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.analysis.TreeModel;
25 import jalview.datamodel.AlignmentAnnotation;
26 import jalview.datamodel.AlignmentExportData;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.AlignmentView;
29 import jalview.datamodel.ColumnSelection;
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.Iterator;
43 import java.util.List;
50 public interface AlignViewportI extends ViewStyleI
54 * Get the ranges object containing details of the start and end sequences and
59 ViewportRanges getRanges();
62 * calculate the height for visible annotation, revalidating bounds where
63 * necessary ABSTRACT GUI METHOD
65 * @return total height of annotation
67 int calcPanelHeight();
70 * Answers true if the viewport has at least one column selected
74 boolean hasSelectedColumns();
77 * Answers true if the viewport has at least one hidden column
81 boolean hasHiddenColumns();
83 boolean isValidCharWidth();
85 boolean isShowConsensusHistogram();
87 boolean isShowSequenceLogo();
89 boolean isNormaliseSequenceLogo();
91 boolean isShowInformationHistogram();
93 boolean isShowHMMSequenceLogo();
95 boolean isNormaliseHMMSequenceLogo();
97 ColourSchemeI getGlobalColourScheme();
100 * Returns an object that describes colouring (including any thresholding or
101 * fading) of the alignment
105 ResidueShaderI getResidueShading();
107 AlignmentI getAlignment();
109 ColumnSelection getColumnSelection();
111 ProfilesI getSequenceConsensusHash();
114 * Get consensus data table for the cDNA complement of this alignment (if any)
118 Hashtable<String, Object>[] getComplementConsensusHash();
120 Hashtable<String, Object>[] getRnaStructureConsensusHash();
122 boolean isIgnoreGapsConsensus();
124 boolean isIgnoreBelowBackground();
126 boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
128 AlignmentAnnotation getAlignmentQualityAnnot();
130 AlignmentAnnotation getAlignmentConservationAnnotation();
133 * get the container for alignment consensus annotation
137 AlignmentAnnotation getAlignmentConsensusAnnotation();
140 * get the container for alignment gap annotation
144 AlignmentAnnotation getAlignmentGapAnnotation();
147 * get the container for cDNA complement consensus annotation
151 AlignmentAnnotation getComplementConsensusAnnotation();
154 * Test to see if viewport is still open and active
156 * @return true indicates that all references to viewport should be dropped
161 * Dispose of all references or resources held by the viewport
166 * get the associated calculation thread manager for the view
170 AlignCalcManagerI2 getCalcManager();
173 * get the percentage gaps allowed in a conservation calculation
176 public int getConsPercGaps();
179 * set the consensus result object for the viewport
183 void setSequenceConsensusHash(ProfilesI hconsensus);
186 * Set the cDNA complement consensus for the viewport
190 void setComplementConsensusHash(Hashtable<String, Object>[] hconsensus);
194 * @return the alignment annotation row for the structure consensus
197 AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
200 * set the Rna structure consensus result object for the viewport
202 * @param hStrucConsensus
204 void setRnaStructureConsensusHash(
205 Hashtable<String, Object>[] hStrucConsensus);
208 * Sets the colour scheme for the background alignment (as distinct from
209 * sub-groups, which may have their own colour schemes). A null value is used
210 * for no residue colour (white).
214 void setGlobalColourScheme(ColourSchemeI cs);
216 Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
218 void setHiddenRepSequences(
219 Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
222 * hides or shows dynamic annotation rows based on groups and group and
223 * alignment associated auto-annotation state flags apply the current
224 * group/autoannotation settings to the alignment view. Usually you should
225 * call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to
226 * ensure the annotation panel bounds are set correctly.
228 * @param applyGlobalSettings
229 * - apply to all autoannotation rows or just the ones associated
230 * with the current visible region
231 * @param preserveNewGroupSettings
232 * - don't apply global settings to groups which don't already have
233 * group associated annotation
235 void updateGroupAnnotationSettings(boolean applyGlobalSettings,
236 boolean preserveNewGroupSettings);
238 void setSequenceColour(SequenceI seq, Color col);
240 Color getSequenceColour(SequenceI seq);
242 void updateSequenceIdColours();
244 SequenceGroup getSelectionGroup();
247 * get the currently selected sequence objects or all the sequences in the
248 * alignment. TODO: change to List<>
250 * @return array of references to sequence objects
252 SequenceI[] getSequenceSelection();
254 void clearSequenceColours();
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);
446 * configure the feature renderer with predefined feature settings
448 * @param featureSettings
450 public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
453 * Apply the given feature settings on top of existing feature settings.
455 public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings);
458 * check if current selection group is defined on the view, or is simply a
461 * @return true if group is defined on the alignment
463 boolean isSelectionDefinedGroup();
467 * @return true if there are search results on the view
469 boolean hasSearchResults();
472 * set the search results for the view
475 * - or null to clear current results
477 void setSearchResults(SearchResultsI results);
480 * get search results for this view (if any)
482 * @return search results or null
484 SearchResultsI getSearchResults();
487 * Updates view settings with the given font. You may need to call
488 * AlignmentPanel.fontChanged to update the layout geometry.
491 * when true, charWidth/height is set according to font metrics
493 void setFont(Font newFont, boolean b);
496 * Answers true if split screen protein and cDNA use the same font
501 boolean isProteinFontAsCdna();
504 * Set the flag for whether split screen protein and cDNA use the same font
509 void setProteinFontAsCdna(boolean b);
511 void setHmmProfiles(ProfilesI info);
513 ProfilesI getHmmProfiles();
516 * Registers and starts a worker thread to calculate Information Content
517 * annotation, if it is not already registered
521 void initInformationWorker(AlignmentViewPanel ap);
523 boolean isInfoLetterHeight();
525 public abstract TreeModel getCurrentTree();
528 * Answers a data bean containing data for export as configured by the
534 AlignmentExportData getAlignExportData(AlignExportSettingsI options);
536 public abstract void setCurrentTree(TreeModel tree);
540 * - set the flag for updating structures on next repaint
542 void setUpdateStructures(boolean update);
546 * @return true if structure views will be updated on next refresh
548 boolean isUpdateStructures();
551 * check if structure views need to be updated, and clear the flag afterwards.
553 * @return if an update is needed
555 boolean needToUpdateStructureViews();
558 * Adds sequencegroup to the alignment in the view. Also adds a group to the
559 * complement view if one is defined.
561 * @param sequenceGroup
562 * - a group defined on sequences in the alignment held by the view
564 void addSequenceGroup(SequenceGroup sequenceGroup);
567 * Returns an interator over the [start, end] column positions of the visible
568 * regions of the alignment
570 * @param selectedRegionOnly
571 * if true, and the view has a selection region, then only the
572 * intersection of visible columns with the selection region is
576 Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);