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.ColourSchemeI;
36 import java.awt.Color;
37 import java.util.Hashtable;
38 import java.util.List;
45 public interface AlignViewportI extends ViewStyleI
51 * calculate the height for visible annotation, revalidating bounds where
52 * necessary ABSTRACT GUI METHOD
54 * @return total height of annotation
56 public int calcPanelHeight();
59 * Answers true if the viewport has at least one column selected
63 boolean hasSelectedColumns();
66 * Answers true if the viewport has at least one hidden column
70 boolean hasHiddenColumns();
72 boolean isValidCharWidth();
74 boolean isShowConsensusHistogram();
76 boolean isShowSequenceLogo();
78 boolean isNormaliseSequenceLogo();
80 ColourSchemeI getGlobalColourScheme();
82 AlignmentI getAlignment();
84 ColumnSelection getColumnSelection();
86 ProfilesI getSequenceConsensusHash();
89 * Get consensus data table for the cDNA complement of this alignment (if any)
93 Hashtable[] getComplementConsensusHash();
95 Hashtable[] getRnaStructureConsensusHash();
97 boolean isIgnoreGapsConsensus();
99 boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
101 AlignmentAnnotation getAlignmentQualityAnnot();
103 AlignmentAnnotation getAlignmentConservationAnnotation();
106 * get the container for alignment consensus annotation
110 AlignmentAnnotation getAlignmentConsensusAnnotation();
113 * get the container for alignment gap annotation
117 AlignmentAnnotation getAlignmentGapAnnotation();
120 * get the container for cDNA complement consensus annotation
124 AlignmentAnnotation getComplementConsensusAnnotation();
127 * Test to see if viewport is still open and active
129 * @return true indicates that all references to viewport should be dropped
134 * Dispose of all references or resources held by the viewport
139 * get the associated calculation thread manager for the view
143 AlignCalcManagerI getCalcManager();
146 * get the percentage gaps allowed in a conservation calculation
149 public int getConsPercGaps();
152 * set the consensus result object for the viewport
156 void setSequenceConsensusHash(ProfilesI hconsensus);
159 * Set the cDNA complement consensus for the viewport
163 void setComplementConsensusHash(Hashtable[] hconsensus);
167 * @return the alignment annotatino row for the structure consensus
170 AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
173 * set the Rna structure consensus result object for the viewport
175 * @param hStrucConsensus
177 void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
180 * set global colourscheme
184 void setGlobalColourScheme(ColourSchemeI rhc);
186 Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
188 void setHiddenRepSequences(
189 Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
192 * hides or shows dynamic annotation rows based on groups and group and
193 * alignment associated auto-annotation state flags apply the current
194 * group/autoannotation settings to the alignment view. Usually you should
195 * call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to
196 * ensure the annotation panel bounds are set correctly.
198 * @param applyGlobalSettings
199 * - apply to all autoannotation rows or just the ones associated
200 * with the current visible region
201 * @param preserveNewGroupSettings
202 * - don't apply global settings to groups which don't already have
203 * group associated annotation
205 void updateGroupAnnotationSettings(boolean applyGlobalSettings,
206 boolean preserveNewGroupSettings);
208 void setSequenceColour(SequenceI seq, Color col);
210 Color getSequenceColour(SequenceI seq);
212 void updateSequenceIdColours();
214 SequenceGroup getSelectionGroup();
217 * get the currently selected sequence objects or all the sequences in the
218 * alignment. TODO: change to List<>
220 * @return array of references to sequence objects
222 SequenceI[] getSequenceSelection();
224 void clearSequenceColours();
227 * This method returns the visible alignment as text, as seen on the GUI, ie
228 * if columns are hidden they will not be returned in the result. Use this for
229 * calculating trees, PCA, redundancy etc on views which contain hidden
234 CigarArray getViewAsCigars(boolean selectedRegionOnly);
237 * return a compact representation of the current alignment selection to pass
238 * to an analysis function
240 * @param selectedOnly
241 * boolean true to just return the selected view
242 * @return AlignmentView
244 AlignmentView getAlignmentView(boolean selectedOnly);
247 * return a compact representation of the current alignment selection to pass
248 * to an analysis function
250 * @param selectedOnly
251 * boolean true to just return the selected view
253 * boolean true to annotate the alignment view with groups on the
254 * alignment (and intersecting with selected region if selectedOnly
256 * @return AlignmentView
258 AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
261 * This method returns the visible alignment as text, as seen on the GUI, ie
262 * if columns are hidden they will not be returned in the result. Use this for
263 * calculating trees, PCA, redundancy etc on views which contain hidden
264 * columns. This method doesn't exclude hidden sequences from the output.
