
35 import jalview.schemes.ColourSchemeI;
36 import jalview.viewmodel.ViewportRanges;
38 import java.awt.Color;
39 import java.util.Hashtable;
40 import java.util.List;
47 public interface AlignViewportI extends ViewStyleI
51 * Get the ranges object containing details of the start and end sequences and
56 public ViewportRanges getRanges();
59 * calculate the height for visible annotation, revalidating bounds where
60 * necessary ABSTRACT GUI METHOD
62 * @return total height of annotation
64 public int calcPanelHeight();
67 * Answers true if the viewport has at least one column selected
71 boolean hasSelectedColumns();
74 * Answers true if the viewport has at least one hidden column
78 boolean hasHiddenColumns();
80 boolean isValidCharWidth();
82 boolean isShowConsensusHistogram();
84 boolean isShowSequenceLogo();
86 boolean isNormaliseSequenceLogo();
88 ColourSchemeI getGlobalColourScheme();
91 * Returns an object that describes colouring (including any thresholding or
92 * fading) of the alignment
96 ResidueShaderI getResidueShading();
98 AlignmentI getAlignment();
100 ColumnSelection getColumnSelection();
102 ProfilesI getSequenceConsensusHash();
105 * Get consensus data table for the cDNA complement of this alignment (if any)
109 Hashtable[] getComplementConsensusHash();
111 Hashtable[] getRnaStructureConsensusHash();
113 boolean isIgnoreGapsConsensus();
115 boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
117 AlignmentAnnotation getAlignmentQualityAnnot();
119 AlignmentAnnotation getAlignmentConservationAnnotation();
122 * get the container for alignment consensus annotation
126 AlignmentAnnotation getAlignmentConsensusAnnotation();
129 * get the container for alignment gap annotation
133 AlignmentAnnotation getAlignmentGapAnnotation();
136 * get the container for cDNA complement consensus annotation
140 AlignmentAnnotation getComplementConsensusAnnotation();
143 * Test to see if viewport is still open and active
145 * @return true indicates that all references to viewport should be dropped
150 * Dispose of all references or resources held by the viewport
155 * get the associated calculation thread manager for the view
159 AlignCalcManagerI getCalcManager();
162 * get the percentage gaps allowed in a conservation calculation
165 public int getConsPercGaps();
168 * set the consensus result object for the viewport
172 void setSequenceConsensusHash(ProfilesI hconsensus);
175 * Set the cDNA complement consensus for the viewport
179 void setComplementConsensusHash(Hashtable[] hconsensus);
183 * @return the alignment annotation row for the structure consensus
186 AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
189 * set the Rna structure consensus result object for the viewport
191 * @param hStrucConsensus
193 void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
196 * Sets the colour scheme for the background alignment (as distinct from
197 * sub-groups, which may have their own colour schemes). A null value is used
198 * for no residue colour (white).
202 void setGlobalColourScheme(ColourSchemeI cs);
204 Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
206 void setHiddenRepSequences(
207 Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
210 * hides or shows dynamic annotation rows based on groups and group and
211 * alignment associated auto-annotation state flags apply the current
212 * group/autoannotation settings to the alignment view. Usually you should
213 * call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to
214 * ensure the annotation panel bounds are set correctly.
216 * @param applyGlobalSettings
217 * - apply to all autoannotation rows or just the ones associated
218 * with the current visible region
219 * @param preserveNewGroupSettings
220 * - don't apply global settings to groups which don't already have
221 * group associated annotation
223 void updateGroupAnnotationSettings(boolean applyGlobalSettings,
224 boolean preserveNewGroupSettings);
226 void setSequenceColour(SequenceI seq, Color col);
228 Color getSequenceColour(SequenceI seq);
230 void updateSequenceIdColours();
232 SequenceGroup getSelectionGroup();
235 * get the currently selected sequence objects or all the sequences in the
236 * alignment. TODO: change to List<>
238 * @return array of references to sequence objects
240 SequenceI[] getSequenceSelection();
242 void clearSequenceColours();
245 * This method returns the visible alignment as text, as seen on the GUI, ie
246 * if columns are hidden they will not be returned in the result. Use this for
247 * calculating trees, PCA, redundancy etc on views which contain hidden
252 CigarArray getViewAsCigars(boolean selectedRegionOnly);
255 * return a compact representation of the current alignment selection to pass
256 * to an analysis function
258 * @param selectedOnly
259 * boolean true to just return the selected view
260 * @return AlignmentView
262 AlignmentView getAlignmentView(boolean selectedOnly);
265 * return a compact representation of the current alignment selection to pass
266 * to an analysis function
268 * @param selectedOnly
269 * boolean true to just return the selected view
271 * boolean true to annotate the alignment view with groups on the
272 * alignment (and intersecting with selected region if selectedOnly
274 * @return AlignmentView
276 AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
279 * This method returns the visible alignment as text, as seen on the GUI, ie
280 * if columns are hidden they will not be returned in the result. Use this for
281 * calculating trees, PCA, redundancy etc on views which contain hidden
282 * columns. This method doesn't exclude hidden sequences from the output.
