2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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.SequenceCollectionI;
30 import jalview.datamodel.SequenceGroup;
31 import jalview.datamodel.SequenceI;
32 import jalview.schemes.ColourSchemeI;
34 import java.awt.Color;
35 import java.util.Hashtable;
36 import java.util.List;
43 public interface AlignViewportI extends ViewStyleI
53 * calculate the height for visible annotation, revalidating bounds where
54 * necessary ABSTRACT GUI METHOD
56 * @return total height of annotation
58 public int calcPanelHeight();
60 boolean hasHiddenColumns();
62 boolean isValidCharWidth();
64 boolean isShowConsensusHistogram();
66 boolean isShowSequenceLogo();
68 boolean isNormaliseSequenceLogo();
70 ColourSchemeI getGlobalColourScheme();
72 AlignmentI getAlignment();
74 ColumnSelection getColumnSelection();
76 Hashtable[] getSequenceConsensusHash();
78 Hashtable[] getRnaStructureConsensusHash();
80 boolean isIgnoreGapsConsensus();
82 boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
84 AlignmentAnnotation getAlignmentQualityAnnot();
86 AlignmentAnnotation getAlignmentConservationAnnotation();
89 * get the container for alignment consensus annotation
93 AlignmentAnnotation getAlignmentConsensusAnnotation();
96 * Test to see if viewport is still open and active
98 * @return true indicates that all references to viewport should be dropped
103 * get the associated calculation thread manager for the view
107 AlignCalcManagerI getCalcManager();
110 * get the percentage gaps allowed in a conservation calculation
113 public int getConsPercGaps();
116 * set the consensus result object for the viewport
120 void setSequenceConsensusHash(Hashtable[] hconsensus);
124 * @return the alignment annotatino row for the structure consensus
127 AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
130 * set the Rna structure consensus result object for the viewport
132 * @param hStrucConsensus
134 void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
137 * set global colourscheme
141 void setGlobalColourScheme(ColourSchemeI rhc);
143 Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
145 void setHiddenRepSequences(
146 Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
149 * hides or shows dynamic annotation rows based on groups and group and
150 * alignment associated auto-annotation state flags apply the current
151 * group/autoannotation settings to the alignment view. Usually you should
152 * call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to
153 * ensure the annotation panel bounds are set correctly.
155 * @param applyGlobalSettings
156 * - apply to all autoannotation rows or just the ones associated
157 * with the current visible region
158 * @param preserveNewGroupSettings
159 * - don't apply global settings to groups which don't already have
160 * group associated annotation
162 void updateGroupAnnotationSettings(boolean applyGlobalSettings,
163 boolean preserveNewGroupSettings);
166 * @return true if a reference sequence is set and should be displayed
168 public boolean isDisplayReferenceSeq();
171 * @return set the flag for displaying reference sequences when they are
174 public void setDisplayReferenceSeq(boolean displayReferenceSeq);
177 * @return true if colourschemes should render according to reference sequence
178 * rather than consensus if available
180 public boolean isColourByReferenceSeq();
183 * @return true set flag for deciding if colourschemes should render according
184 * to reference sequence rather than consensus if available
186 public void setColourByReferenceSeq(boolean colourByReferenceSeq);
188 void setSequenceColour(SequenceI seq, Color col);
190 Color getSequenceColour(SequenceI seq);
192 void updateSequenceIdColours();
194 SequenceGroup getSelectionGroup();
197 * get the currently selected sequence objects or all the sequences in the
198 * alignment. TODO: change to List<>
200 * @return array of references to sequence objects
202 SequenceI[] getSequenceSelection();
204 void clearSequenceColours();
207 * This method returns the visible alignment as text, as seen on the GUI, ie
208 * if columns are hidden they will not be returned in the result. Use this for
209 * calculating trees, PCA, redundancy etc on views which contain hidden
214 CigarArray getViewAsCigars(boolean selectedRegionOnly);
217 * return a compact representation of the current alignment selection to pass
218 * to an analysis function
220 * @param selectedOnly
221 * boolean true to just return the selected view
222 * @return AlignmentView
224 AlignmentView getAlignmentView(boolean selectedOnly);
227 * return a compact representation of the current alignment selection to pass
228 * to an analysis function
230 * @param selectedOnly
231 * boolean true to just return the selected view
233 * boolean true to annotate the alignment view with groups on the
234 * alignment (and intersecting with selected region if selectedOnly
236 * @return AlignmentView
238 AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
241 * This method returns the visible alignment as text, as seen on the GUI, ie
242 * if columns are hidden they will not be returned in the result. Use this for
243 * calculating trees, PCA, redundancy etc on views which contain hidden
248 String[] getViewAsString(boolean selectedRegionOnly);
250 void setSelectionGroup(SequenceGroup sg);
252 char getGapCharacter();
254 void setColumnSelection(ColumnSelection cs);
256 void setConservation(Conservation cons);
259 * get a copy of the currently visible alignment annotation
260 * @param selectedOnly if true - trim to selected regions on the alignment
261 * @return an empty list or new alignment annotation objects shown only visible columns trimmed to selected region only
263 List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
264 boolean selectedOnly);
266 FeaturesDisplayedI getFeaturesDisplayed();
268 String getSequenceSetId();
270 boolean isShowSequenceFeatures();
272 void setShowSequenceFeatures(boolean b);
277 * indicating if annotation panel shown below alignment
280 void setShowAnnotation(boolean b);
283 * flag indicating if annotation panel shown below alignment
287 boolean isShowAnnotation();
289 boolean isRightAlignIds();
291 void setRightAlignIds(boolean rightAlignIds);
293 boolean areFeaturesDisplayed();
295 void setShowSequenceFeaturesHeight(boolean selected);
297 boolean isShowSequenceFeaturesHeight();
299 void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI);
301 void alignmentChanged(AlignmentViewPanel ap);
304 * @return the padGaps
312 void setPadGaps(boolean padGaps);
315 * return visible region boundaries within given column range
318 * first column (inclusive, from 0)
320 * last column (exclusive)
321 * @return int[][] range of {start,end} visible positions TODO: change to list
324 int[][] getVisibleRegionBoundaries(int min, int max);
327 * This method returns an array of new SequenceI objects derived from the
328 * whole alignment or just the current selection with start and end points
331 * @note if you need references to the actual SequenceI objects in the
332 * alignment or currently selected then use getSequenceSelection()
333 * @return selection as new sequenceI objects
335 SequenceI[] getSelectionAsNewSequence();
337 void invertColumnSelection();
340 * broadcast selection to any interested parties
342 void sendSelection();
345 * calculate the row position for alignmentIndex if all hidden sequences were
348 * @param alignmentIndex
349 * @return adjusted row position
351 int adjustForHiddenSeqs(int alignmentIndex);
353 boolean hasHiddenRows();
357 * @return a copy of this view's current display settings
359 public ViewStyleI getViewStyle();
362 * update the view's display settings with the given style set
364 * @param settingsForView
366 public void setViewStyle(ViewStyleI settingsForView);