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.AlignmentI;
27 import jalview.datamodel.AlignmentView;
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;
36 import jalview.viewmodel.ViewportRanges;
38 import java.awt.Color;
40 import java.util.Hashtable;
41 import java.util.Iterator;
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 * 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
252 * @return AlignmentView
254 AlignmentView getAlignmentView(boolean selectedOnly);
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
263 * boolean true to annotate the alignment view with groups on the
264 * alignment (and intersecting with selected region if selectedOnly
266 * @return AlignmentView
268 AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
271 * @return an alignment view, optionally without a complement view
272 * @param selectedOnly
274 * @param withComplement - false if no complement view required
276 AlignmentView getAlignmentViewWithComplement(boolean selectedOnly,
277 boolean markGroups, boolean withComplement);
280 * This method returns the visible alignment as text, as seen on the GUI, ie
281 * if columns are hidden they will not be returned in the result. Use this for
282 * calculating trees, PCA, redundancy etc on views which contain hidden
283 * columns. This method doesn't exclude hidden sequences from the output.
285 * @param selectedRegionOnly
286 * - determines if only the selected region or entire alignment is
290 String[] getViewAsString(boolean selectedRegionOnly);
293 * This method returns the visible alignment as text, as seen on the GUI, ie
294 * if columns are hidden they will not be returned in the result. Use this for
295 * calculating trees, PCA, redundancy etc on views which contain hidden
298 * @param selectedRegionOnly
299 * - determines if only the selected region or entire alignment is
301 * @param isExportHiddenSeqs
302 * - determines if hidden sequences would be exported or not.
306 String[] getViewAsString(boolean selectedRegionOnly,
307 boolean isExportHiddenSeqs);
309 void setSelectionGroup(SequenceGroup sg);
311 char getGapCharacter();
313 void setColumnSelection(ColumnSelection cs);
315 void setConservation(Conservation cons);
318 * get a copy of the currently visible alignment annotation
320 * @param selectedOnly
321 * if true - trim to selected regions on the alignment
322 * @return an empty list or new alignment annotation objects shown only
323 * visible columns trimmed to selected region only
325 List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
326 boolean selectedOnly);
328 FeaturesDisplayedI getFeaturesDisplayed();
330 String getSequenceSetId();
332 boolean areFeaturesDisplayed();
334 void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI);
336 void alignmentChanged(AlignmentViewPanel ap);
339 * @return the padGaps
347 void setPadGaps(boolean padGaps);
350 * return visible region boundaries within given column range
353 * first column (inclusive, from 0)
355 * last column (exclusive)
356 * @return int[][] range of {start,end} visible positions
358 List<int[]> getVisibleRegionBoundaries(int min, int max);
361 * This method returns an array of new SequenceI objects derived from the
362 * whole alignment or just the current selection with start and end points
365 * @note if you need references to the actual SequenceI objects in the
366 * alignment or currently selected then use getSequenceSelection()
367 * @return selection as new sequenceI objects
369 SequenceI[] getSelectionAsNewSequence();
371 void invertColumnSelection();
374 * broadcast selection to any interested parties
376 void sendSelection();
379 * calculate the row position for alignmentIndex if all hidden sequences were
382 * @param alignmentIndex
383 * @return adjusted row position
385 int adjustForHiddenSeqs(int alignmentIndex);
387 boolean hasHiddenRows();
391 * @return a copy of this view's current display settings
393 public ViewStyleI getViewStyle();
396 * update the view's display settings with the given style set
398 * @param settingsForView
400 public void setViewStyle(ViewStyleI settingsForView);
403 * Returns a viewport which holds the cDna for this (protein), or vice versa,
404 * or null if none is set.
408 AlignViewportI getCodingComplement();
411 * Sets the viewport which holds the cDna for this (protein), or vice versa.
412 * Implementation should guarantee that the reciprocal relationship is always
413 * set, i.e. each viewport is the complement of the other.
415 void setCodingComplement(AlignViewportI sl);
418 * Answers true if viewport hosts DNA/RNA, else false.
422 boolean isNucleotide();
425 * Returns an id guaranteed to be unique for this viewport.
432 * Return true if view should scroll to show the highlighted region of a
437 boolean isFollowHighlight();
440 * Set whether view should scroll to show the highlighted region of a sequence
442 void setFollowHighlight(boolean b);
445 * configure the feature renderer with predefined feature settings
447 * @param featureSettings
449 public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
452 * Apply the given feature settings on top of existing feature settings.
454 public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings);
457 * check if current selection group is defined on the view, or is simply a
460 * @return true if group is defined on the alignment
462 boolean isSelectionDefinedGroup();
466 * @return true if there are search results on the view
468 boolean hasSearchResults();
471 * set the search results for the view
474 * - or null to clear current results
476 void setSearchResults(SearchResultsI results);
479 * get search results for this view (if any)
481 * @return search results or null
483 SearchResultsI getSearchResults();
486 * Updates view settings with the given font. You may need to call
487 * AlignmentPanel.fontChanged to update the layout geometry.
490 * when true, charWidth/height is set according to font metrics
492 void setFont(Font newFont, boolean b);
495 * Answers true if split screen protein and cDNA use the same font
500 boolean isProteinFontAsCdna();
503 * Set the flag for whether split screen protein and cDNA use the same font
508 void setProteinFontAsCdna(boolean b);
510 public abstract TreeModel getCurrentTree();
512 public abstract void setCurrentTree(TreeModel tree);
516 * - set the flag for updating structures on next repaint
518 void setUpdateStructures(boolean update);
522 * @return true if structure views will be updated on next refresh
524 boolean isUpdateStructures();
527 * check if structure views need to be updated, and clear the flag afterwards.
529 * @return if an update is needed
531 boolean needToUpdateStructureViews();
534 * Adds sequencegroup to the alignment in the view. Also adds a group to the
535 * complement view if one is defined.
537 * @param sequenceGroup
538 * - a group defined on sequences in the alignment held by the view
540 void addSequenceGroup(SequenceGroup sequenceGroup);
543 * Returns an interator over the [start, end] column positions of the visible
544 * regions of the alignment
546 * @param selectedRegionOnly
547 * if true, and the view has a selection region,
548 * then only the intersection of visible columns
549 * with the selection region is returned
552 Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);