284 * @param selectedRegionOnly
285 * - determines if only the selected region or entire alignment is
289 String[] getViewAsString(boolean selectedRegionOnly);
292 * This method returns the visible alignment as text, as seen on the GUI, ie
293 * if columns are hidden they will not be returned in the result. Use this for
294 * calculating trees, PCA, redundancy etc on views which contain hidden
297 * @param selectedRegionOnly
298 * - determines if only the selected region or entire alignment is
300 * @param isExportHiddenSeqs
301 * - determines if hidden sequences would be exported or not.
305 String[] getViewAsString(boolean selectedRegionOnly,
306 boolean isExportHiddenSeqs);
308 void setSelectionGroup(SequenceGroup sg);
310 char getGapCharacter();
312 void setColumnSelection(ColumnSelection cs);
314 void setConservation(Conservation cons);
317 * get a copy of the currently visible alignment annotation
319 * @param selectedOnly
320 * if true - trim to selected regions on the alignment
321 * @return an empty list or new alignment annotation objects shown only
322 * visible columns trimmed to selected region only
324 List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
325 boolean selectedOnly);
327 FeaturesDisplayedI getFeaturesDisplayed();
329 String getSequenceSetId();
331 boolean areFeaturesDisplayed();
333 void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI);
335 void alignmentChanged(AlignmentViewPanel ap);
338 * @return the padGaps
346 void setPadGaps(boolean padGaps);
349 * return visible region boundaries within given column range
352 * first column (inclusive, from 0)
354 * last column (exclusive)
355 * @return int[][] range of {start,end} visible positions
357 List<int[]> getVisibleRegionBoundaries(int min, int max);
360 * This method returns an array of new SequenceI objects derived from the
361 * whole alignment or just the current selection with start and end points
364 * @note if you need references to the actual SequenceI objects in the
365 * alignment or currently selected then use getSequenceSelection()
366 * @return selection as new sequenceI objects
368 SequenceI[] getSelectionAsNewSequence();
370 void invertColumnSelection();
373 * broadcast selection to any interested parties
375 void sendSelection();
378 * calculate the row position for alignmentIndex if all hidden sequences were
381 * @param alignmentIndex
382 * @return adjusted row position
384 int adjustForHiddenSeqs(int alignmentIndex);
386 boolean hasHiddenRows();
390 * @return a copy of this view's current display settings
392 public ViewStyleI getViewStyle();
395 * update the view's display settings with the given style set
397 * @param settingsForView
399 public void setViewStyle(ViewStyleI settingsForView);
402 * Returns a viewport which holds the cDna for this (protein), or vice versa,
403 * or null if none is set.
407 AlignViewportI getCodingComplement();
410 * Sets the viewport which holds the cDna for this (protein), or vice versa.
411 * Implementation should guarantee that the reciprocal relationship is always
412 * set, i.e. each viewport is the complement of the other.
414 void setCodingComplement(AlignViewportI sl);
417 * Answers true if viewport hosts DNA/RNA, else false.
421 boolean isNucleotide();
424 * Returns an id guaranteed to be unique for this viewport.
431 * Return true if view should scroll to show the highlighted region of a
436 boolean isFollowHighlight();
439 * Set whether view should scroll to show the highlighted region of a sequence
441 void setFollowHighlight(boolean b);
443 public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
446 * check if current selection group is defined on the view, or is simply a
449 * @return true if group is defined on the alignment
451 boolean isSelectionDefinedGroup();
455 * @return true if there are search results on the view
457 boolean hasSearchResults();
460 * set the search results for the view
463 * - or null to clear current results
465 void setSearchResults(SearchResultsI results);
468 * get search results for this view (if any)
470 * @return search results or null
472 SearchResultsI getSearchResults();