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.schemes.CollectionColourSchemeI;
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();
83 CollectionColourSchemeI getViewportColourScheme();
85 AlignmentI getAlignment();
87 ColumnSelection getColumnSelection();
89 ProfilesI getSequenceConsensusHash();
92 * Get consensus data table for the cDNA complement of this alignment (if any)
96 Hashtable[] getComplementConsensusHash();
98 Hashtable[] getRnaStructureConsensusHash();
100 boolean isIgnoreGapsConsensus();
102 boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
104 AlignmentAnnotation getAlignmentQualityAnnot();
106 AlignmentAnnotation getAlignmentConservationAnnotation();
109 * get the container for alignment consensus annotation
113 AlignmentAnnotation getAlignmentConsensusAnnotation();
116 * get the container for cDNA complement consensus annotation
120 AlignmentAnnotation getComplementConsensusAnnotation();
123 * Test to see if viewport is still open and active
125 * @return true indicates that all references to viewport should be dropped
130 * Dispose of all references or resources held by the viewport
135 * get the associated calculation thread manager for the view
139 AlignCalcManagerI getCalcManager();
142 * get the percentage gaps allowed in a conservation calculation
145 public int getConsPercGaps();
148 * set the consensus result object for the viewport
152 void setSequenceConsensusHash(ProfilesI hconsensus);
155 * Set the cDNA complement consensus for the viewport
159 void setComplementConsensusHash(Hashtable[] hconsensus);
163 * @return the alignment annotatino row for the structure consensus
166 AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
169 * set the Rna structure consensus result object for the viewport
171 * @param hStrucConsensus
173 void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
176 * set global colourscheme
180 void setGlobalColourScheme(ColourSchemeI rhc);
182 Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
184 void setHiddenRepSequences(
185 Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
188 * hides or shows dynamic annotation rows based on groups and group and
189 * alignment associated auto-annotation state flags apply the current
190 * group/autoannotation settings to the alignment view. Usually you should
191 * call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to
192 * ensure the annotation panel bounds are set correctly.
194 * @param applyGlobalSettings
195 * - apply to all autoannotation rows or just the ones associated
196 * with the current visible region
197 * @param preserveNewGroupSettings
198 * - don't apply global settings to groups which don't already have
199 * group associated annotation
201 void updateGroupAnnotationSettings(boolean applyGlobalSettings,
202 boolean preserveNewGroupSettings);
204 void setSequenceColour(SequenceI seq, Color col);
206 Color getSequenceColour(SequenceI seq);
208 void updateSequenceIdColours();
210 SequenceGroup getSelectionGroup();
213 * get the currently selected sequence objects or all the sequences in the
214 * alignment. TODO: change to List<>
216 * @return array of references to sequence objects
218 SequenceI[] getSequenceSelection();
220 void clearSequenceColours();
223 * This method returns the visible alignment as text, as seen on the GUI, ie
224 * if columns are hidden they will not be returned in the result. Use this for
225 * calculating trees, PCA, redundancy etc on views which contain hidden
230 CigarArray getViewAsCigars(boolean selectedRegionOnly);
233 * return a compact representation of the current alignment selection to pass
234 * to an analysis function
236 * @param selectedOnly
237 * boolean true to just return the selected view
238 * @return AlignmentView
240 AlignmentView getAlignmentView(boolean selectedOnly);
243 * return a compact representation of the current alignment selection to pass
244 * to an analysis function
246 * @param selectedOnly
247 * boolean true to just return the selected view
249 * boolean true to annotate the alignment view with groups on the
250 * alignment (and intersecting with selected region if selectedOnly
252 * @return AlignmentView
254 AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
257 * This method returns the visible alignment as text, as seen on the GUI, ie
258 * if columns are hidden they will not be returned in the result. Use this for
259 * calculating trees, PCA, redundancy etc on views which contain hidden
260 * columns. This method doesn't exclude hidden sequences from the output.
262 * @param selectedRegionOnly
263 * - determines if only the selected region or entire alignment is
267 String[] getViewAsString(boolean selectedRegionOnly);
270 * This method returns the visible alignment as text, as seen on the GUI, ie
271 * if columns are hidden they will not be returned in the result. Use this for
272 * calculating trees, PCA, redundancy etc on views which contain hidden
275 * @param selectedRegionOnly
276 * - determines if only the selected region or entire alignment is
278 * @param isExportHiddenSeqs
279 * - determines if hidden sequences would be exported or not.
283 String[] getViewAsString(boolean selectedRegionOnly,
284 boolean isExportHiddenSeqs);
286 void setSelectionGroup(SequenceGroup sg);
288 char getGapCharacter();
290 void setColumnSelection(ColumnSelection cs);
292 void setConservation(Conservation cons);
295 * get a copy of the currently visible alignment annotation
297 * @param selectedOnly
298 * if true - trim to selected regions on the alignment
299 * @return an empty list or new alignment annotation objects shown only
300 * visible columns trimmed to selected region only
302 List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
303 boolean selectedOnly);
305 FeaturesDisplayedI getFeaturesDisplayed();
307 String getSequenceSetId();
309 boolean areFeaturesDisplayed();
311 void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI);
313 void alignmentChanged(AlignmentViewPanel ap);
316 * @return the padGaps
324 void setPadGaps(boolean padGaps);
327 * return visible region boundaries within given column range
330 * first column (inclusive, from 0)
332 * last column (exclusive)
333 * @return int[][] range of {start,end} visible positions
335 List<int[]> getVisibleRegionBoundaries(int min, int max);
338 * This method returns an array of new SequenceI objects derived from the
339 * whole alignment or just the current selection with start and end points
342 * @note if you need references to the actual SequenceI objects in the
343 * alignment or currently selected then use getSequenceSelection()
344 * @return selection as new sequenceI objects
346 SequenceI[] getSelectionAsNewSequence();
348 void invertColumnSelection();
351 * broadcast selection to any interested parties
353 void sendSelection();
356 * calculate the row position for alignmentIndex if all hidden sequences were
359 * @param alignmentIndex
360 * @return adjusted row position
362 int adjustForHiddenSeqs(int alignmentIndex);
364 boolean hasHiddenRows();
368 * @return a copy of this view's current display settings
370 public ViewStyleI getViewStyle();
373 * update the view's display settings with the given style set
375 * @param settingsForView
377 public void setViewStyle(ViewStyleI settingsForView);
380 * Returns a viewport which holds the cDna for this (protein), or vice versa,
381 * or null if none is set.
385 AlignViewportI getCodingComplement();
388 * Sets the viewport which holds the cDna for this (protein), or vice versa.
389 * Implementation should guarantee that the reciprocal relationship is always
390 * set, i.e. each viewport is the complement of the other.
392 void setCodingComplement(AlignViewportI sl);
395 * Answers true if viewport hosts DNA/RNA, else false.
399 boolean isNucleotide();
402 * Returns an id guaranteed to be unique for this viewport.
409 * Return true if view should scroll to show the highlighted region of a
414 boolean isFollowHighlight();
417 * Set whether view should scroll to show the highlighted region of a sequence
419 void setFollowHighlight(boolean b);
421 public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
424 * check if current selection group is defined on the view, or is simply a
427 * @return true if group is defined on the alignment
429 boolean isSelectionDefinedGroup();
433 * @return true if there are search results on the view
435 boolean hasSearchResults();
438 * set the search results for the view
441 * - or null to clear current results
443 void setSearchResults(SearchResultsI results);
446 * get search results for this view (if any)
448 * @return search results or null
450 SearchResultsI getSearchResults();