/*
- * 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.
*
*/
package jalview.viewmodel;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeaturesDisplayedI;
+import jalview.api.ViewStyleI;
+import jalview.commands.CommandI;
+import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Annotation;
+import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.SearchResults;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.PIDColourScheme;
-import jalview.schemes.ResidueProperties;
+import jalview.structure.CommandListener;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
+import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
+import jalview.workers.ComplementConsensusThread;
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
import java.awt.Color;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayDeque;
import java.util.ArrayList;
import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
-import java.util.Vector;
/**
* base class holding visualization and analysis attributes and common logic for
* @author jimp
*
*/
-public abstract class AlignmentViewport implements AlignViewportI
+public abstract class AlignmentViewport implements AlignViewportI,
+ CommandListener, VamsasSource
{
- /**
- * alignment displayed in the viewport. Please use get/setter
- */
- protected AlignmentI alignment;
-
- protected String sequenceSetID;
+ protected ViewStyleI viewStyle = new ViewStyle();
/**
- * probably unused indicator that view is of a dataset rather than an
- * alignment
+ * A viewport that hosts the cDna view of this (protein), or vice versa (if
+ * set).
*/
- protected boolean isDataset = false;
-
- private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
-
- protected ColumnSelection colSel = new ColumnSelection();
-
- public boolean autoCalculateConsensus = true;
+ AlignViewportI codingComplement = null;
- protected boolean autoCalculateStrucConsensus = true;
+ FeaturesDisplayedI featuresDisplayed = null;
- protected boolean ignoreGapsInConsensusCalculation = false;
+ protected Deque<CommandI> historyList = new ArrayDeque<CommandI>();
- protected ColourSchemeI globalColourScheme = null;
+ protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
/**
- * gui state - changes to colour scheme propagated to all groups
+ * @param name
+ * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
*/
- private boolean colourAppliesToAllGroups;
+ @Override
+ public void setFontName(String name)
+ {
+ viewStyle.setFontName(name);
+ }
/**
- * @param value
- * indicating if subsequent colourscheme changes will be propagated
- * to all groups
+ * @param style
+ * @see jalview.api.ViewStyleI#setFontStyle(int)
*/
- public void setColourAppliesToAllGroups(boolean b)
+ @Override
+ public void setFontStyle(int style)
{
- colourAppliesToAllGroups = b;
+ viewStyle.setFontStyle(style);
}
/**
- *
- *
- * @return flag indicating if colourchanges propagated to all groups
+ * @param size
+ * @see jalview.api.ViewStyleI#setFontSize(int)
*/
- public boolean getColourAppliesToAllGroups()
+ @Override
+ public void setFontSize(int size)
{
- return colourAppliesToAllGroups;
+ viewStyle.setFontSize(size);
}
- boolean abovePIDThreshold = false;
-
/**
- * GUI state
- *
- * @return true if percent identity threshold is applied to shading
+ * @return
+ * @see jalview.api.ViewStyleI#getFontStyle()
*/
- public boolean getAbovePIDThreshold()
+ @Override
+ public int getFontStyle()
{
- return abovePIDThreshold;
+ return viewStyle.getFontStyle();
}
/**
- * GUI state
- *
- *
- * @param b
- * indicate if percent identity threshold is applied to shading
+ * @return
+ * @see jalview.api.ViewStyleI#getFontName()
*/
- public void setAbovePIDThreshold(boolean b)
+ @Override
+ public String getFontName()
{
- abovePIDThreshold = b;
+ return viewStyle.getFontName();
}
- int threshold;
-
/**
- * DOCUMENT ME!
- *
- * @param thresh
- * DOCUMENT ME!
+ * @return
+ * @see jalview.api.ViewStyleI#getFontSize()
*/
- public void setThreshold(int thresh)
+ @Override
+ public int getFontSize()
{
- threshold = thresh;
+ return viewStyle.getFontSize();
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @param upperCasebold
+ * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
*/
- public int getThreshold()
+ @Override
+ public void setUpperCasebold(boolean upperCasebold)
{
- return threshold;
+ viewStyle.setUpperCasebold(upperCasebold);
}
- int increment;
-
/**
- *
- * @param inc
- * set the scalar for bleaching colourschemes according to degree of
- * conservation
+ * @return
+ * @see jalview.api.ViewStyleI#isUpperCasebold()
*/
- public void setIncrement(int inc)
+ @Override
+ public boolean isUpperCasebold()
{
- increment = inc;
+ return viewStyle.isUpperCasebold();
}
/**
- * GUI State
- *
- * @return get scalar for bleaching colourschemes by conservation
+ * @return
+ * @see jalview.api.ViewStyleI#isSeqNameItalics()
*/
- public int getIncrement()
+ @Override
+ public boolean isSeqNameItalics()
{
- return increment;
+ return viewStyle.isSeqNameItalics();
}
- boolean conservationColourSelected = false;
-
/**
- * GUI state
- *
- * @return true if conservation based shading is enabled
+ * @param colourByReferenceSeq
+ * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
*/
- public boolean getConservationSelected()
+ @Override
+ public void setColourByReferenceSeq(boolean colourByReferenceSeq)
{
- return conservationColourSelected;
+ viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
}
/**
- * GUI state
- *
* @param b
- * enable conservation based shading
+ * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
*/
- public void setConservationSelected(boolean b)
+ @Override
+ public void setColourAppliesToAllGroups(boolean b)
{
- conservationColourSelected = b;
+ viewStyle.setColourAppliesToAllGroups(b);
}
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
+ */
@Override
- public void setGlobalColourScheme(ColourSchemeI cs)
+ public boolean getColourAppliesToAllGroups()
{
- // TODO: logic refactored from AlignFrame changeColour -
- // autorecalc stuff should be changed to rely on the worker system
- // check to see if we should implement a changeColour(cs) method rather than
- // put th logic in here
- // - means that caller decides if they want to just modify state and defer
- // calculation till later or to do all calculations in thread.
- // via changecolour
- globalColourScheme = cs;
- boolean recalc = false;
- if (cs != null)
- {
- cs.setConservationApplied(recalc = getConservationSelected());
- if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
- {
- recalc = true;
- cs.setThreshold(threshold, ignoreGapsInConsensusCalculation);
- }
- else
- {
- cs.setThreshold(0, ignoreGapsInConsensusCalculation);
- }
- if (recalc)
- {
- cs.setConsensus(hconsensus);
- cs.setConservation(hconservation);
- }
- cs.alignmentChanged(alignment, hiddenRepSequences);
- }
- if (getColourAppliesToAllGroups())
- {
- for (SequenceGroup sg : getAlignment().getGroups())
- {
- if (cs == null)
- {
- sg.cs = null;
- continue;
- }
- sg.cs = cs.applyTo(sg, getHiddenRepSequences());
- sg.setConsPercGaps(ConsPercGaps);
- if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
- {
- sg.cs.setThreshold(threshold, getIgnoreGapsConsensus());
- recalc = true;
- }
- else
- {
- sg.cs.setThreshold(0, getIgnoreGapsConsensus());
- }
-
- if (getConservationSelected())
- {
- sg.cs.setConservationApplied(true);
- recalc = true;
- }
- else
- {
- sg.cs.setConservation(null);
- // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
- }
- if (recalc)
- {
- sg.recalcConservation();
- }
- else
- {
- sg.cs.alignmentChanged(sg, hiddenRepSequences);
- }
- }
- }
-
+ return viewStyle.getColourAppliesToAllGroups();
}
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
+ */
@Override
- public ColourSchemeI getGlobalColourScheme()
+ public boolean getAbovePIDThreshold()
{
- return globalColourScheme;
+ return viewStyle.getAbovePIDThreshold();
}
- protected AlignmentAnnotation consensus;
-
- protected AlignmentAnnotation strucConsensus;
-
- protected AlignmentAnnotation conservation;
-
- protected AlignmentAnnotation quality;
-
- protected AlignmentAnnotation[] groupConsensus;
-
- protected AlignmentAnnotation[] groupConservation;
-
/**
- * results of alignment consensus analysis for visible portion of view
+ * @param inc
+ * @see jalview.api.ViewStyleI#setIncrement(int)
*/
- protected Hashtable[] hconsensus = null;
+ @Override
+ public void setIncrement(int inc)
+ {
+ viewStyle.setIncrement(inc);
+ }
/**
- * results of secondary structure base pair consensus for visible portion of
- * view
+ * @return
+ * @see jalview.api.ViewStyleI#getIncrement()
*/
- protected Hashtable[] hStrucConsensus = null;
-
- protected Conservation hconservation = null;
-
@Override
- public void setConservation(Conservation cons)
+ public int getIncrement()
{
- hconservation = cons;
+ return viewStyle.getIncrement();
}
/**
- * percentage gaps allowed in a column before all amino acid properties should
- * be considered unconserved
+ * @param b
+ * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
*/
- int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
@Override
- public int getConsPercGaps()
+ public void setConservationSelected(boolean b)
{
- return ConsPercGaps;
+ viewStyle.setConservationSelected(b);
}
+ /**
+ * @param show
+ * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
+ */
@Override
- public void setSequenceConsensusHash(Hashtable[] hconsensus)
+ public void setShowHiddenMarkers(boolean show)
{
- this.hconsensus = hconsensus;
-
+ viewStyle.setShowHiddenMarkers(show);
