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;
37 import java.awt.Color;
38 import java.util.Hashtable;
39 import java.util.List;
46 public interface AlignViewportI extends ViewStyleI
52 * calculate the height for visible annotation, revalidating bounds where
53 * necessary ABSTRACT GUI METHOD
55 * @return total height of annotation
57 public int calcPanelHeight();
60 * Answers true if the viewport has at least one column selected
64 boolean hasSelectedColumns();
67 * Answers true if the viewport has at least one hidden column
71 boolean hasHiddenColumns();
73 boolean isValidCharWidth();
75 boolean isShowConsensusHistogram();
77 boolean isShowSequenceLogo();
79 boolean isNormaliseSequenceLogo();
81 ColourSchemeI getGlobalColourScheme();
84 * Returns an object that describes colouring (including any thresholding or
85 * fading) of the alignment
89 ResidueShaderI getResidueShading();
91 AlignmentI getAlignment();
93 ColumnSelection getColumnSelection();
95 ProfilesI getSequenceConsensusHash();
98 * Get consensus data table for the cDNA complement of this alignment (if any)
102 Hashtable[] getComplementConsensusHash();
104 Hashtable[] getRnaStructureConsensusHash();
106 boolean isIgnoreGapsConsensus();
108 boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
110 AlignmentAnnotation getAlignmentQualityAnnot();
112 AlignmentAnnotation getAlignmentConservationAnnotation();
115 * get the container for alignment consensus annotation
119 AlignmentAnnotation getAlignmentConsensusAnnotation();
122 * get the container for alignment gap annotation
126 AlignmentAnnotation getAlignmentGapAnnotation();
129 * get the container for cDNA complement consensus annotation
133 AlignmentAnnotation getComplementConsensusAnnotation();
136 * Test to see if viewport is still open and active
138 * @return true indicates that all references to viewport should be dropped
143 * Dispose of all references or resources held by the viewport
148 * get the associated calculation thread manager for the view
152 AlignCalcManagerI getCalcManager();
155 * get the percentage gaps allowed in a conservation calculation
158 public int getConsPercGaps();
161 * set the consensus result object for the viewport
165 void setSequenceConsensusHash(ProfilesI hconsensus);
168 * Set the cDNA complement consensus for the viewport
172 void setComplementConsensusHash(Hashtable[] hconsensus);
176 * @return the alignment annotation row for the structure consensus
179 AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
182 * set the Rna structure consensus result object for the viewport
184 * @param hStrucConsensus
186 void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
189 * Sets the colour scheme for the background alignment (as distinct from
190 * sub-groups, which may have their own colour schemes). A null value is used
191 * for no residue colour (white).
195 void setGlobalColourScheme(ColourSchemeI cs);
197 Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
199 void setHiddenRepSequences(
200 Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
203 * hides or shows dynamic annotation rows based on groups and group and
204 * alignment associated auto-annotation state flags apply the current
205 * group/autoannotation settings to the alignment view. Usually you should
206 * call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to
207 * ensure the annotation panel bounds are set correctly.
209 * @param applyGlobalSettings
210 * - apply to all autoannotation rows or just the ones associated
211 * with the current visible region
212 * @param preserveNewGroupSettings
213 * - don't apply global settings to groups which don't already have
214 * group associated annotation
216 void updateGroupAnnotationSettings(boolean applyGlobalSettings,
217 boolean preserveNewGroupSettings);
219 void setSequenceColour(SequenceI seq, Color col);
221 Color getSequenceColour(SequenceI seq);
223 void updateSequenceIdColours();
225 SequenceGroup getSelectionGroup();
228 * get the currently selected sequence objects or all the sequences in the
229 * alignment. TODO: change to List<>
231 * @return array of references to sequence objects
233 SequenceI[] getSequenceSelection();
235 void clearSequenceColours();
238 * This method returns the visible alignment as text, as seen on the GUI, ie
239 * if columns are hidden they will not be returned in the result. Use this for
240 * calculating trees, PCA, redundancy etc on views which contain hidden
245 CigarArray getViewAsCigars(boolean selectedRegionOnly);
248 * return a compact representation of the current alignment selection to pass
249 * to an analysis function
251 * @param selectedOnly
252 * boolean true to just return the selected view
253 * @return AlignmentView
255 AlignmentView getAlignmentView(boolean selectedOnly);
258 * return a compact representation of the current alignment selection to pass
259 * to an analysis function
261 * @param selectedOnly
262 * boolean true to just return the selected view
264 * boolean true to annotate the alignment view with groups on the
265 * alignment (and intersecting with selected region if selectedOnly
267 * @return AlignmentView
269 AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
272 * This method returns the visible alignment as text, as seen on the GUI, ie
273 * if columns are hidden they will not be returned in the result. Use this for
274 * calculating trees, PCA, redundancy etc on views which contain hidden
275 * columns. This method doesn't exclude hidden sequences from the output.