266 * @param selectedRegionOnly
267 * - determines if only the selected region or entire alignment is
271 String[] getViewAsString(boolean selectedRegionOnly);
274 * This method returns the visible alignment as text, as seen on the GUI, ie
275 * if columns are hidden they will not be returned in the result. Use this for
276 * calculating trees, PCA, redundancy etc on views which contain hidden
279 * @param selectedRegionOnly
280 * - determines if only the selected region or entire alignment is
282 * @param isExportHiddenSeqs
283 * - determines if hidden sequences would be exported or not.
287 String[] getViewAsString(boolean selectedRegionOnly,
288 boolean isExportHiddenSeqs);
290 void setSelectionGroup(SequenceGroup sg);
292 char getGapCharacter();
294 void setColumnSelection(ColumnSelection cs);
296 void setConservation(Conservation cons);
299 * get a copy of the currently visible alignment annotation
301 * @param selectedOnly
302 * if true - trim to selected regions on the alignment
303 * @return an empty list or new alignment annotation objects shown only
304 * visible columns trimmed to selected region only
306 List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
307 boolean selectedOnly);
309 FeaturesDisplayedI getFeaturesDisplayed();
311 String getSequenceSetId();
313 boolean areFeaturesDisplayed();
315 void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI);
317 void alignmentChanged(AlignmentViewPanel ap);
320 * @return the padGaps
328 void setPadGaps(boolean padGaps);
331 * return visible region boundaries within given column range
334 * first column (inclusive, from 0)
336 * last column (exclusive)
337 * @return int[][] range of {start,end} visible positions
339 List<int[]> getVisibleRegionBoundaries(int min, int max);
342 * This method returns an array of new SequenceI objects derived from the
343 * whole alignment or just the current selection with start and end points
346 * @note if you need references to the actual SequenceI objects in the
347 * alignment or currently selected then use getSequenceSelection()
348 * @return selection as new sequenceI objects
350 SequenceI[] getSelectionAsNewSequence();
352 void invertColumnSelection();
355 * broadcast selection to any interested parties
357 void sendSelection();
360 * calculate the row position for alignmentIndex if all hidden sequences were
363 * @param alignmentIndex
364 * @return adjusted row position
366 int adjustForHiddenSeqs(int alignmentIndex);
368 boolean hasHiddenRows();
372 * @return a copy of this view's current display settings
374 public ViewStyleI getViewStyle();
377 * update the view's display settings with the given style set
379 * @param settingsForView
381 public void setViewStyle(ViewStyleI settingsForView);
384 * Returns a viewport which holds the cDna for this (protein), or vice versa,
385 * or null if none is set.
389 AlignViewportI getCodingComplement();
392 * Sets the viewport which holds the cDna for this (protein), or vice versa.
393 * Implementation should guarantee that the reciprocal relationship is always
394 * set, i.e. each viewport is the complement of the other.
396 void setCodingComplement(AlignViewportI sl);
399 * Answers true if viewport hosts DNA/RNA, else false.
403 boolean isNucleotide();
406 * Returns an id guaranteed to be unique for this viewport.
413 * Return true if view should scroll to show the highlighted region of a
418 boolean isFollowHighlight();
421 * Set whether view should scroll to show the highlighted region of a sequence
423 void setFollowHighlight(boolean b);
425 public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
428 * check if current selection group is defined on the view, or is simply a
431 * @return true if group is defined on the alignment
433 boolean isSelectionDefinedGroup();
437 * @return true if there are search results on the view
439 boolean hasSearchResults();
442 * set the search results for the view
445 * - or null to clear current results
447 void setSearchResults(SearchResultsI results);
450 * get search results for this view (if any)
452 * @return search results or null
454 SearchResultsI getSearchResults();