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.ContactListI;
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;
39 import java.awt.Color;
41 import java.util.Hashtable;
42 import java.util.List;
49 public interface AlignViewportI extends ViewStyleI
53 * Get the ranges object containing details of the start and end sequences and
58 public ViewportRanges getRanges();
61 * calculate the height for visible annotation, revalidating bounds where
62 * necessary ABSTRACT GUI METHOD
64 * @return total height of annotation
66 public int calcPanelHeight();
69 * Answers true if the viewport has at least one column selected
73 boolean hasSelectedColumns();
76 * Answers true if the viewport has at least one hidden column
80 boolean hasHiddenColumns();
82 boolean isValidCharWidth();
84 boolean isShowConsensusHistogram();
86 boolean isShowSequenceLogo();
88 boolean isNormaliseSequenceLogo();
90 ColourSchemeI getGlobalColourScheme();
93 * Returns an object that describes colouring (including any thresholding or
94 * fading) of the alignment
98 ResidueShaderI getResidueShading();
100 AlignmentI getAlignment();
102 ColumnSelection getColumnSelection();
104 ProfilesI getSequenceConsensusHash();
107 * Get consensus data table for the cDNA complement of this alignment (if any)
111 Hashtable[] getComplementConsensusHash();
113 Hashtable[] getRnaStructureConsensusHash();
115 boolean isIgnoreGapsConsensus();
117 boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
119 AlignmentAnnotation getAlignmentQualityAnnot();
121 AlignmentAnnotation getAlignmentConservationAnnotation();
124 * get the container for alignment consensus annotation
128 AlignmentAnnotation getAlignmentConsensusAnnotation();
131 * get the container for alignment gap annotation
135 AlignmentAnnotation getAlignmentGapAnnotation();
138 * get the container for cDNA complement consensus annotation
142 AlignmentAnnotation getComplementConsensusAnnotation();
145 * Test to see if viewport is still open and active
147 * @return true indicates that all references to viewport should be dropped
152 * Dispose of all references or resources held by the viewport
157 * get the associated calculation thread manager for the view
161 AlignCalcManagerI getCalcManager();
164 * get the percentage gaps allowed in a conservation calculation
167 public int getConsPercGaps();
170 * set the consensus result object for the viewport
174 void setSequenceConsensusHash(ProfilesI hconsensus);
177 * Set the cDNA complement consensus for the viewport
181 void setComplementConsensusHash(Hashtable[] hconsensus);
185 * @return the alignment annotation row for the structure consensus
188 AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
191 * set the Rna structure consensus result object for the viewport
193 * @param hStrucConsensus
195 void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
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).
204 void setGlobalColourScheme(ColourSchemeI cs);
206 Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
208 void setHiddenRepSequences(
209 Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
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.
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
225 void updateGroupAnnotationSettings(boolean applyGlobalSettings,
226 boolean preserveNewGroupSettings);
228 void setSequenceColour(SequenceI seq, Color col);
230 Color getSequenceColour(SequenceI seq);
232 void updateSequenceIdColours();
234 SequenceGroup getSelectionGroup();
237 * get the currently selected sequence objects or all the sequences in the
238 * alignment. TODO: change to List<>
240 * @return array of references to sequence objects
242 SequenceI[] getSequenceSelection();
244 void clearSequenceColours();
247 * This method returns the visible alignment as text, as seen on the GUI, ie
248 * if columns are hidden they will not be returned in the result. Use this for
249 * calculating trees, PCA, redundancy etc on views which contain hidden
254 CigarArray getViewAsCigars(boolean selectedRegionOnly);
257 * return a compact representation of the current alignment selection to pass
258 * to an analysis function
260 * @param selectedOnly
261 * boolean true to just return the selected view
262 * @return AlignmentView
264 AlignmentView getAlignmentView(boolean selectedOnly);
267 * return a compact representation of the current alignment selection to pass
268 * to an analysis function
270 * @param selectedOnly
271 * boolean true to just return the selected view
273 * boolean true to annotate the alignment view with groups on the
274 * alignment (and intersecting with selected region if selectedOnly
276 * @return AlignmentView
278 AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
281 * This method returns the visible alignment as text, as seen on the GUI, ie
282 * if columns are hidden they will not be returned in the result. Use this for
283 * calculating trees, PCA, redundancy etc on views which contain hidden
284 * columns. This method doesn't exclude hidden sequences from the output.
