X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=bd7d53dadae700248dcedacab65cc5192e1a801b;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=54a1d6fb1838b9d6239290cc17ea98fc6a39ffdc;hpb=e8ede151da126e8fe205392c64f1604d80adda6d;p=jalview.git diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java index 54a1d6f..bd7d53d 100644 --- a/src/jalview/api/AlignViewportI.java +++ b/src/jalview/api/AlignViewportI.java @@ -1,41 +1,70 @@ -/** +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.api; -import java.util.Hashtable; -import java.util.Map; - +import jalview.analysis.Conservation; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; -import jalview.datamodel.AnnotatedCollectionI; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.CigarArray; import jalview.datamodel.ColumnSelection; import jalview.datamodel.SequenceCollectionI; +import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.schemes.ColourSchemeI; -import jalview.schemes.RNAHelicesColour; + +import java.awt.Color; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; /** * @author jimp - * + * */ -public interface AlignViewportI +public interface AlignViewportI extends ViewStyleI { - int getCharWidth(); - int getEndRes(); - int getCharHeight(); - /** * calculate the height for visible annotation, revalidating bounds where * necessary ABSTRACT GUI METHOD - * + * * @return total height of annotation */ public int calcPanelHeight(); + /** + * Answers true if the viewport has at least one column selected + * + * @return + */ + boolean hasSelectedColumns(); + + /** + * Answers true if the viewport has at least one hidden column + * + * @return + */ boolean hasHiddenColumns(); boolean isValidCharWidth(); @@ -54,34 +83,56 @@ public interface AlignViewportI Hashtable[] getSequenceConsensusHash(); - Hashtable[] getRnaStructureConsensusHash(); + /** + * Get consensus data table for the cDNA complement of this alignment (if any) + * + * @return + */ + Hashtable[] getComplementConsensusHash(); - boolean getIgnoreGapsConsensus(); + Hashtable[] getRnaStructureConsensusHash(); - boolean getCentreColumnLabels(); + boolean isIgnoreGapsConsensus(); boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation); AlignmentAnnotation getAlignmentQualityAnnot(); AlignmentAnnotation getAlignmentConservationAnnotation(); + /** * get the container for alignment consensus annotation + * * @return */ AlignmentAnnotation getAlignmentConsensusAnnotation(); /** + * get the container for cDNA complement consensus annotation + * + * @return + */ + AlignmentAnnotation getComplementConsensusAnnotation(); + + /** * Test to see if viewport is still open and active - * @return true indicates that all references to viewport should be dropped + * + * @return true indicates that all references to viewport should be dropped */ boolean isClosed(); + + /** + * Dispose of all references or resources held by the viewport + */ + void dispose(); + /** * get the associated calculation thread manager for the view + * * @return */ AlignCalcManagerI getCalcManager(); - + /** * get the percentage gaps allowed in a conservation calculation * @@ -90,24 +141,35 @@ public interface AlignViewportI /** * set the consensus result object for the viewport + * * @param hconsensus */ void setSequenceConsensusHash(Hashtable[] hconsensus); /** + * Set the cDNA complement consensus for the viewport + * + * @param hconsensus + */ + void setComplementConsensusHash(Hashtable[] hconsensus); + + /** * - * @return the alignment annotatino row for the structure consensus calculation + * @return the alignment annotatino row for the structure consensus + * calculation */ AlignmentAnnotation getAlignmentStrucConsensusAnnotation(); /** * set the Rna structure consensus result object for the viewport - * @param hStrucConsensus + * + * @param hStrucConsensus */ void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus); /** * set global colourscheme + * * @param rhc */ void setGlobalColourScheme(ColourSchemeI rhc); @@ -117,4 +179,247 @@ public interface AlignViewportI void setHiddenRepSequences( Map hiddenRepSequences); + /** + * hides or shows dynamic annotation rows based on groups and group and + * alignment associated auto-annotation state flags apply the current + * group/autoannotation settings to the alignment view. Usually you should + * call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to + * ensure the annotation panel bounds are set correctly. + * + * @param applyGlobalSettings + * - apply to all autoannotation rows or just the ones associated + * with the current visible region + * @param preserveNewGroupSettings + * - don't apply global settings to groups which don't already have + * group associated annotation + */ + void updateGroupAnnotationSettings(boolean applyGlobalSettings, + boolean preserveNewGroupSettings); + + void setSequenceColour(SequenceI seq, Color col); + + Color getSequenceColour(SequenceI seq); + + void updateSequenceIdColours(); + + SequenceGroup getSelectionGroup(); + + /** + * get the currently selected sequence objects or all the sequences in the + * alignment. TODO: change to List<> + * + * @return array of references to sequence objects + */ + SequenceI[] getSequenceSelection(); + + void clearSequenceColours(); + + /** + * This method returns the visible alignment as text, as seen on the GUI, ie + * if columns are hidden they will not be returned in the result. Use this for + * calculating