}
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
+ */
@Override
- public Hashtable[] getSequenceConsensusHash()
+ public boolean getShowHiddenMarkers()
{
- return hconsensus;
+ return viewStyle.getShowHiddenMarkers();
}
+ /**
+ * @param b
+ * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
+ */
@Override
- public Hashtable[] getRnaStructureConsensusHash()
+ public void setScaleRightWrapped(boolean b)
{
- return hStrucConsensus;
+ viewStyle.setScaleRightWrapped(b);
}
+ /**
+ * @param b
+ * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
+ */
@Override
- public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
+ public void setScaleLeftWrapped(boolean b)
{
- this.hStrucConsensus = hStrucConsensus;
-
+ viewStyle.setScaleLeftWrapped(b);
}
+ /**
+ * @param b
+ * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
+ */
@Override
- public AlignmentAnnotation getAlignmentQualityAnnot()
+ public void setScaleAboveWrapped(boolean b)
{
- return quality;
+ viewStyle.setScaleAboveWrapped(b);
}
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
+ */
@Override
- public AlignmentAnnotation getAlignmentConservationAnnotation()
+ public boolean getScaleLeftWrapped()
{
- return conservation;
+ return viewStyle.getScaleLeftWrapped();
}
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
+ */
@Override
- public AlignmentAnnotation getAlignmentConsensusAnnotation()
+ public boolean getScaleAboveWrapped()
{
- return consensus;
+ return viewStyle.getScaleAboveWrapped();
}
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getScaleRightWrapped()
+ */
@Override
- public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
+ public boolean getScaleRightWrapped()
{
- return strucConsensus;
+ return viewStyle.getScaleRightWrapped();
}
- protected AlignCalcManagerI calculator = new AlignCalcManager();
+ /**
+ * @param b
+ * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
+ */
+ @Override
+ public void setAbovePIDThreshold(boolean b)
+ {
+ viewStyle.setAbovePIDThreshold(b);
+ }
/**
- * trigger update of conservation annotation
+ * @param thresh
+ * @see jalview.api.ViewStyleI#setThreshold(int)
*/
- public void updateConservation(final AlignmentViewPanel ap)
+ @Override
+ public void setThreshold(int thresh)
{
- // see note in mantis : issue number 8585
- if (alignment.isNucleotide() || conservation == null
- || !autoCalculateConsensus)
- {
- return;
- }
- if (calculator
- .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
- {
- calculator.registerWorker(new jalview.workers.ConservationThread(
- this, ap));
- }
+ viewStyle.setThreshold(thresh);
}
/**
- * trigger update of consensus annotation
+ * @return
+ * @see jalview.api.ViewStyleI#getThreshold()
*/
- public void updateConsensus(final AlignmentViewPanel ap)
+ @Override
+ public int getThreshold()
{
- // see note in mantis : issue number 8585
- if (consensus == null || !autoCalculateConsensus)
- {
- return;
- }
- if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
- {
- calculator.registerWorker(new ConsensusThread(this, ap));
- }
- }
-
- // --------START Structure Conservation
- public void updateStrucConsensus(final AlignmentViewPanel ap)
- {
- if (autoCalculateStrucConsensus && strucConsensus == null
- && alignment.isNucleotide() && alignment.hasRNAStructure())
- {
- // secondary structure has been added - so init the consensus line
- initRNAStructure();
- }
-
- // see note in mantis : issue number 8585
- if (strucConsensus == null || !autoCalculateStrucConsensus)
- {
- return;
- }
- if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
- {
- calculator.registerWorker(new StrucConsensusThread(this, ap));
- }
- }
-
- public boolean isCalcInProgress()
- {
- return calculator.isWorking();
+ return viewStyle.getThreshold();
}
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getShowJVSuffix()
+ */
@Override
- public boolean isCalculationInProgress(
- AlignmentAnnotation alignmentAnnotation)
+ public boolean getShowJVSuffix()
{
- if (!alignmentAnnotation.autoCalculated)
- {
- return false;
- }
- if (calculator.workingInvolvedWith(alignmentAnnotation))
- {
- // System.err.println("grey out ("+alignmentAnnotation.label+")");
- return true;
- }
- return false;
+ return viewStyle.getShowJVSuffix();
}
+ /**
+ * @param b
+ * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
+ */
@Override
- public boolean isClosed()
+ public void setShowJVSuffix(boolean b)
{
- // TODO: check that this isClosed is only true after panel is closed, not
- // before it is fully constructed.
- return alignment == null;
+ viewStyle.setShowJVSuffix(b);
}
+ /**
+ * @param state
+ * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
+ */
@Override
- public AlignCalcManagerI getCalcManager()
+ public void setWrapAlignment(boolean state)
{
- return calculator;
+ viewStyle.setWrapAlignment(state);
}
/**
- * should conservation rows be shown for groups
- */
- protected boolean showGroupConservation = false;
-
- /**
- * should consensus rows be shown for groups
- */
- protected boolean showGroupConsensus = false;
-
- /**
- * should consensus profile be rendered by default
- */
- protected boolean showSequenceLogo = false;
-
- /**
- * should consensus profile be rendered normalised to row height
- */
- protected boolean normaliseSequenceLogo = false;
-
- /**
- * should consensus histograms be rendered by default
- */
- protected boolean showConsensusHistogram = true;
-
- /**
- * @return the showConsensusProfile
+ * @param state
+ * @see jalview.api.ViewStyleI#setShowText(boolean)
*/
@Override
- public boolean isShowSequenceLogo()
+ public void setShowText(boolean state)
{
- return showSequenceLogo;
+ viewStyle.setShowText(state);
}
/**
- * @param showSequenceLogo
- * the new value
+ * @param state
+ * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
*/
- public void setShowSequenceLogo(boolean showSequenceLogo)
+ @Override
+ public void setRenderGaps(boolean state)
{
- if (showSequenceLogo != this.showSequenceLogo)
- {
- // TODO: decouple settings setting from calculation when refactoring
- // annotation update method from alignframe to viewport
- this.showSequenceLogo = showSequenceLogo;
- calculator.updateAnnotationFor(ConsensusThread.class);
- calculator.updateAnnotationFor(StrucConsensusThread.class);
- }
- this.showSequenceLogo = showSequenceLogo;
+ viewStyle.setRenderGaps(state);
}
/**
- * @param showConsensusHistogram
- * the showConsensusHistogram to set
+ * @return
+ * @see jalview.api.ViewStyleI#getColourText()
*/
- public void setShowConsensusHistogram(boolean showConsensusHistogram)
+ @Override
+ public boolean getColourText()
{
- this.showConsensusHistogram = showConsensusHistogram;
+ return viewStyle.getColourText();
}
/**
- * @return the showGroupConservation
+ * @param state
+ * @see jalview.api.ViewStyleI#setColourText(boolean)
*/
- public boolean isShowGroupConservation()
+ @Override
+ public void setColourText(boolean state)
{
- return showGroupConservation;
+ viewStyle.setColourText(state);
}
/**
- * @param showGroupConservation
- * the showGroupConservation to set
+ * @return
+ * @see jalview.api.ViewStyleI#getWrapAlignment()
*/
- public void setShowGroupConservation(boolean showGroupConservation)
+ @Override
+ public boolean getWrapAlignment()
{
- this.showGroupConservation = showGroupConservation;
+ return viewStyle.getWrapAlignment();
}
/**
- * @return the showGroupConsensus
+ * @return
+ * @see jalview.api.ViewStyleI#getShowText()
*/
- public boolean isShowGroupConsensus()
+ @Override
+ public boolean getShowText()
{
- return showGroupConsensus;
+ return viewStyle.getShowText();
}
/**
- * @param showGroupConsensus
- * the showGroupConsensus to set
+ * @return
+ * @see jalview.api.ViewStyleI#getWrappedWidth()
*/
- public void setShowGroupConsensus(boolean showGroupConsensus)
+ @Override
+ public int getWrappedWidth()
{
- this.showGroupConsensus = showGroupConsensus;
+ return viewStyle.getWrappedWidth();
}
/**
- *
- * @return flag to indicate if the consensus histogram should be rendered by
- * default
+ * @param w
+ * @see jalview.api.ViewStyleI#setWrappedWidth(int)
*/
@Override
- public boolean isShowConsensusHistogram()
+ public void setWrappedWidth(int w)
{
- return this.showConsensusHistogram;
+ viewStyle.setWrappedWidth(w);
}
/**
- * show non-conserved residues only
- */
- protected boolean showUnconserved = false;
-
- /**
- * when set, updateAlignment will always ensure sequences are of equal length
- */
- private boolean padGaps = false;
-
- /**
- * when set, alignment should be reordered according to a newly opened tree
+ * @return
+ * @see jalview.api.ViewStyleI#getCharHeight()
*/
- public boolean sortByTree = false;
-
- public boolean getShowUnconserved()
- {
- return showUnconserved;
- }
-
- public void setShowUnconserved(boolean showunconserved)
+ @Override
+ public int getCharHeight()
{
- showUnconserved = showunconserved;
+ return viewStyle.getCharHeight();
}
/**
- * @param showNonconserved
- * the showUnconserved to set
+ * @param h
+ * @see jalview.api.ViewStyleI#setCharHeight(int)
*/
- public void setShowunconserved(boolean displayNonconserved)
+ @Override
+ public void setCharHeight(int h)
{
- this.showUnconserved = displayNonconserved;
+ viewStyle.setCharHeight(h);
}
/**
- *
- *
- * @return null or the currently selected sequence region
+ * @return
+ * @see jalview.api.ViewStyleI#getCharWidth()
*/
@Override
- public SequenceGroup getSelectionGroup()
+ public int getCharWidth()
{
- return selectionGroup;
+ return viewStyle.getCharWidth();
}
/**
- * Set the selection group for this window.
