*/
package jalview.viewmodel;
+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 jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.api.AlignCalcManagerI;
import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenSequences;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.schemes.Blosum62ColourScheme;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
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.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
-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;
-
/**
* 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,
CommandListener, VamsasSource
{
+ protected ViewportRanges ranges;
+
protected ViewStyleI viewStyle = new ViewStyle();
/**
protected boolean ignoreGapsInConsensusCalculation = false;
- protected ColourSchemeI globalColourScheme = null;
+ protected ResidueShaderI residueShading;
@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
+ // put the 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;
+
+ /*
+ * only instantiate alignment colouring once, thereafter update it;
+ * this means that any conservation or PID threshold settings
+ * persist when the alignment colour scheme is changed
+ */
+ if (residueShading == null)
+ {
+ residueShading = new ResidueShader(viewStyle);
+ }
+ residueShading.setColourScheme(cs);
+
+ // TODO: do threshold and increment belong in ViewStyle or ResidueShader?
+ // ...problem: groups need these, but do not currently have a ViewStyle
+
if (cs != null)
{
- cs.setConservationApplied(recalc = getConservationSelected());
- if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
+ if (getConservationSelected())
{
- recalc = true;
- cs.setThreshold(viewStyle.getThreshold(),
- ignoreGapsInConsensusCalculation);
+ residueShading.setConservation(hconservation);
}
- else
- {
- cs.setThreshold(0, ignoreGapsInConsensusCalculation);
- }
- if (recalc)
- {
- cs.setConsensus(hconsensus);
- cs.setConservation(hconservation);
- }
- cs.alignmentChanged(alignment, hiddenRepSequences);
+ residueShading.alignmentChanged(alignment, hiddenRepSequences);
}
+
+ /*
+ * if 'apply colour to all groups' is selected... do so
+ * (but don't transfer any colour threshold settings to groups)
+ */
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
+ /*
+ * retain any colour thresholds per group while
+ * changing choice of colour scheme (JAL-2386)
+ */
+ sg.setColourScheme(cs);
+ if (cs != null)
{
- 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);
+ sg.getGroupColourScheme()
+ .alignmentChanged(sg, hiddenRepSequences);
}
}
}
@Override
public ColourSchemeI getGlobalColourScheme()
{
- return globalColourScheme;
+ return residueShading == null ? null : residueShading
+ .getColourScheme();
+ }
+
+ @Override
+ public ResidueShaderI getResidueShading()
+ {
+ return residueShading;
}
protected AlignmentAnnotation consensus;
protected AlignmentAnnotation complementConsensus;
+ protected AlignmentAnnotation gapcounts;
+
protected AlignmentAnnotation strucConsensus;
protected AlignmentAnnotation conservation;
/**
* results of alignment consensus analysis for visible portion of view
*/
- protected Hashtable[] hconsensus = null;
+ protected ProfilesI hconsensus = null;
/**
* results of cDNA complement consensus visible portion of view
}
@Override
- public void setSequenceConsensusHash(Hashtable[] hconsensus)
+ public void setSequenceConsensusHash(ProfilesI hconsensus)
{
this.hconsensus = hconsensus;
}
}
@Override
- public Hashtable[] getSequenceConsensusHash()
+ public ProfilesI getSequenceConsensusHash()
{
return hconsensus;
}
}
@Override
+ public AlignmentAnnotation getAlignmentGapAnnotation()
+ {
+ return gapcounts;
+ }
+
+ @Override
public AlignmentAnnotation getComplementConsensusAnnotation()
{
return complementConsensus;
public void updateConservation(final AlignmentViewPanel ap)
{
// see note in mantis : issue number 8585
- if (alignment.isNucleotide() || conservation == null
+ if (alignment.isNucleotide()
+ || (conservation == null && quality == null)
|| !autoCalculateConsensus)
{
return;
&& !al.getCodonFrames().isEmpty())
{
/*
- * fudge - check first mapping is protein-to-nucleotide
+ * fudge - check first for protein-to-nucleotide mappings
* (we don't want to do this for protein-to-protein)
*/
- AlignedCodonFrame mapping = al.getCodonFrames().iterator().next();
- // 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)
+ 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)
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;
+ // colour scheme may hold reference to consensus
+ residueShading = null;
+ // TODO remove listeners from changeSupport?
+ changeSupport = null;
+ setAlignment(null);
+ }
+
@Override
public boolean isClosed()
{
}
/**
- * Set the selection group for this window.
+ * Set the selection group for this window. Also sets the current alignment as
+ * the context for the group, if it does not already have one.