trees, PCA, redundancy etc on views which contain hidden + * columns. + * + * @return String[] + */ + CigarArray getViewAsCigars(boolean selectedRegionOnly); + + /** + * return a compact representation of the current alignment selection to pass + * to an analysis function + * + * @param selectedOnly + * boolean true to just return the selected view + * @return AlignmentView + */ + AlignmentView getAlignmentView(boolean selectedOnly); + + /** + * return a compact representation of the current alignment selection to pass + * to an analysis function + * + * @param selectedOnly + * boolean true to just return the selected view + * @param markGroups + * boolean true to annotate the alignment view with groups on the + * alignment (and intersecting with selected region if selectedOnly + * is true) + * @return AlignmentView + */ + AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups); + + /** + * This method returns the visible alignment as text, as seen on the GUI, ie + * if columns are hidden they will not be returned in the result. Use this for + * calculating trees, PCA, redundancy etc on views which contain hidden + * columns. This method doesn't exclude hidden sequences from the output. + * + * @param selectedRegionOnly + * - determines if only the selected region or entire alignment is + * exported + * @return String[] + */ + String[] getViewAsString(boolean selectedRegionOnly); + + /** + * This method returns the visible alignment as text, as seen on the GUI, ie + * if columns are hidden they will not be returned in the result. Use this for + * calculating trees, PCA, redundancy etc on views which contain hidden + * columns. + * + * @param selectedRegionOnly + * - determines if only the selected region or entire alignment is + * exported + * @param isExportHiddenSeqs + * - determines if hidden sequences would be exported or not. + * + * @return String[] + */ + String[] getViewAsString(boolean selectedRegionOnly, + boolean isExportHiddenSeqs); + + void setSelectionGroup(SequenceGroup sg); + + char getGapCharacter(); + + void setColumnSelection(ColumnSelection cs); + + void setConservation(Conservation cons); + + /** + * get a copy of the currently visible alignment annotation + * + * @param selectedOnly + * if true - trim to selected regions on the alignment + * @return an empty list or new alignment annotation objects shown only + * visible columns trimmed to selected region only + */ + List getVisibleAlignmentAnnotation( + boolean selectedOnly); + + FeaturesDisplayedI getFeaturesDisplayed(); + + String getSequenceSetId(); + + boolean areFeaturesDisplayed(); + + void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI); + + void alignmentChanged(AlignmentViewPanel ap); + + /** + * @return the padGaps + */ + boolean isPadGaps(); + + /** + * @param padGaps + * the padGaps to set + */ + void setPadGaps(boolean padGaps); + + /** + * return visible region boundaries within given column range + * + * @param min + * first column (inclusive, from 0) + * @param max + * last column (exclusive) + * @return int[][] range of {start,end} visible positions + */ + List getVisibleRegionBoundaries(int min, int max); + + /** + * This method returns an array of new SequenceI objects derived from the + * whole alignment or just the current selection with start and end points + * adjusted + * + * @note if you need references to the actual SequenceI objects in the + * alignment or currently selected then use getSequenceSelection() + * @return selection as new sequenceI objects + */ + SequenceI[] getSelectionAsNewSequence(); + + void invertColumnSelection(); + + /** + * broadcast selection to any interested parties + */ + void sendSelection(); + + /** + * calculate the row position for alignmentIndex if all hidden sequences were + * shown + * + * @param alignmentIndex + * @return adjusted row position + */ + int adjustForHiddenSeqs(int alignmentIndex); + + boolean hasHiddenRows(); + + /** + * + * @return a copy of this view's current display settings + */ + public ViewStyleI getViewStyle(); + + /** + * update the view's display settings with the given style set + * + * @param settingsForView + */ + public void setViewStyle(ViewStyleI settingsForView); + + /** + * Returns a viewport which holds the cDna for this (protein), or vice versa, + * or null if none is set. + * + * @return + */ + AlignViewportI getCodingComplement(); + + /** + * Sets the viewport which holds the cDna for this (protein), or vice versa. + * Implementation should guarantee that the reciprocal relationship is always + * set, i.e. each viewport is the complement of the other. + */ + void setCodingComplement(AlignViewportI sl); + + /** + * Answers true if viewport hosts DNA/RNA, else false. + * + * @return + */ + boolean isNucleotide(); + + /** + * Returns an id guaranteed to be unique for this viewport. + * + * @return + */ + String getViewId(); + + /** + * Return true if view should scroll to show the highlighted region of a + * sequence + * + * @return + */ + boolean isFollowHighlight(); + + /** + * Set whether view should scroll to show the highlighted region of a sequence + */ + void setFollowHighlight(boolean b); + + public void applyFeaturesStyle(FeatureSettingsModelI featureSettings); + + /** + * check if current selection group is defined on the view, or is simply a + * temporary group. + * + * @return true if group is defined on the alignment + */ + boolean isSelectionDefinedGroup(); }