- *
- * @param sg
- * - group holding references to sequences in this alignment view
- *
+ * @param w
+ * @see jalview.api.ViewStyleI#setCharWidth(int)
*/
@Override
- public void setSelectionGroup(SequenceGroup sg)
+ public void setCharWidth(int w)
{
- selectionGroup = sg;
+ viewStyle.setCharWidth(w);
}
- public void setHiddenColumns(ColumnSelection colsel)
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getShowBoxes()
+ */
+ @Override
+ public boolean getShowBoxes()
{
- this.colSel = colsel;
+ return viewStyle.getShowBoxes();
}
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getShowUnconserved()
+ */
@Override
- public ColumnSelection getColumnSelection()
+ public boolean getShowUnconserved()
{
- return colSel;
+ return viewStyle.getShowUnconserved();
}
+ /**
+ * @param showunconserved
+ * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
+ */
@Override
- public void setColumnSelection(ColumnSelection colSel)
+ public void setShowUnconserved(boolean showunconserved)
{
- this.colSel = colSel;
- if (colSel != null)
- {
- updateHiddenColumns();
- }
+ viewStyle.setShowUnconserved(showunconserved);
}
/**
- *
- * @return
+ * @param default1
+ * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
*/
@Override
- public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
+ public void setSeqNameItalics(boolean default1)
{
- return hiddenRepSequences;
+ viewStyle.setSeqNameItalics(default1);
}
+ /**
+ * alignment displayed in the viewport. Please use get/setter
+ */
+ protected AlignmentI alignment;
+
@Override
- public void setHiddenRepSequences(
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public AlignmentI getAlignment()
{
- this.hiddenRepSequences = hiddenRepSequences;
+ return alignment;
}
@Override
- public boolean hasHiddenColumns()
+ public char getGapCharacter()
{
- return colSel != null && colSel.hasHiddenColumns();
+ return alignment.getGapCharacter();
}
- public void updateHiddenColumns()
- {
- // this method doesn't really do anything now. But - it could, since a
- // column Selection could be in the process of modification
- // hasHiddenColumns = colSel.hasHiddenColumns();
- }
+ protected String sequenceSetID;
- protected boolean hasHiddenRows = false;
+ /**
+ * probably unused indicator that view is of a dataset rather than an
+ * alignment
+ */
+ protected boolean isDataset = false;
- @Override
- public boolean hasHiddenRows()
+ public void setDataset(boolean b)
{
- return hasHiddenRows;
+ isDataset = b;
}
- protected SequenceGroup selectionGroup;
-
- public void setSequenceSetId(String newid)
+ public boolean isDataset()
{
- if (sequenceSetID != null)
- {
- System.err
- .println("Warning - overwriting a sequenceSetId for a viewport!");
- }
- sequenceSetID = new String(newid);
+ return isDataset;
}
- @Override
- public String getSequenceSetId()
- {
- if (sequenceSetID == null)
- {
- sequenceSetID = alignment.hashCode() + "";
- }
+ private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
- return sequenceSetID;
- }
+ protected ColumnSelection colSel = new ColumnSelection();
- /**
- * unique viewId for synchronizing state (e.g. with stored Jalview Project)
- *
- */
- protected String viewId = null;
+ public boolean autoCalculateConsensus = true;
- public String getViewId()
- {
- if (viewId == null)
- {
- viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
- }
- return viewId;
- }
+ protected boolean autoCalculateStrucConsensus = true;
- public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
+ protected boolean ignoreGapsInConsensusCalculation = false;
+
+ protected ColourSchemeI globalColourScheme = null;
+
+ @Override
+ public void setGlobalColourScheme(ColourSchemeI cs)
+ {
+ // TODO: logic refactored from AlignFrame changeColour -
+ // TODO: autorecalc stuff should be changed to rely on the worker system
+ // check to see if we should implement a changeColour(cs) method rather than
+ // put th logic in here
+ // - means that caller decides if they want to just modify state and defer
+ // calculation till later or to do all calculations in thread.
