/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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 java.awt.Color;
+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.Set;
+
+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.Sequence;
import jalview.datamodel.SequenceCollectionI;
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.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.util.ArrayList;
-import java.util.BitSet;
-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
* an active alignment view displayed in the GUI
*
*/
public abstract class AlignmentViewport implements AlignViewportI,
- ViewStyleI
+ ViewStyleI, CommandListener, VamsasSource
{
protected ViewStyleI viewStyle = new ViewStyle();
-
+
+ /**
+ * A viewport that hosts the cDna view of this (protein), or vice versa (if
+ * set).
+ */
+ AlignViewportI codingComplement = null;
+
+ FeaturesDisplayedI featuresDisplayed = null;
+
+ protected Deque<CommandI> historyList = new ArrayDeque<CommandI>();
+
+ protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
+
+ /**
+ * @param name
+ * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
+ */
+ public void setFontName(String name)
+ {
+ viewStyle.setFontName(name);
+ }
+
+ /**
+ * @param style
+ * @see jalview.api.ViewStyleI#setFontStyle(int)
+ */
+ public void setFontStyle(int style)
+ {
+ viewStyle.setFontStyle(style);
+ }
+
+ /**
+ * @param size
+ * @see jalview.api.ViewStyleI#setFontSize(int)
+ */
+ public void setFontSize(int size)
+ {
+ viewStyle.setFontSize(size);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getFontStyle()
+ */
+ public int getFontStyle()
+ {
+ return viewStyle.getFontStyle();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getFontName()
+ */
+ public String getFontName()
+ {
+ return viewStyle.getFontName();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getFontSize()
+ */
+ public int getFontSize()
+ {
+ return viewStyle.getFontSize();
+ }
+
/**
* @param upperCasebold
* @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
|| cs instanceof Blosum62ColourScheme)
{
sg.cs.setThreshold(viewStyle.getThreshold(),
- getIgnoreGapsConsensus());
+ isIgnoreGapsConsensus());
recalc = true;
}
else
{
- sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+ sg.cs.setThreshold(0, isIgnoreGapsConsensus());
}
if (getConservationSelected())
protected AlignmentAnnotation consensus;
+ protected AlignmentAnnotation complementConsensus;
+
protected AlignmentAnnotation strucConsensus;
protected AlignmentAnnotation conservation;
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
*/
public void setSequenceConsensusHash(Hashtable[] hconsensus)
{
this.hconsensus = hconsensus;
+ }
+ @Override
+ public void setComplementConsensusHash(Hashtable[] hconsensus)
+ {
+ this.hcomplementConsensus = hconsensus;
}
@Override
}
@Override
+ public Hashtable[] getComplementConsensusHash()
+ {
+ return hcomplementConsensus;
+ }
+
+ @Override
public Hashtable[] getRnaStructureConsensusHash()
{
return hStrucConsensus;
}
@Override
+ public AlignmentAnnotation getComplementConsensusAnnotation()
+ {
+ return complementConsensus;
+ }
+
+ @Override
public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
{
return strucConsensus;
{
calculator.registerWorker(new ConsensusThread(this, ap));
}
+
+ /*
+ * A separate thread to compute cDNA consensus for a protein alignment
+ */
+ final AlignmentI al = this.getAlignment();
+ if (!al.isNucleotide() && al.getCodonFrames() != null
+ && !al.getCodonFrames().isEmpty())
+ {
+ if (calculator
+ .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+ {
+ calculator.registerWorker(new ComplementConsensusThread(this, ap));
+ }
+ }
}
// --------START Structure Conservation
// 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;
*/
protected String viewId = null;
+ @Override
public String getViewId()
{
if (viewId == null)
}
@Override
- public boolean getIgnoreGapsConsensus()
+ public boolean isIgnoreGapsConsensus()
{
return ignoreGapsInConsensusCalculation;
}
protected boolean showConsensus = true;
- Hashtable sequenceColours;
+ private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
+
+ protected SequenceAnnotationOrder sortAnnotationsBy = null;
+
+ protected boolean showAutocalculatedAbove;
/**
* Property change listener for changes in alignment
}
@Override
- public abstract void sendSelection();
-
- @Override
public void invertColumnSelection()
{
colSel.invertColumnSelection(0, alignment.getWidth());
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
@Override
- public jalview.datamodel.CigarArray getViewAsCigars(
+ public CigarArray getViewAsCigars(
boolean selectedRegionOnly)
{
- return new jalview.datamodel.CigarArray(alignment, colSel,
+ return new CigarArray(alignment, colSel,
(selectedRegionOnly ? selectionGroup : null));
}
@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[]
+ 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
{
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.
