/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
*
* 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.
+ * 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/>.
+ * 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.awt.Color;
-import java.util.Hashtable;
-import java.util.Map;
-
+import jalview.analysis.Conservation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
+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
*/
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();
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 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
boolean isClosed();
/**
+ * Dispose of all references or resources held by the viewport
+ */
+ void dispose();
+
+ /**
* get the associated calculation thread manager for the view
*
* @return
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
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<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);
+
+ 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();
}
git://source.jalview.org / jalview.git / blobdiff