+ // via changecolour
+ globalColourScheme = cs;
+ boolean recalc = false;
+ if (cs != null)
+ {
+ recalc = getConservationSelected();
+ if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
+ {
+ recalc = true;
+ cs.setThreshold(viewStyle.getThreshold(),
+ ignoreGapsInConsensusCalculation);
+ }
+ else
+ {
+ cs.setThreshold(0, ignoreGapsInConsensusCalculation);
+ }
+ if (recalc)
+ {
+ cs.setConsensus(hconsensus);
+ cs.setConservation(hconservation);
+ }
+ cs.setConservationApplied(getConservationSelected());
+ cs.alignmentChanged(alignment, hiddenRepSequences);
+ }
+ if (getColourAppliesToAllGroups())
+ {
+ for (SequenceGroup sg : getAlignment().getGroups())
+ {
+ if (cs == null)
+ {
+ sg.cs = null;
+ continue;
+ }
+ sg.cs = cs.applyTo(sg, getHiddenRepSequences());
+ sg.setConsPercGaps(ConsPercGaps);
+ if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
+ {
+ sg.cs.setThreshold(viewStyle.getThreshold(),
+ isIgnoreGapsConsensus());
+ recalc = true;
+ }
+ else
+ {
+ sg.cs.setThreshold(0, isIgnoreGapsConsensus());
+ }
+
+ if (getConservationSelected())
+ {
+ sg.cs.setConservationApplied(true);
+ recalc = true;
+ }
+ else
+ {
+ sg.cs.setConservation(null);
+ // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+ }
+ if (recalc)
+ {
+ sg.recalcConservation();
+ }
+ else
+ {
+ sg.cs.alignmentChanged(sg, hiddenRepSequences);
+ }
+ }
+ }
+ }
+
+ @Override
+ public ColourSchemeI getGlobalColourScheme()
+ {
+ return globalColourScheme;
+ }
+
+ protected AlignmentAnnotation consensus;
+
+ protected AlignmentAnnotation complementConsensus;
+
+ protected AlignmentAnnotation strucConsensus;
+
+ protected AlignmentAnnotation conservation;
+
+ protected AlignmentAnnotation quality;
+
+ protected AlignmentAnnotation[] groupConsensus;
+
+ protected AlignmentAnnotation[] groupConservation;
+
+ /**
+ * results of alignment consensus analysis for visible portion of view
+ */
+ protected Hashtable[] hconsensus = null;
+
+ /**
+ * results of cDNA complement consensus visible portion of view
+ */
+ protected Hashtable[] hcomplementConsensus = null;
+
+ /**
+ * results of secondary structure base pair consensus for visible portion of
+ * view
+ */
+ protected Hashtable[] hStrucConsensus = null;
+
+ protected Conservation hconservation = null;
+
+ @Override
+ public void setConservation(Conservation cons)
+ {
+ hconservation = cons;
+ }
+
+ /**
+ * percentage gaps allowed in a column before all amino acid properties should
+ * be considered unconserved
+ */
+ int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+
+ @Override
+ public int getConsPercGaps()
+ {
+ return ConsPercGaps;
+ }
+
+ @Override
+ public void setSequenceConsensusHash(Hashtable[] hconsensus)
+ {
+ this.hconsensus = hconsensus;
+ }
+
+ @Override
+ public void setComplementConsensusHash(Hashtable[] hconsensus)
+ {
+ this.hcomplementConsensus = hconsensus;
+ }
+
+ @Override
+ public Hashtable[] getSequenceConsensusHash()
+ {
+ return hconsensus;
+ }
+
+ @Override
+ public Hashtable[] getComplementConsensusHash()
+ {
+ return hcomplementConsensus;
+ }
+
+ @Override
+ public Hashtable[] getRnaStructureConsensusHash()
+ {
+ return hStrucConsensus;
+ }
+
+ @Override
+ public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
+ {
+ this.hStrucConsensus = hStrucConsensus;
+
+ }
+
+ @Override
+ public AlignmentAnnotation getAlignmentQualityAnnot()
+ {
+ return quality;
+ }
+
+ @Override
+ public AlignmentAnnotation getAlignmentConservationAnnotation()
+ {
+ return conservation;
+ }
+
+ @Override
+ public AlignmentAnnotation getAlignmentConsensusAnnotation()
+ {
+ return consensus;
+ }
+
+ @Override
+ public AlignmentAnnotation getComplementConsensusAnnotation()
+ {
+ return complementConsensus;
+ }
+
+ @Override
+ public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
+ {
+ return strucConsensus;
+ }
+
+ protected AlignCalcManagerI calculator = new AlignCalcManager();
+
+ /**
+ * trigger update of conservation annotation
+ */
+ public void updateConservation(final AlignmentViewPanel ap)
+ {
+ // see note in mantis : issue number 8585
+ if (alignment.isNucleotide()
+ || (conservation == null && quality == null)
+ || !autoCalculateConsensus)
+ {
+ return;
+ }
+ if (calculator
+ .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
+ {
+ calculator.registerWorker(new jalview.workers.ConservationThread(
+ this, ap));
+ }
+ }
+
+ /**
+ * trigger update of consensus annotation
+ */
+ public void updateConsensus(final AlignmentViewPanel ap)
+ {
+ // see note in mantis : issue number 8585
+ if (consensus == null || !autoCalculateConsensus)
+ {
+ return;
+ }
+ if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
+ {
+ calculator.registerWorker(new ConsensusThread(this, ap));
+ }
+
+ /*
+ * A separate thread to compute cDNA consensus for a protein alignment
+ * which has mapping to cDNA
+ */
+ final AlignmentI al = this.getAlignment();
+ if (!al.isNucleotide() && al.getCodonFrames() != null
+ && !al.getCodonFrames().isEmpty())
+ {
+ /*
+ * fudge - check first for protein-to-nucleotide mappings
+ * (we don't want to do this for protein-to-protein)
+ */
+ boolean doConsensus = false;
+ for (AlignedCodonFrame mapping : al.getCodonFrames())
+ {
+ // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
+ MapList[] mapLists = mapping.getdnaToProt();
+ // mapLists can be empty if project load has not finished resolving seqs
+ if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+ {
+ doConsensus = true;
+ break;
+ }
+ }
+ if (doConsensus)
+ {
+ if (calculator
+ .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+ {
+ calculator
+ .registerWorker(new ComplementConsensusThread(this, ap));
+ }
+ }
+ }
+ }
+
+ // --------START Structure Conservation
+ public void updateStrucConsensus(final AlignmentViewPanel ap)
+ {
+ if (autoCalculateStrucConsensus && strucConsensus == null
+ && alignment.isNucleotide() && alignment.hasRNAStructure())
+ {
+ // secondary structure has been added - so init the consensus line
+ initRNAStructure();
+ }
+
+ // see note in mantis : issue number 8585
+ if (strucConsensus == null || !autoCalculateStrucConsensus)
+ {
+ return;
+ }
+ if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
+ {
+ calculator.registerWorker(new StrucConsensusThread(this, ap));
+ }
+ }
+
+ public boolean isCalcInProgress()
+ {
+ return calculator.isWorking();
+ }
+
+ @Override
+ public boolean isCalculationInProgress(
+ AlignmentAnnotation alignmentAnnotation)
+ {
+ if (!alignmentAnnotation.autoCalculated)
+ {
+ return false;
+ }
+ if (calculator.workingInvolvedWith(alignmentAnnotation))
+ {
+ // System.err.println("grey out ("+alignmentAnnotation.label+")");
+ return true;
+ }
+ return false;
+ }
+
+ public void setAlignment(AlignmentI align)
+ {
+ this.alignment = align;
+ }
+
+ /**
+ * Clean up references when this viewport is closed
+ */
+ @Override
+ public void dispose()
+ {
+ /*
+ * defensively null out references to large objects in case
+ * this object is not garbage collected (as if!)
+ */
+ consensus = null;
+ complementConsensus = null;
+ strucConsensus = null;
+ conservation = null;
+ quality = null;
+ groupConsensus = null;
+ groupConservation = null;
+ hconsensus = null;
+ hcomplementConsensus = null;
+ // TODO removed listeners from changeSupport?
+ changeSupport = null;
+ setAlignment(null);
+ }
+
+ @Override
+ public boolean isClosed()
+ {
+ // TODO: check that this isClosed is only true after panel is closed, not
+ // before it is fully constructed.
+ return alignment == null;
+ }
+
+ @Override
+ public AlignCalcManagerI getCalcManager()
+ {
+ return calculator;
+ }
+
+ /**
+ * should conservation rows be shown for groups
+ */
+ protected boolean showGroupConservation = false;
+
+ /**
+ * should consensus rows be shown for groups
+ */
+ protected boolean showGroupConsensus = false;
+
+ /**
+ * should consensus profile be rendered by default
+ */
+ protected boolean showSequenceLogo = false;
+
+ /**
+ * should consensus profile be rendered normalised to row height
+ */
+ protected boolean normaliseSequenceLogo = false;
+
+ /**
+ * should consensus histograms be rendered by default
+ */
+ protected boolean showConsensusHistogram = true;
+
+ /**
+ * @return the showConsensusProfile
+ */
+ @Override
+ public boolean isShowSequenceLogo()
+ {
+ return showSequenceLogo;
+ }
+
+ /**
+ * @param showSequenceLogo
+ * the new value
+ */
+ public void setShowSequenceLogo(boolean showSequenceLogo)
+ {
+ if (showSequenceLogo != this.showSequenceLogo)
+ {
+ // TODO: decouple settings setting from calculation when refactoring
+ // annotation update method from alignframe to viewport
+ this.showSequenceLogo = showSequenceLogo;
+ calculator.updateAnnotationFor(ConsensusThread.class);
+ calculator.updateAnnotationFor(ComplementConsensusThread.class);
+ calculator.updateAnnotationFor(StrucConsensusThread.class);
+ }
+ this.showSequenceLogo = showSequenceLogo;
+ }
+
+ /**
+ * @param showConsensusHistogram
+ * the showConsensusHistogram to set
+ */
+ public void setShowConsensusHistogram(boolean showConsensusHistogram)
+ {
+ this.showConsensusHistogram = showConsensusHistogram;
+ }
+
+ /**
+ * @return the showGroupConservation
+ */
+ public boolean isShowGroupConservation()
+ {
+ return showGroupConservation;
+ }
+
+ /**
+ * @param showGroupConservation
+ * the showGroupConservation to set
+ */
+ public void setShowGroupConservation(boolean showGroupConservation)
+ {
+ this.showGroupConservation = showGroupConservation;
+ }
+
+ /**
+ * @return the showGroupConsensus
+ */
+ public boolean isShowGroupConsensus()
+ {
+ return showGroupConsensus;
+ }
+
+ /**
+ * @param showGroupConsensus
+ * the showGroupConsensus to set
+ */
+ public void setShowGroupConsensus(boolean showGroupConsensus)
+ {
+ this.showGroupConsensus = showGroupConsensus;
+ }
+
+ /**
+ *
+ * @return flag to indicate if the consensus histogram should be rendered by
+ * default
+ */
+ @Override
+ public boolean isShowConsensusHistogram()
+ {
+ return this.showConsensusHistogram;
+ }
+
+ /**
+ * when set, updateAlignment will always ensure sequences are of equal length
+ */
+ private boolean padGaps = false;
+
+ /**
+ * when set, alignment should be reordered according to a newly opened tree
+ */
+ public boolean sortByTree = false;
+
+ /**
+ *
+ *
+ * @return null or the currently selected sequence region
+ */
+ @Override
+ public SequenceGroup getSelectionGroup()
+ {
+ return selectionGroup;
+ }
+
+ /**
+ * Set the selection group for this window.