*
* @param sg
* - group holding references to sequences in this alignment view
public void setSelectionGroup(SequenceGroup sg)
{
selectionGroup = sg;
+ if (sg != null && sg.getContext() == null)
+ {
+ sg.setContext(alignment);
+ }
}
public void setHiddenColumns(ColumnSelection colsel)
}
@Override
+ public boolean hasSelectedColumns()
+ {
+ ColumnSelection columnSelection = getColumnSelection();
+ return columnSelection != null && columnSelection.hasSelectedColumns();
+ }
+
+ @Override
public boolean hasHiddenColumns()
{
return colSel != null && colSel.hasHiddenColumns();
if (ap != null)
{
updateConsensus(ap);
- if (globalColourScheme != null)
+ if (residueShading != null)
{
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+ residueShading.setThreshold(residueShading.getThreshold(),
ignoreGapsInConsensusCalculation);
}
}
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;
+ protected boolean showOccupancy = true;
+
private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
protected SequenceAnnotationOrder sortAnnotationsBy = null;
*/
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 boolean isHiddenRepSequence(SequenceI seq)
{
return (hiddenRepSequences != null && hiddenRepSequences
- .containsKey(seq));
+ .containsKey(seq));
}
/**
selectionGroup.setEndRes(alWidth - 1);
}
- resetAllColourSchemes();
+ updateAllColourSchemes();
calculator.restartWorkers();
// alignment.adjustSequenceAnnotations();
}
/**
* reset scope and do calculations for all applied colourschemes on alignment
*/
- void resetAllColourSchemes()
+ void updateAllColourSchemes()
{
- ColourSchemeI cs = globalColourScheme;
- if (cs != null)
+ ResidueShaderI rs = residueShading;
+ if (rs != null)
{
- cs.alignmentChanged(alignment, hiddenRepSequences);
+ rs.alignmentChanged(alignment, hiddenRepSequences);
- cs.setConsensus(hconsensus);
- if (cs.conservationApplied())
+ rs.setConsensus(hconsensus);
+ if (rs.conservationApplied())
{
- cs.setConservation(Conservation.calculateConservation("All",
- ResidueProperties.propHash, 3, alignment.getSequences(), 0,
- alignment.getWidth(), false, getConsPercGaps(), false));
+ rs.setConservation(Conservation.calculateConservation("All",
+ alignment.getSequences(), 0, alignment.getWidth(), false,
+ getConsPercGaps(), false));
}
}
consensus = new AlignmentAnnotation("Consensus", "PID",
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
+ initGapCounts();
initComplementConsensus();
}
}
/**
- * If this is a protein alignment and there are mappings to cDNA, add the cDNA
- * consensus annotation.
+ * If this is a protein alignment and there are mappings to cDNA, adds the
+ * cDNA consensus annotation and returns true, else returns false.
*/
- public void initComplementConsensus()
+ public boolean initComplementConsensus()
{
if (!alignment.isNucleotide())
{
.getCodonFrames();
if (codonMappings != null && !codonMappings.isEmpty())
{
- // fudge: check mappings are not protein-to-protein
- // TODO: nicer
- AlignedCodonFrame mapping = codonMappings.iterator().next();
- MapList[] mapLists = mapping.getdnaToProt();
- // mapLists can be empty if project load has not finished resolving seqs
- if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+ 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);
+ return true;
}
}
}
+ return false;
}
private void initConsensus(AlignmentAnnotation aa)
}
}
+ // these should be extracted from the view model - style and settings for
+ // derived annotation
+ private void initGapCounts()
+ {
+ if (showOccupancy)
+ {
+ gapcounts = new AlignmentAnnotation("Occupancy",
+ "Number of aligned positions", new Annotation[1], 0f,
+ alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
+ gapcounts.hasText = true;
+ gapcounts.autoCalculated = true;
+ gapcounts.scaleColLabel = true;
+ gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+
+ alignment.addAnnotation(gapcounts);
+ }
+ }
+
private void initConservation()
{
if (showConservation)
public void setViewStyle(ViewStyleI settingsForView)
{
viewStyle = new ViewStyle(settingsForView);
+ if (residueShading != null)
+ {
+ residueShading.setConservationApplied(settingsForView
+ .isConservationColourSelected());
+ }
}
@Override
this.followHighlight = b;
}
- public int getStartRes()
- {
- return startRes;
- }
-
@Override
- public int getEndRes()
+ public ViewportRanges getRanges()
{
- 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;
+ return ranges;
}
/**
* the SearchResults to add to
* @return the offset (below top of visible region) of the matched sequence
*/
- protected int findComplementScrollTarget(SearchResults sr)
+ protected int findComplementScrollTarget(SearchResultsI sr)
{
final AlignViewportI complement = getCodingComplement();
if (complement == null || !complement.isFollowHighlight())
* locate 'middle' column (true middle if an odd number visible, left of
* middle if an even number visible)
*/
- int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
+ int middleColumn = ranges.getStartRes()
+ + (ranges.getEndRes() - ranges.getStartRes()) / 2;
final HiddenSequences hiddenSequences = getAlignment()
.getHiddenSequences();
* all gapped visible regions
*/
int lastSeq = alignment.getHeight() - 1;
- for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+ List<AlignedCodonFrame> seqMappings = null;
+ for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
{
sequence = getAlignment().getSequenceAt(seqNo);
if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
{
continue;
}
- List<AlignedCodonFrame> seqMappings = MappingUtils
- .findMappingsForSequence(sequence, mappings);
+ seqMappings = MappingUtils
+ .findMappingsForSequenceAndOthers(sequence, mappings,
+ getCodingComplement().getAlignment().getSequences());
if (!seqMappings.isEmpty())
{
break;
}
}
- if (sequence == null)
+ 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), mappings);
+ sequence.findPosition(middleColumn), seqMappings);
return seqOffset;
}
public void expandColSelection(SequenceGroup sg, boolean wholewidth)
{
int sgs, sge;
- if (sg != null
- && (sgs = sg.getStartRes()) >= 0
+ if (sg != null && (sgs = sg.getStartRes()) >= 0
&& sg.getStartRes() <= (sge = sg.getEndRes())
- && (colSel == null || colSel.getSelected() == null || colSel
- .getSelected().size() == 0))
+ && !this.hasSelectedColumns())
{
if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
{
}
}
+ /**
+ * 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;
+ }
+
+ /**
+ * null, or currently highlighted results on this view
+ */
+ private SearchResultsI searchResults = null;
+ @Override
+ public boolean hasSearchResults()
+ {
+ return searchResults != null;
+ }
+
+ @Override
+ public void setSearchResults(SearchResultsI results)
+ {
+ searchResults = results;
+ }
+
+ @Override
+ public SearchResultsI getSearchResults()
+ {
+ return searchResults;
+ }
}
git://source.jalview.org / jalview.git / blobdiff