277 * @param selectedRegionOnly
278 * - determines if only the selected region or entire alignment is
282 String[] getViewAsString(boolean selectedRegionOnly);
285 * This method returns the visible alignment as text, as seen on the GUI, ie
286 * if columns are hidden they will not be returned in the result. Use this for
287 * calculating trees, PCA, redundancy etc on views which contain hidden
290 * @param selectedRegionOnly
291 * - determines if only the selected region or entire alignment is
293 * @param isExportHiddenSeqs
294 * - determines if hidden sequences would be exported or not.
298 String[] getViewAsString(boolean selectedRegionOnly,
299 boolean isExportHiddenSeqs);
301 void setSelectionGroup(SequenceGroup sg);
303 char getGapCharacter();
305 void setColumnSelection(ColumnSelection cs);
307 void setConservation(Conservation cons);
310 * get a copy of the currently visible alignment annotation
312 * @param selectedOnly
313 * if true - trim to selected regions on the alignment
314 * @return an empty list or new alignment annotation objects shown only
315 * visible columns trimmed to selected region only
317 List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
318 boolean selectedOnly);
320 FeaturesDisplayedI getFeaturesDisplayed();
322 String getSequenceSetId();
324 boolean areFeaturesDisplayed();
326 void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI);
328 void alignmentChanged(AlignmentViewPanel ap);
331 * @return the padGaps
339 void setPadGaps(boolean padGaps);
342 * return visible region boundaries within given column range
345 * first column (inclusive, from 0)
347 * last column (exclusive)
348 * @return int[][] range of {start,end} visible positions
350 List<int[]> getVisibleRegionBoundaries(int min, int max);
353 * This method returns an array of new SequenceI objects derived from the
354 * whole alignment or just the current selection with start and end points
357 * @note if you need references to the actual SequenceI objects in the
358 * alignment or currently selected then use getSequenceSelection()
359 * @return selection as new sequenceI objects
361 SequenceI[] getSelectionAsNewSequence();
363 void invertColumnSelection();
366 * broadcast selection to any interested parties
368 void sendSelection();
371 * calculate the row position for alignmentIndex if all hidden sequences were
374 * @param alignmentIndex
375 * @return adjusted row position
377 int adjustForHiddenSeqs(int alignmentIndex);
379 boolean hasHiddenRows();
383 * @return a copy of this view's current display settings
385 public ViewStyleI getViewStyle();
388 * update the view's display settings with the given style set
390 * @param settingsForView
392 public void setViewStyle(ViewStyleI settingsForView);
395 * Returns a viewport which holds the cDna for this (protein), or vice versa,
396 * or null if none is set.
400 AlignViewportI getCodingComplement();
403 * Sets the viewport which holds the cDna for this (protein), or vice versa.
404 * Implementation should guarantee that the reciprocal relationship is always
405 * set, i.e. each viewport is the complement of the other.
407 void setCodingComplement(AlignViewportI sl);
410 * Answers true if viewport hosts DNA/RNA, else false.
414 boolean isNucleotide();
417 * Returns an id guaranteed to be unique for this viewport.
424 * Return true if view should scroll to show the highlighted region of a
429 boolean isFollowHighlight();
432 * Set whether view should scroll to show the highlighted region of a sequence
434 void setFollowHighlight(boolean b);
436 public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
439 * check if current selection group is defined on the view, or is simply a
442 * @return true if group is defined on the alignment
444 boolean isSelectionDefinedGroup();
448 * @return true if there are search results on the view
450 boolean hasSearchResults();
453 * set the search results for the view
456 * - or null to clear current results
458 void setSearchResults(SearchResultsI results);
461 * get search results for this view (if any)
463 * @return search results or null
465 SearchResultsI getSearchResults();