+ */
+ protected void initComplementConsensus()
{
+ if (!alignment.isNucleotide())
+ {
+ final Set<AlignedCodonFrame> codonMappings = alignment
+ .getCodonFrames();
+ if (codonMappings != null && !codonMappings.isEmpty())
+ {
+ 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)
viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
}
+ @Override
public boolean isColourByReferenceSeq()
{
return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
}
-
@Override
public Color getSequenceColour(SequenceI seq)
{
- Color sqc = Color.white;
- if (sequenceColours != null)
- {
- sqc = (Color) sequenceColours.get(seq);
- if (sqc == null)
- {
- sqc = Color.white;
- }
- }
- return sqc;
+ Color sqc = sequenceColours.get(seq);
+ return (sqc == null ? Color.white : sqc);
}
@Override
public void setSequenceColour(SequenceI seq, Color col)
{
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
-
if (col == null)
{
sequenceColours.remove(seq);
@Override
public void updateSequenceIdColours()
{
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
for (SequenceGroup sg : alignment.getGroups())
{
if (sg.idColour != null)
@Override
public void clearSequenceColours()
{
- sequenceColours = null;
+ sequenceColours.clear();
};
- FeaturesDisplayedI featuresDisplayed = null;
+ @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 viewStyle.isShowColourText();
}
-
/**
* @return
* @see jalview.api.ViewStyleI#isShowSeqFeaturesHeight()
viewStyle.setTextColour2(textColour2);
}
+ @Override
+ public ViewStyleI getViewStyle()
+ {
+ return new ViewStyle(viewStyle);
+ }
+
+ @Override
+ public void setViewStyle(ViewStyleI settingsForView)
+ {
+ viewStyle = new ViewStyle(settingsForView);
+ }
+
+ @Override
+ public boolean sameStyle(ViewStyleI them)
+ {
+ return viewStyle.sameStyle(them);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#getIdWidth()
+ */
+ public int getIdWidth()
+ {
+ return viewStyle.getIdWidth();
+ }
+
+ /**
+ * @param i
+ * @see jalview.api.ViewStyleI#setIdWidth(int)
+ */
+ public void setIdWidth(int i)
+ {
+ viewStyle.setIdWidth(i);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isCentreColumnLabels()
+ */
+ public boolean isCentreColumnLabels()
+ {
+ return viewStyle.isCentreColumnLabels();
+ }
+
+ /**
+ * @param centreColumnLabels
+ * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
+ */
+ public void setCentreColumnLabels(boolean centreColumnLabels)
+ {
+ viewStyle.setCentreColumnLabels(centreColumnLabels);
+ }
+
+ /**
+ * @param showdbrefs
+ * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
+ */
+ public void setShowDBRefs(boolean showdbrefs)
+ {
+ viewStyle.setShowDBRefs(showdbrefs);
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isShowDBRefs()
+ */
+ public boolean isShowDBRefs()
+ {
+ return viewStyle.isShowDBRefs();
+ }
+
+ /**
+ * @return
+ * @see jalview.api.ViewStyleI#isShowNPFeats()
+ */
+ public boolean isShowNPFeats()
+ {
+ return viewStyle.isShowNPFeats();
+ }
+
+ /**
+ * @param shownpfeats
+ * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
+ */
+ 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()
+ {
+ return this.redoList;
+ }
+
+ @Override
+ public VamsasSource getVamsasSource()
+ {
+ return this;
+ }
+
+ public SequenceAnnotationOrder getSortAnnotationsBy()
+ {
+ return sortAnnotationsBy;
+ }
+
+ public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+ {
+ this.sortAnnotationsBy = sortAnnotationsBy;
+ }
+
+ public boolean isShowAutocalculatedAbove()
+ {
+ return showAutocalculatedAbove;
+ }
+
+ public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
+ {
+ this.showAutocalculatedAbove = showAutocalculatedAbove;
+ }
}
git://source.jalview.org / jalview.git / blobdiff