+ *
+ * @param sg
+ * - group holding references to sequences in this alignment view
+ *
+ */
+ @Override
+ public void setSelectionGroup(SequenceGroup sg)
+ {
+ selectionGroup = sg;
+ }
+
+ public void setHiddenColumns(ColumnSelection colsel)
+ {
+ this.colSel = colsel;
+ }
+
+ @Override
+ public ColumnSelection getColumnSelection()
+ {
+ return colSel;
+ }
+
+ @Override
+ public void setColumnSelection(ColumnSelection colSel)
+ {
+ this.colSel = colSel;
+ if (colSel != null)
+ {
+ updateHiddenColumns();
+ }
+ isColSelChanged(true);
+ }
+
+ /**
+ *
+ * @return
+ */
+ @Override
+ public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
+ {
+ return hiddenRepSequences;
+ }
+
+ @Override
+ public void setHiddenRepSequences(
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ this.hiddenRepSequences = hiddenRepSequences;
+ }
+
+ @Override
+ public boolean hasSelectedColumns()
+ {
+ ColumnSelection columnSelection = getColumnSelection();
+ return columnSelection != null && columnSelection.hasSelectedColumns();
+ }
+
+ @Override
+ public boolean hasHiddenColumns()
+ {
+ return colSel != null && colSel.hasHiddenColumns();
+ }
+
+ public void updateHiddenColumns()
+ {
+ // this method doesn't really do anything now. But - it could, since a
+ // column Selection could be in the process of modification
+ // hasHiddenColumns = colSel.hasHiddenColumns();
+ }
+
+ @Override
+ public boolean hasHiddenRows()
+ {
+ return alignment.getHiddenSequences().getSize() > 0;
+ }
+
+ protected SequenceGroup selectionGroup;
+
+ public void setSequenceSetId(String newid)
+ {
+ if (sequenceSetID != null)
+ {
+ System.err
+ .println("Warning - overwriting a sequenceSetId for a viewport!");
+ }
+ sequenceSetID = new String(newid);
+ }
+
+ @Override
+ public String getSequenceSetId()
+ {
+ if (sequenceSetID == null)
+ {
+ sequenceSetID = alignment.hashCode() + "";
+ }
+
+ return sequenceSetID;
+ }
+
+ /**
+ * unique viewId for synchronizing state (e.g. with stored Jalview Project)
+ *
+ */
+ protected String viewId = null;
+
+ @Override
+ public String getViewId()
+ {
+ if (viewId == null)
+ {
+ viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
+ }
+ return viewId;
+ }
+
+ public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
{
ignoreGapsInConsensusCalculation = b;
if (ap != null)
*/
public boolean isColSelChanged(boolean b)
{
- int hc = (colSel == null || colSel.size() == 0) ? -1 : colSel
- .hashCode();
+ int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
if (hc != -1 && hc != colselhash)
{
if (b)
}
@Override
- public boolean getIgnoreGapsConsensus()
+ public boolean isIgnoreGapsConsensus()
{
return ignoreGapsInConsensusCalculation;
}
- // / property change stuff
-
+ // property change stuff
// JBPNote Prolly only need this in the applet version.
- private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+ private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
this);
protected boolean showConservation = true;
protected boolean showConsensus = true;
- Hashtable sequenceColours;
+ private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
+
+ protected SequenceAnnotationOrder sortAnnotationsBy = null;
+
+ protected boolean showAutocalculatedAbove;
+
+ /**
+ * when set, view will scroll to show the highlighted position
+ */
+ private boolean followHighlight = true;
+
+ // TODO private with getters and setters?
+ public int startRes;
+
+ public int endRes;
+
+ public int startSeq;
+
+ public int endSeq;
/**
* Property change listener for changes in alignment
public void hideSelectedColumns()
{
- if (colSel.size() < 1)
+ if (colSel.isEmpty())
{
return;
}
colSel.hideSelectedColumns();
setSelectionGroup(null);
-
+ isColSelChanged(true);
}
public void hideColumns(int start, int end)
{
colSel.hideColumns(start, end);
}
+ isColSelChanged(true);
}
public void showColumn(int col)
{
colSel.revealHiddenColumns(col);
-
+ isColSelChanged(true);
}
public void showAllHiddenColumns()
{
colSel.revealAllHiddenColumns();
+ isColSelChanged(true);
}
// common hide/show seq stuff
setSequenceAnnotationsVisible(seq, true);
}
- hasHiddenRows = false;
hiddenRepSequences = null;
firePropertyChange("alignment", null, alignment.getSequences());
public void showSequence(int index)
{
List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
- index,
- hiddenRepSequences);
+ index, hiddenRepSequences);
if (tmp.size() > 0)
{
if (selectionGroup == null)
selectionGroup.addSequence(seq, false);
setSequenceAnnotationsVisible(seq, true);
}
- // JBPNote: refactor: only update flag if we modified visiblity (used to
- // do this regardless)
- if (alignment.getHiddenSequences().getSize() < 1)
- {
- hasHiddenRows = false;
- }
firePropertyChange("alignment", null, alignment.getSequences());
sendSelection();
}
alignment.getHiddenSequences().hideSequence(seq[i]);
setSequenceAnnotationsVisible(seq[i], false);
}
- hasHiddenRows = true;
firePropertyChange("alignment", null, alignment.getSequences());
}
}
/**
+ * Hides the specified sequence, or the sequences it represents
+ *
+ * @param sequence
+ * the sequence to hide, or keep as representative
+ * @param representGroup
+ * if true, hide the current selection group except for the
+ * representative sequence
+ */
+ public void hideSequences(SequenceI sequence, boolean representGroup)
+ {
+ if (selectionGroup == null || selectionGroup.getSize() < 1)
+ {
+ hideSequence(new SequenceI[] { sequence });
+ return;
+ }
+
+ if (representGroup)
+ {
+ hideRepSequences(sequence, selectionGroup);
+ setSelectionGroup(null);
+ return;
+ }
+
+ int gsize = selectionGroup.getSize();
+ SequenceI[] hseqs = selectionGroup.getSequences().toArray(
+ new SequenceI[gsize]);
+
+ hideSequence(hseqs);
+ setSelectionGroup(null);
+ sendSelection();
+ }
+
+ /**
* Set visibility for any annotations for the given sequence.