286 * @param selectedRegionOnly
287 * - determines if only the selected region or entire alignment is
291 String[] getViewAsString(boolean selectedRegionOnly);
294 * This method returns the visible alignment as text, as seen on the GUI, ie
295 * if columns are hidden they will not be returned in the result. Use this for
296 * calculating trees, PCA, redundancy etc on views which contain hidden
299 * @param selectedRegionOnly
300 * - determines if only the selected region or entire alignment is
302 * @param isExportHiddenSeqs
303 * - determines if hidden sequences would be exported or not.
307 String[] getViewAsString(boolean selectedRegionOnly,
308 boolean isExportHiddenSeqs);
310 void setSelectionGroup(SequenceGroup sg);
312 char getGapCharacter();
314 void setColumnSelection(ColumnSelection cs);
316 void setConservation(Conservation cons);
319 * get a copy of the currently visible alignment annotation
321 * @param selectedOnly
322 * if true - trim to selected regions on the alignment
323 * @return an empty list or new alignment annotation objects shown only
324 * visible columns trimmed to selected region only
326 List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
327 boolean selectedOnly);
329 FeaturesDisplayedI getFeaturesDisplayed();
331 String getSequenceSetId();
333 boolean areFeaturesDisplayed();
335 void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI);
337 void alignmentChanged(AlignmentViewPanel ap);
340 * @return the padGaps
348 void setPadGaps(boolean padGaps);
351 * return visible region boundaries within given column range
354 * first column (inclusive, from 0)
356 * last column (exclusive)
357 * @return int[][] range of {start,end} visible positions
359 List<int[]> getVisibleRegionBoundaries(int min, int max);
362 * This method returns an array of new SequenceI objects derived from the
363 * whole alignment or just the current selection with start and end points
366 * @note if you need references to the actual SequenceI objects in the
367 * alignment or currently selected then use getSequenceSelection()
368 * @return selection as new sequenceI objects
370 SequenceI[] getSelectionAsNewSequence();
372 void invertColumnSelection();
375 * broadcast selection to any interested parties
377 void sendSelection();
380 * calculate the row position for alignmentIndex if all hidden sequences were
383 * @param alignmentIndex
384 * @return adjusted row position
386 int adjustForHiddenSeqs(int alignmentIndex);
388 boolean hasHiddenRows();
392 * @return a copy of this view's current display settings
394 public ViewStyleI getViewStyle();
397 * update the view's display settings with the given style set
399 * @param settingsForView
401 public void setViewStyle(ViewStyleI settingsForView);
404 * Returns a viewport which holds the cDna for this (protein), or vice versa,
405 * or null if none is set.
409 AlignViewportI getCodingComplement();
412 * Sets the viewport which holds the cDna for this (protein), or vice versa.
413 * Implementation should guarantee that the reciprocal relationship is always
414 * set, i.e. each viewport is the complement of the other.
416 void setCodingComplement(AlignViewportI sl);
419 * Answers true if viewport hosts DNA/RNA, else false.
423 boolean isNucleotide();
426 * Returns an id guaranteed to be unique for this viewport.
433 * Return true if view should scroll to show the highlighted region of a
438 boolean isFollowHighlight();
441 * Set whether view should scroll to show the highlighted region of a sequence
443 void setFollowHighlight(boolean b);
445 public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
448 * check if current selection group is defined on the view, or is simply a
451 * @return true if group is defined on the alignment
453 boolean isSelectionDefinedGroup();
457 * @return true if there are search results on the view
459 boolean hasSearchResults();
462 * set the search results for the view
465 * - or null to clear current results
467 void setSearchResults(SearchResultsI results);
470 * get search results for this view (if any)
472 * @return search results or null
474 SearchResultsI getSearchResults();
476 ContactListI getContactList(AlignmentAnnotation _aa, int column);
479 * Updates view settings with the given font. You may need to call
480 * AlignmentPanel.fontChanged to update the layout geometry.
483 * when true, charWidth/height is set according to font metrics
485 void setFont(Font newFont, boolean b);
488 * Answers true if split screen protein and cDNA use the same font
493 boolean isProteinFontAsCdna();
496 * Set the flag for whether split screen protein and cDNA use the same font
501 void setProteinFontAsCdna(boolean b);