package jalview.api;
import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactListI;
+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.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;
public interface AlignViewportI extends ViewStyleI
{
- int getEndRes();
+ /**
+ * 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();
/**
* Get consensus data table for the cDNA complement of this alignment (if any)
*
* @return
*/
- Hashtable[] getComplementConsensusHash();
+ Hashtable<String, Object>[] getComplementConsensusHash();
- Hashtable[] getRnaStructureConsensusHash();
+ Hashtable<String, Object>[] getRnaStructureConsensusHash();
boolean isIgnoreGapsConsensus();
AlignmentAnnotation getAlignmentConsensusAnnotation();
/**
+ * get the container for alignment gap annotation
+ *
+ * @return
+ */
+ AlignmentAnnotation getAlignmentGapAnnotation();
+
+ /**
* get the container for cDNA complement consensus annotation
*
* @return
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);
+ void setComplementConsensusHash(Hashtable<String, Object>[] hconsensus);
/**
*
- * @return the alignment annotatino row for the structure consensus
+ * @return the alignment annotation row for the structure consensus
* calculation
*/
AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
*
* @param hStrucConsensus
*/
- void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
+ void setRnaStructureConsensusHash(
+ Hashtable<String, Object>[] 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 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
*
* 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);
+ String[] getViewAsString(boolean selectedRegionOnly,
+ boolean isExportHiddenSeqs);
void setSelectionGroup(SequenceGroup sg);
* 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();
+
+ ContactListI getContactList(AlignmentAnnotation _aa, int column);
+
+ /**
+ * 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);
+
+ TreeModel getCurrentTree();
+
+ void setCurrentTree(TreeModel tree);
+
+ /**
+ * Answers a data bean containing data for export as configured by the
+ * supplied options
+ *
+ * @param options
+ * @return
+ */
+ AlignmentExportData getAlignExportData(AlignExportSettingsI options);
+
+ /**
+ * @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