*
* @param sequenceI
protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
boolean visible)
{
- for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
+ AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+ if (anns != null)
{
- if (ann.sequenceRef == sequenceI)
+ for (AlignmentAnnotation ann : anns)
{
- ann.visible = visible;
+ if (ann.sequenceRef == sequenceI)
+ {
+ ann.visible = visible;
+ }
}
}
}
if (hiddenRepSequences == null)
{
- hiddenRepSequences = new Hashtable();
+ hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
}
hiddenRepSequences.put(repSequence, sg);
}
+ /**
+ *
+ * @return null or the current reference sequence
+ */
+ public SequenceI getReferenceSeq()
+ {
+ return alignment.getSeqrep();
+ }
+
+ /**
+ * @param seq
+ * @return true iff seq is the reference for the alignment
+ */
+ public boolean isReferenceSeq(SequenceI seq)
+ {
+ return alignment.getSeqrep() == seq;
+ }
+
+ /**
+ *
+ * @param seq
+ * @return true if there are sequences represented by this sequence that are
+ * currently hidden
+ */
public boolean isHiddenRepSequence(SequenceI seq)
{
- return alignment.getSeqrep()==seq || (hiddenRepSequences != null
- && hiddenRepSequences.containsKey(seq));
+ return (hiddenRepSequences != null && hiddenRepSequences
+ .containsKey(seq));
}
+ /**
+ *
+ * @param seq
+ * @return null or a sequence group containing the sequences that seq
+ * represents
+ */
public SequenceGroup getRepresentedSequences(SequenceI seq)
{
return (SequenceGroup) (hiddenRepSequences == null ? null
}
@Override
- public abstract void sendSelection();
-
- @Override
public void invertColumnSelection()
{
colSel.invertColumnSelection(0, alignment.getWidth());
}
-
@Override
public SequenceI[] getSelectionAsNewSequence()
{
AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
for (int i = 0; i < sequences.length; i++)
{
- sequences[i] = new Sequence(sequences[i], annots); // construct new
- // sequence with
- // subset of visible
- // annotation
+ // construct new sequence with subset of visible annotation
+ sequences[i] = new Sequence(sequences[i], annots);
}
}
else
return sequences;
}
-
@Override
public SequenceI[] getSequenceSelection()
{
return sequences;
}
-
@Override
- public jalview.datamodel.CigarArray getViewAsCigars(
- boolean selectedRegionOnly)
+ public CigarArray getViewAsCigars(boolean selectedRegionOnly)
{
- return new jalview.datamodel.CigarArray(alignment, colSel,
+ return new CigarArray(alignment, colSel,
(selectedRegionOnly ? selectionGroup : null));
}
-
@Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly)
return getAlignmentView(selectedOnly, false);
}
-
@Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly, boolean markGroups)
markGroups);
}
-
@Override
public String[] getViewAsString(boolean selectedRegionOnly)
{
+ return getViewAsString(selectedRegionOnly, true);
+ }
+
+ @Override
+ public String[] getViewAsString(boolean selectedRegionOnly,
+ boolean exportHiddenSeqs)
+ {
String[] selection = null;
SequenceI[] seqs = null;
int i, iSize;
}
else
{
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth();
+ if (hasHiddenRows() && exportHiddenSeqs)
+ {
+ AlignmentI fullAlignment = alignment.getHiddenSequences()
+ .getFullAlignment();
+ iSize = fullAlignment.getHeight();
+ seqs = fullAlignment.getSequencesArray();
+ end = fullAlignment.getWidth();
+ }
+ else
+ {
+ iSize = alignment.getHeight();
+ seqs = alignment.getSequencesArray();
+ end = alignment.getWidth();
+ }
}
selection = new String[iSize];
return selection;
}
-
@Override
- public int[][] getVisibleRegionBoundaries(int min, int max)
+ public List<int[]> getVisibleRegionBoundaries(int min, int max)
{
- Vector regions = new Vector();
+ ArrayList<int[]> regions = new ArrayList<int[]>();
int start = min;
int end = max;
}
}
- regions.addElement(new int[]
- { start, end });
+ regions.add(new int[] { start, end });
if (colSel != null && colSel.hasHiddenColumns())
{
int[][] startEnd = new int[regions.size()][2];
- regions.copyInto(startEnd);
-
- return startEnd;
-
+ return regions;
}
@Override
- public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(boolean selectedOnly)
+ public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
+ boolean selectedOnly)
{
ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
AlignmentAnnotation[] aa;
- if ((aa=alignment.getAlignmentAnnotation())!=null)
+ if ((aa = alignment.getAlignmentAnnotation()) != null)
{
- for (AlignmentAnnotation annot:aa)
+ for (AlignmentAnnotation annot : aa)
{
AlignmentAnnotation clone = new AlignmentAnnotation(annot);
- if (selectedOnly && selectionGroup!=null)
+ if (selectedOnly && selectionGroup != null)
+ {
+ colSel.makeVisibleAnnotation(selectionGroup.getStartRes(),
+ selectionGroup.getEndRes(), clone);
+ }
+ else
{
- colSel.makeVisibleAnnotation(selectionGroup.getStartRes(), selectionGroup.getEndRes(),clone);
- } else {
colSel.makeVisibleAnnotation(clone);
}
ala.add(clone);
return ala;
}
-
@Override
public boolean isPadGaps()
{
return padGaps;
}
-
@Override
public void setPadGaps(boolean padGaps)
{
cs.setConsensus(hconsensus);
if (cs.conservationApplied())
{
- cs.setConservation(Conservation.calculateConservation("All",
- ResidueProperties.propHash, 3, alignment.getSequences(), 0,
- alignment.getWidth(), false, getConsPercGaps(), false));
+ cs.setConservation(Conservation.calculateConservation("All", 3,
+ alignment.getSequences(), 0, alignment.getWidth(), false,
+ getConsPercGaps(), false));
}
}
{
initRNAStructure();
}
- initConsensus();
+ consensus = new AlignmentAnnotation("Consensus", "PID",
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ initConsensus(consensus);
+
+ initComplementConsensus();
}
}
- private void initConsensus()
+ /**
+ * If this is a protein alignment and there are mappings to cDNA, add the cDNA
+ * consensus annotation.
+ */
+ public void initComplementConsensus()
{
+ if (!alignment.isNucleotide())
+ {
+ final List<AlignedCodonFrame> codonMappings = alignment
+ .getCodonFrames();
+ if (codonMappings != null && !codonMappings.isEmpty())
+ {
+ boolean doConsensus = false;
+ for (AlignedCodonFrame mapping : codonMappings)
+ {
+ // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
+ MapList[] mapLists = mapping.getdnaToProt();
+ // mapLists can be empty if project load has not finished resolving
+ // seqs
+ if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+ {
+ doConsensus = true;
+ break;
+ }
+ }
+ if (doConsensus)
+ {
+ complementConsensus = new AlignmentAnnotation("cDNA Consensus",
+ "PID for cDNA", new Annotation[1], 0f, 100f,
+ AlignmentAnnotation.BAR_GRAPH);
+ initConsensus(complementConsensus);
+ }
+ }
+ }
+ }
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
+ private void initConsensus(AlignmentAnnotation aa)
+ {
+ aa.hasText = true;
+ aa.autoCalculated = true;
if (showConsensus)
{
- alignment.addAnnotation(consensus);
+ alignment.addAnnotation(aa);
}
}
public int calcPanelHeight()
{
// setHeight of panels
- AlignmentAnnotation[] aa = getAlignment().getAlignmentAnnotation();
+ AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation();
int height = 0;
int charHeight = getCharHeight();
- if (aa != null)
+ if (anns != null)
{
BitSet graphgrp = new BitSet();
- for (int i = 0; i < aa.length; i++)
+ for (AlignmentAnnotation aa : anns)
{
- if (aa[i] == null)
+ if (aa == null)
{
System.err.println("Null annotation row: ignoring.");
continue;
}
- if (!aa[i].visible)
+ if (!aa.visible)
{
continue;
}
- if (aa[i].graphGroup > -1)
+ if (aa.graphGroup > -1)
{
- if (graphgrp.get(aa[i].graphGroup))
+ if (graphgrp.get(aa.graphGroup))
{
continue;
}
else
{
- graphgrp.set(aa[i].graphGroup);
+ graphgrp.set(aa.graphGroup);
}
}
- aa[i].height = 0;
+ aa.height = 0;
- if (aa[i].hasText)
+ if (aa.hasText)
{
- aa[i].height += charHeight;
+ aa.height += charHeight;
}
- if (aa[i].hasIcons)
+ if (aa.hasIcons)
{
- aa[i].height += 16;
+ aa.height += 16;
}
- if (aa[i].graph > 0)
+ if (aa.graph > 0)
{
- aa[i].height += aa[i].graphHeight;
+ aa.height += aa.graphHeight;
}
- if (aa[i].height == 0)
+ if (aa.height == 0)
{
- aa[i].height = 20;
+ aa.height = 20;
}
- height += aa[i].height;
+ height += aa.height;
}
}
if (height == 0)
}
oldrfs.clear();
}
+
+ @Override
+ public boolean isDisplayReferenceSeq()
+ {
+ return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
+ }
+
+ @Override
+ public void setDisplayReferenceSeq(boolean displayReferenceSeq)
+ {
+ viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
+ }
+
+ @Override
+ public boolean isColourByReferenceSeq()
+ {
+ return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
+ }
+
+ @Override
+ public Color getSequenceColour(SequenceI seq)
+ {
+ Color sqc = sequenceColours.get(seq);
+ return (sqc == null ? Color.white : sqc);
+ }
+
+ @Override
+ public void setSequenceColour(SequenceI seq, Color col)
+ {
+ if (col == null)
+ {
+ sequenceColours.remove(seq);
+ }
+ else
+ {
+ sequenceColours.put(seq, col);
+ }
+ }
+
+ @Override
+ public void updateSequenceIdColours()
+ {
+ for (SequenceGroup sg : alignment.getGroups())
+ {
+ if (sg.idColour != null)
+ {
+ for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
+ {
+ sequenceColours.put(s, sg.idColour);
+ }
+ }
+ }
+ }
+
+ @Override
+ public void clearSequenceColours()
+ {
+ sequenceColours.clear();
+ };
+
+ @Override
+ public AlignViewportI getCodingComplement()
+ {
+ return this.codingComplement;
+ }
+
+ /**
+ * Set this as the (cDna/protein) complement of the given viewport. Also
+ * ensures the reverse relationship is set on the given viewport.
