X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=f92160e66d29b95717eb5f173e8a50242fcf6b2d;hb=f2b03e9fecf41886ebf5f747fd4be02edf042bee;hp=f6036de376dab361cb92bad5620e227658df2577;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java index f6036de..f92160e 100644 --- a/src/jalview/api/AlignViewportI.java +++ b/src/jalview/api/AlignViewportI.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,11 +20,6 @@ */ package jalview.api; -import java.awt.Color; -import java.util.Hashtable; -import java.util.List; -import java.util.Map; - import jalview.analysis.Conservation; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; @@ -36,19 +31,19 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.schemes.ColourSchemeI; +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 @@ -57,6 +52,18 @@ public interface AlignViewportI */ 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(); @@ -75,11 +82,16 @@ 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); @@ -95,6 +107,13 @@ public interface AlignViewportI 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 @@ -122,6 +141,13 @@ public interface AlignViewportI 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 @@ -164,25 +190,86 @@ public interface AlignViewportI void updateGroupAnnotationSettings(boolean applyGlobalSettings, boolean preserveNewGroupSettings); - void setSequenceColour(SequenceI seq, Color col); + void setSequenceColour(SequenceI seq, ColorI col); - Color getSequenceColour(SequenceI seq); + ColorI 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); @@ -194,10 +281,139 @@ public interface AlignViewportI /** * 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 + * + * @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(); }