-/**
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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.analysis.TreeModel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.RNAHelicesColour;
+import jalview.viewmodel.ViewportRanges;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
/**
* @author jimp
*
*/
-public interface AlignViewportI
+public interface AlignViewportI extends ViewStyleI
{
- int getCharWidth();
-
- int getEndRes();
-
- int getCharHeight();
+ /**
+ * Get the ranges object containing details of the start and end sequences and
+ * residues
+ *
+ * @return
+ */
+ public ViewportRanges getRanges();
/**
* calculate the height for visible annotation, revalidating bounds where
*/
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();
ColourSchemeI getGlobalColourScheme();
+ /**
+ * Returns an object that describes colouring (including any thresholding or
+ * fading) of the alignment
+ *
+ * @return
+ */
+ ResidueShaderI getResidueShading();
+
AlignmentI getAlignment();
ColumnSelection getColumnSelection();
- Hashtable[] getSequenceConsensusHash();
+ ProfilesI 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 getAlignmentConsensusAnnotation();
/**
+ * get the container for alignment gap annotation
+ *
+ * @return
+ */
+ AlignmentAnnotation getAlignmentGapAnnotation();
+
+ /**
+ * 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
boolean isClosed();
/**
+ * Dispose of all references or resources held by the viewport
+ */
+ void dispose();
+
+ /**
* get the associated calculation thread manager for the view
*
* @return
*
* @param hconsensus
*/
- void setSequenceConsensusHash(Hashtable[] hconsensus);
+ void setSequenceConsensusHash(ProfilesI hconsensus);
+
+ /**
+ * Set the cDNA complement consensus for the viewport
+ *
+ * @param hconsensus
+ */
+ void setComplementConsensusHash(Hashtable[] hconsensus);
/**
*
- * @return the alignment annotatino row for the structure consensus
+ * @return the alignment annotation row for the structure consensus
* calculation
*/
AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
/**
- * set global colourscheme
+ * Sets the colour scheme for the background alignment (as distinct from
+ * sub-groups, which may have their own colour schemes). A null value is used
+ * for no residue colour (white).
*
- * @param rhc
+ * @param cs
*/
- void setGlobalColourScheme(ColourSchemeI rhc);
+ void setGlobalColourScheme(ColourSchemeI cs);
Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
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();
+
+ /**
+ * 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);
+
+ /**
+ * @return an alignment view, optionally without a complement view
+ * @param selectedOnly
+ * @param markGroups
+ * @param withComplement - false if no complement view required
+ */
+ AlignmentView getAlignmentViewWithComplement(boolean selectedOnly,
+ boolean markGroups, boolean withComplement);
+
+ /**
+ * 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<AlignmentAnnotation> 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<int[]> 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);
+
+ /**
+ * configure the feature renderer with predefined feature settings
+ *
+ * @param featureSettings
+ */
+ public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
+
+ /**
+ * Apply the given feature settings on top of existing feature settings.
+ */
+ public void mergeFeaturesStyle(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();
+
+ /**
+ *
+ * @return true if there are search results on the view
+ */
+ boolean hasSearchResults();
+
+ /**
+ * set the search results for the view
+ *
+ * @param results
+ * - or null to clear current results
+ */
+ void setSearchResults(SearchResultsI results);
+
+ /**
+ * get search results for this view (if any)
+ *
+ * @return search results or null
+ */
+ SearchResultsI getSearchResults();
+
+ /**
+ * Updates view settings with the given font. You may need to call
+ * AlignmentPanel.fontChanged to update the layout geometry.
+ *
+ * @param setGrid
+ * when true, charWidth/height is set according to font metrics
+ */
+ void setFont(Font newFont, boolean b);
+
+ /**
+ * Answers true if split screen protein and cDNA use the same font
+ *
+ * @return
+ */
+ @Override
+ boolean isProteinFontAsCdna();
+
+ /**
+ * Set the flag for whether split screen protein and cDNA use the same font
+ *
+ * @return
+ */
+ @Override
+ void setProteinFontAsCdna(boolean b);
+
+ public abstract TreeModel getCurrentTree();
+
+ public abstract void setCurrentTree(TreeModel tree);
+
+ /**
+ * @param update
+ * - set the flag for updating structures on next repaint
+ */
+ void setUpdateStructures(boolean update);
+
+ /**
+ *
+ * @return true if structure views will be updated on next refresh
+ */
+ boolean isUpdateStructures();
+
+ /**
+ * check if structure views need to be updated, and clear the flag afterwards.
+ *
+ * @return if an update is needed
+ */
+ boolean needToUpdateStructureViews();
+
+ /**
+ * Adds sequencegroup to the alignment in the view. Also adds a group to the
+ * complement view if one is defined.
+ *
+ * @param sequenceGroup
+ * - a group defined on sequences in the alignment held by the view
+ */
+ void addSequenceGroup(SequenceGroup sequenceGroup);
+
+ /**
+ * Returns an interator over the [start, end] column positions of the visible
+ * regions of the alignment
+ *
+ * @param selectedRegionOnly
+ * if true, and the view has a selection region,
+ * then only the intersection of visible columns
+ * with the selection region is returned
+ * @return
+ */
+ Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
}
git://source.jalview.org / jalview.git / blobdiff