+ */
+ @Override
+ public void setCodingComplement(AlignViewportI av)
+ {
+ if (this == av)
+ {
+ System.err.println("Ignoring recursive setCodingComplement request");
+ }
+ else
+ {
+ this.codingComplement = av;
+ // avoid infinite recursion!
+ if (av.getCodingComplement() != this)
+ {
+ av.setCodingComplement(this);
+ }
+ }
+ }
+
+ @Override
+ public boolean isNucleotide()
+ {
+ return getAlignment() == null ? false : getAlignment().isNucleotide();
+ }
+
+ @Override
+ public FeaturesDisplayedI getFeaturesDisplayed()
+ {
+ return featuresDisplayed;
+ }
+
+ @Override
+ public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
+ {
+ featuresDisplayed = featuresDisplayedI;
+ }
+
+ @Override
+ public boolean areFeaturesDisplayed()
+ {
+ return featuresDisplayed != null
+ && featuresDisplayed.getRegisteredFeaturesCount() > 0;
+ }
+
+ /**
+ * set the flag
+ *
+ * @param b
+ * features are displayed if true
+ */
+ @Override
+ public void setShowSequenceFeatures(boolean b)
+ {
+ viewStyle.setShowSequenceFeatures(b);
+ }
+
+ @Override
+ public boolean isShowSequenceFeatures()
+ {
+ return viewStyle.isShowSequenceFeatures();
+ }
+
+ @Override
+ public void setShowSequenceFeaturesHeight(boolean selected)
+ {
+ viewStyle.setShowSequenceFeaturesHeight(selected);
+ }
+
+ @Override
+ public boolean isShowSequenceFeaturesHeight()
+ {
+ return viewStyle.isShowSequenceFeaturesHeight();
+ }
+
+ @Override
+ public void setShowAnnotation(boolean b)
+ {
+ viewStyle.setShowAnnotation(b);
+ }
+
+ @Override
+ public boolean isShowAnnotation()
+ {
+ return viewStyle.isShowAnnotation();
+ }
+
+ @Override
+ public boolean isRightAlignIds()
+ {
+ return viewStyle.isRightAlignIds();
+ }
+
+ @Override
+ public void setRightAlignIds(boolean rightAlignIds)
+ {
+ viewStyle.setRightAlignIds(rightAlignIds);
+ }
+
+ @Override
+ public boolean getConservationSelected()
+ {
+ return viewStyle.getConservationSelected();
+ }
+
+ @Override
+ public void setShowBoxes(boolean state)
+ {
+ viewStyle.setShowBoxes(state);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getTextColour()
+ */
+ @Override
+ public Color getTextColour()
+ {
+ return viewStyle.getTextColour();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getTextColour2()
+ */
+ @Override
+ public Color getTextColour2()
+ {
+ return viewStyle.getTextColour2();
+ }
+
/**
- * show the reference sequence in the alignment view
+ * @return
+ * @see jalview.api.ViewStyleI#getThresholdTextColour()
*/
- private boolean displayReferenceSeq=false;
+ @Override
+ public int getThresholdTextColour()
+ {
+ return viewStyle.getThresholdTextColour();
+ }
+
/**
- * colour according to the reference sequence defined on the alignment
+ * @return
+ * @see jalview.api.ViewStyleI#isConservationColourSelected()
*/
- private boolean colourByReferenceSeq=false;
+ @Override
+ public boolean isConservationColourSelected()
+ {
+ return viewStyle.isConservationColourSelected();
+ }
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isRenderGaps()
+ */
@Override
- public boolean isDisplayReferenceSeq()
+ public boolean isRenderGaps()
{
- return alignment.hasSeqrep() && displayReferenceSeq;
+ return viewStyle.isRenderGaps();
}
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isShowColourText()
+ */
@Override
- public void setDisplayReferenceSeq(boolean displayReferenceSeq)
+ public boolean isShowColourText()
{
- this.displayReferenceSeq = displayReferenceSeq;
+ return viewStyle.isShowColourText();
}
- public boolean isColourByReferenceSeq()
+ /**
+ * @param conservationColourSelected
+ * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
+ */
+ @Override
+ public void setConservationColourSelected(
+ boolean conservationColourSelected)
{
- return alignment.hasSeqrep() && colourByReferenceSeq;
+ viewStyle.setConservationColourSelected(conservationColourSelected);
}
- public void setColourByReferenceSeq(boolean colourByReferenceSeq)
+ /**
+ * @param showColourText
+ * @see jalview.api.ViewStyleI#setShowColourText(boolean)
+ */
+ @Override
+ public void setShowColourText(boolean showColourText)
{
- this.colourByReferenceSeq = colourByReferenceSeq;
+ viewStyle.setShowColourText(showColourText);
}
+ /**
+ * @param textColour
+ * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
+ */
@Override
- public Color getSequenceColour(SequenceI seq)
+ public void setTextColour(Color textColour)
{
- Color sqc = Color.white;
- if (sequenceColours != null)
- {
- sqc = (Color) sequenceColours.get(seq);
- if (sqc == null)
- {
- sqc = Color.white;
- }
- }
- return sqc;
+ viewStyle.setTextColour(textColour);
}
+ /**
+ * @param thresholdTextColour
+ * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
+ */
@Override
- public void setSequenceColour(SequenceI seq, Color col)
+ public void setThresholdTextColour(int thresholdTextColour)
{
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
+ viewStyle.setThresholdTextColour(thresholdTextColour);
+ }
- if (col == null)
- {
- sequenceColours.remove(seq);
- }
- else
- {
- sequenceColours.put(seq, col);
- }
+ /**
+ * @param textColour2
+ * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
+ */
+ @Override
+ public void setTextColour2(Color textColour2)
+ {
+ viewStyle.setTextColour2(textColour2);
}
@Override
- public void updateSequenceIdColours()
+ public ViewStyleI getViewStyle()
{
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
- for (SequenceGroup sg : alignment.getGroups())
- {
- if (sg.idColour != null)
- {
- for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
- {
- sequenceColours.put(s, sg.idColour);
- }
- }
- }
+ return new ViewStyle(viewStyle);
}
@Override
- public void clearSequenceColours()
+ public void setViewStyle(ViewStyleI settingsForView)
{
- sequenceColours = null;
- };
+ viewStyle = new ViewStyle(settingsForView);
+ }
- FeaturesDisplayedI featuresDisplayed = null;
+ @Override
+ public boolean sameStyle(ViewStyleI them)
+ {
+ return viewStyle.sameStyle(them);
+ }
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getIdWidth()
+ */
@Override
- public FeaturesDisplayedI getFeaturesDisplayed()
+ public int getIdWidth()
{
- return featuresDisplayed;
+ return viewStyle.getIdWidth();
}
+ /**
+ * @param i
+ * @see jalview.api.ViewStyleI#setIdWidth(int)
+ */
@Override
- public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
+ public void setIdWidth(int i)
{
- featuresDisplayed = featuresDisplayedI;
+ viewStyle.setIdWidth(i);
}
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isCentreColumnLabels()
+ */
@Override
- public boolean areFeaturesDisplayed()
+ public boolean isCentreColumnLabels()
{
- return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0;
+ return viewStyle.isCentreColumnLabels();
}
/**
- * display setting for showing/hiding sequence features on alignment view
+ * @param centreColumnLabels
+ * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
*/
- boolean showSequenceFeatures = false;
+ @Override
+ public void setCentreColumnLabels(boolean centreColumnLabels)
+ {
+ viewStyle.setCentreColumnLabels(centreColumnLabels);
+ }
/**
- * set the flag
- *
- * @param b
- * features are displayed if true
+ * @param showdbrefs
+ * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
*/
@Override
- public void setShowSequenceFeatures(boolean b)
+ public void setShowDBRefs(boolean showdbrefs)
{
- showSequenceFeatures = b;
+ viewStyle.setShowDBRefs(showdbrefs);
}
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isShowDBRefs()
+ */
@Override
- public boolean isShowSequenceFeatures()
+ public boolean isShowDBRefs()
{
- return showSequenceFeatures;
+ return viewStyle.isShowDBRefs();
}
- boolean showSeqFeaturesHeight;
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isShowNPFeats()
+ */
+ @Override
+ public boolean isShowNPFeats()
+ {
+ return viewStyle.isShowNPFeats();
+ }
+ /**
+ * @param shownpfeats
+ * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
+ */
@Override
- public void setShowSequenceFeaturesHeight(boolean selected)
+ public void setShowNPFeats(boolean shownpfeats)
+ {
+ viewStyle.setShowNPFeats(shownpfeats);
+ }
+
+ public abstract StructureSelectionManager getStructureSelectionManager();
+
+ /**
+ * Add one command to the command history list.
+ *
+ * @param command
+ */
+ public void addToHistoryList(CommandI command)
+ {
+ if (this.historyList != null)
+ {
+ this.historyList.push(command);
+ broadcastCommand(command, false);
+ }
+ }
+
+ protected void broadcastCommand(CommandI command, boolean undo)
+ {
+ getStructureSelectionManager().commandPerformed(command, undo,
+ getVamsasSource());
+ }
+
+ /**
+ * Add one command to the command redo list.
+ *
+ * @param command
+ */
+ public void addToRedoList(CommandI command)
+ {
+ if (this.redoList != null)
+ {
+ this.redoList.push(command);
+ }
+ broadcastCommand(command, true);
+ }
+
+ /**
+ * Clear the command redo list.
+ */
+ public void clearRedoList()
+ {
+ if (this.redoList != null)
+ {
+ this.redoList.clear();
+ }
+ }
+
+ public void setHistoryList(Deque<CommandI> list)
+ {
+ this.historyList = list;
+ }
+
+ public Deque<CommandI> getHistoryList()
+ {
+ return this.historyList;
+ }
+
+ public void setRedoList(Deque<CommandI> list)
+ {
+ this.redoList = list;
+ }
+
+ public Deque<CommandI> getRedoList()
{
- showSeqFeaturesHeight = selected;
+ return this.redoList;
}
@Override
- public boolean isShowSequenceFeaturesHeight()
+ public VamsasSource getVamsasSource()
+ {
+ return this;
+ }
+
+ public SequenceAnnotationOrder getSortAnnotationsBy()
{
- return showSeqFeaturesHeight;
+ return sortAnnotationsBy;
}
- private boolean showAnnotation = true;
+ public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+ {
+ this.sortAnnotationsBy = sortAnnotationsBy;
+ }
- private boolean rightAlignIds = false;
+ public boolean isShowAutocalculatedAbove()
+ {
+ return showAutocalculatedAbove;
+ }
+ public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
+ {
+ this.showAutocalculatedAbove = showAutocalculatedAbove;
+ }
@Override
- public void setShowAnnotation(boolean b)
+ public boolean isScaleProteinAsCdna()
{
- showAnnotation = b;
+ return viewStyle.isScaleProteinAsCdna();
}
@Override
- public boolean isShowAnnotation()
+ public void setScaleProteinAsCdna(boolean b)
{
- return showAnnotation;
+ viewStyle.setScaleProteinAsCdna(b);
}
+ /**
+ * @return true if view should scroll to show the highlighted region of a
+ * sequence
+ * @return
+ */
@Override
- public boolean isRightAlignIds()
+ public final boolean isFollowHighlight()
{
- return rightAlignIds;
+ return followHighlight;
}
@Override
- public void setRightAlignIds(boolean rightAlignIds)
+ public final void setFollowHighlight(boolean b)
+ {
+ this.followHighlight = b;
+ }
+
+ public int getStartRes()
+ {
+ return startRes;
+ }
+
+ @Override
+ public int getEndRes()
+ {
+ return endRes;
+ }
+
+ public int getStartSeq()
+ {
+ return startSeq;
+ }
+
+ public void setStartRes(int res)
+ {
+ this.startRes = res;
+ }
+
+ public void setStartSeq(int seq)
+ {
+ this.startSeq = seq;
+ }
+
+ public void setEndRes(int res)
+ {
+ if (res > alignment.getWidth() - 1)
+ {
+ // log.System.out.println(" Corrected res from " + res + " to maximum " +
+ // (alignment.getWidth()-1));
+ res = alignment.getWidth() - 1;
+ }
+ if (res < 0)
+ {
+ res = 0;
+ }
+ this.endRes = res;
+ }
+
+ public void setEndSeq(int seq)
+ {
+ if (seq > alignment.getHeight())
+ {
+ seq = alignment.getHeight();
+ }
+ if (seq < 0)
+ {
+ seq = 0;
+ }
+ this.endSeq = seq;
+ }
+
+ public int getEndSeq()
+ {
+ return endSeq;
+ }
+
+ /**
+ * Helper method to populate the SearchResults with the location in the
+ * complementary alignment to scroll to, in order to match this one.
+ *
+ * @param sr
+ * the SearchResults to add to
+ * @return the offset (below top of visible region) of the matched sequence
+ */
+ protected int findComplementScrollTarget(SearchResults sr)
+ {
+ final AlignViewportI complement = getCodingComplement();
+ if (complement == null || !complement.isFollowHighlight())
+ {
+ return 0;
+ }
+ boolean iAmProtein = !getAlignment().isNucleotide();
+ AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement
+ .getAlignment();
+ if (proteinAlignment == null)
+ {
+ return 0;
+ }
+ final List<AlignedCodonFrame> mappings = proteinAlignment
+ .getCodonFrames();
+
+ /*
+ * Heuristic: find the first mapped sequence (if any) with a non-gapped
+ * residue in the middle column of the visible region. Scroll the
+ * complementary alignment to line up the corresponding residue.
+ */
+ int seqOffset = 0;
+ SequenceI sequence = null;
+
+ /*
+ * locate 'middle' column (true middle if an odd number visible, left of
+ * middle if an even number visible)
+ */
+ int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
+ final HiddenSequences hiddenSequences = getAlignment()
+ .getHiddenSequences();
+
+ /*
+ * searching to the bottom of the alignment gives smoother scrolling across
+ * all gapped visible regions
+ */
+ int lastSeq = alignment.getHeight() - 1;
+ List<AlignedCodonFrame> seqMappings = null;
+ for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+ {
+ sequence = getAlignment().getSequenceAt(seqNo);
+ if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
+ {
+ continue;
+ }
+ if (Comparison.isGap(sequence.getCharAt(middleColumn)))
+ {
+ continue;
+ }
+ seqMappings = MappingUtils
+ .findMappingsForSequenceAndOthers(sequence, mappings,
+ getCodingComplement().getAlignment().getSequences());
+ if (!seqMappings.isEmpty())
+ {
+ break;
+ }
+ }
+
+ if (sequence == null || seqMappings == null || seqMappings.isEmpty())
+ {
+ /*
+ * No ungapped mapped sequence in middle column - do nothing
+ */
+ return 0;
+ }
+ MappingUtils.addSearchResults(sr, sequence,
+ sequence.findPosition(middleColumn), seqMappings);
+ return seqOffset;
+ }
+
+ /**
+ * synthesize a column selection if none exists so it covers the given
+ * selection group. if wholewidth is false, no column selection is made if the
+ * selection group covers the whole alignment width.
+ *
+ * @param sg
+ * @param wholewidth
+ */
+ public void expandColSelection(SequenceGroup sg, boolean wholewidth)
{
- this.rightAlignIds = rightAlignIds;
+ int sgs, sge;
+ if (sg != null && (sgs = sg.getStartRes()) >= 0
+ && sg.getStartRes() <= (sge = sg.getEndRes())
+ && !this.hasSelectedColumns())
+ {
+ if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
+ {
+ // do nothing
+ return;
+ }
+ if (colSel == null)
+ {
+ colSel = new ColumnSelection();
+ }
+ for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+ {
+ colSel.addElement(cspos);
+ }
+ }
}
+ /**
+ * hold status of current selection group - defined on alignment or not.
+ */
+ private boolean selectionIsDefinedGroup = false;
+
+ @Override
+ public boolean isSelectionDefinedGroup()
+ {
+ if (selectionGroup == null)
+ {
+ return false;
+ }
+ if (isSelectionGroupChanged(true))
+ {
+ selectionIsDefinedGroup = false;
+ List<SequenceGroup> gps = alignment.getGroups();
+ if (gps == null || gps.size() == 0)
+ {
+ selectionIsDefinedGroup = false;
+ }
+ else
+ {
+ selectionIsDefinedGroup = gps.contains(selectionGroup);
+ }
+ }
+ return selectionGroup.getContext() == alignment
+ || selectionIsDefinedGroup;
+ }
}
git://source.jalview.org / jalview.git / blobdiff