import jalview.datamodel.Annotation;
import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
+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.structure.CommandListener;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.util.Comparison;
import jalview.util.MapList;
import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
import jalview.workers.ComplementConsensusThread;
public abstract class AlignmentViewport implements AlignViewportI,
CommandListener, VamsasSource
{
+ final protected ViewportRanges ranges;
+
protected ViewStyleI viewStyle = new ViewStyle();
/**
FeaturesDisplayedI featuresDisplayed = null;
- protected Deque<CommandI> historyList = new ArrayDeque<CommandI>();
+ protected Deque<CommandI> historyList = new ArrayDeque<>();
+
+ protected Deque<CommandI> redoList = new ArrayDeque<>();
+
+ /**
+ * alignment displayed in the viewport. Please use get/setter
+ */
+ protected AlignmentI alignment;
- protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
+ public AlignmentViewport(AlignmentI al)
+ {
+ setAlignment(al);
+ ranges = new ViewportRanges(al);
+ }
/**
* @param name
public void setWrapAlignment(boolean state)
{
viewStyle.setWrapAlignment(state);
+ ranges.setWrappedMode(state);
}
/**
viewStyle.setSeqNameItalics(default1);
}
- /**
- * alignment displayed in the viewport. Please use get/setter
- */
- protected AlignmentI alignment;
+
@Override
public AlignmentI getAlignment()
protected boolean ignoreGapsInConsensusCalculation = false;
- protected ColourSchemeI globalColourScheme = null;
+ protected ResidueShaderI residueShading = new ResidueShader();
@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)
{
- recalc = getConservationSelected();
- if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
- {
- recalc = true;
- cs.setThreshold(viewStyle.getThreshold(),
- ignoreGapsInConsensusCalculation);
- }
- else
+ if (getConservationSelected())
{
- cs.setThreshold(0, ignoreGapsInConsensusCalculation);
+ residueShading.setConservation(hconservation);
}
- if (recalc)
- {
- cs.setConsensus(hconsensus);
- cs.setConservation(hconservation);
- }
- cs.setConservationApplied(getConservationSelected());
- 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
- {
- sg.cs.setThreshold(0, isIgnoreGapsConsensus());
- }
-
- if (getConservationSelected())
+ /*
+ * retain any colour thresholds per group while
+ * changing choice of colour scheme (JAL-2386)
+ */
+ sg.setColourScheme(cs);
+ if (cs != null)
{
- 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;
groupConservation = null;
hconsensus = null;
hcomplementConsensus = null;
- // TODO removed listeners from changeSupport?
+ // colour scheme may hold reference to consensus
+ residueShading = null;
+ // TODO remove listeners from changeSupport?
changeSupport = null;
setAlignment(null);
}
}
/**
- * 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)
+ public void setHiddenColumns(HiddenColumns hidden)
{
- this.colSel = colsel;
+ this.alignment.setHiddenColumns(hidden);
}
@Override
@Override
public boolean hasHiddenColumns()
{
- return colSel != null && colSel.hasHiddenColumns();
+ return alignment.getHiddenColumns() != null
+ && alignment.getHiddenColumns().hasHiddenColumns();
}
public void updateHiddenColumns()
if (ap != null)
{
updateConsensus(ap);
- if (globalColourScheme != null)
+ if (residueShading != null)
{
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+ residueShading.setThreshold(residueShading.getThreshold(),
ignoreGapsInConsensusCalculation);
}
}
protected boolean showConsensus = true;
- private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
+ protected boolean showOccupancy = true;
+
+ private Map<SequenceI, Color> sequenceColours = new HashMap<>();
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
*
return;
}
- colSel.hideSelectedColumns();
+ colSel.hideSelectedColumns(alignment);
setSelectionGroup(null);
isColSelChanged(true);
}
{
if (start == end)
{
- colSel.hideColumns(start);
+ colSel.hideSelectedColumns(start, alignment.getHiddenColumns());
}
else
{
- colSel.hideColumns(start, end);
+ alignment.getHiddenColumns().hideColumns(start, end);
}
isColSelChanged(true);
}
public void showColumn(int col)
{
- colSel.revealHiddenColumns(col);
+ alignment.getHiddenColumns().revealHiddenColumns(col, colSel);
isColSelChanged(true);
}
public void showAllHiddenColumns()
{
- colSel.revealAllHiddenColumns();
+ alignment.getHiddenColumns().revealAllHiddenColumns(colSel);
isColSelChanged(true);
}
// common hide/show seq stuff
public void showAllHiddenSeqs()
{
+ int startSeq = ranges.getStartSeq();
+ int endSeq = ranges.getEndSeq();
+
if (alignment.getHiddenSequences().getSize() > 0)
{
if (selectionGroup == null)
hiddenRepSequences = null;
+ ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
+
firePropertyChange("alignment", null, alignment.getSequences());
// used to set hasHiddenRows/hiddenRepSequences here, after the property
// changed event
public void showSequence(int index)
{
+ int startSeq = ranges.getStartSeq();
+ int endSeq = ranges.getEndSeq();
+
List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
index, hiddenRepSequences);
if (tmp.size() > 0)
selectionGroup.addSequence(seq, false);
setSequenceAnnotationsVisible(seq, true);
}
+
+ ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
+
firePropertyChange("alignment", null, alignment.getSequences());
sendSelection();
}
public void hideSequence(SequenceI[] seq)
{
+ /*
+ * cache offset to first visible sequence
+ */
+ int startSeq = ranges.getStartSeq();
+
if (seq != null)
{
for (int i = 0; i < seq.length; i++)
alignment.getHiddenSequences().hideSequence(seq[i]);
setSequenceAnnotationsVisible(seq[i], false);
}
+ ranges.setStartSeq(startSeq);
firePropertyChange("alignment", null, alignment.getSequences());
}
}
if (hiddenRepSequences == null)
{
- hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+ hiddenRepSequences = new Hashtable<>();
}
hiddenRepSequences.put(repSequence, sg);
@Override
public void invertColumnSelection()
{
- colSel.invertColumnSelection(0, alignment.getWidth());
+ colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
}
@Override
@Override
public CigarArray getViewAsCigars(boolean selectedRegionOnly)
{
- return new CigarArray(alignment, colSel,
+ return new CigarArray(alignment, alignment.getHiddenColumns(),
(selectedRegionOnly ? selectionGroup : null));
}
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly, boolean markGroups)
{
- return new AlignmentView(alignment, colSel, selectionGroup,
- colSel != null && colSel.hasHiddenColumns(), selectedOnly,
+ return new AlignmentView(alignment, alignment.getHiddenColumns(),
+ selectionGroup, alignment.getHiddenColumns() != null
+ && alignment.getHiddenColumns().hasHiddenColumns(),
+ selectedOnly,
markGroups);
}
}
selection = new String[iSize];
- if (colSel != null && colSel.hasHiddenColumns())
+ if (alignment.getHiddenColumns() != null
+ && alignment.getHiddenColumns().hasHiddenColumns())
{
- selection = colSel.getVisibleSequenceStrings(start, end, seqs);
+ selection = alignment.getHiddenColumns().getVisibleSequenceStrings(
+ start, end, seqs);
}
else
{
@Override
public List<int[]> getVisibleRegionBoundaries(int min, int max)
{
- ArrayList<int[]> regions = new ArrayList<int[]>();
+ ArrayList<int[]> regions = new ArrayList<>();
int start = min;
int end = max;
do
{
- if (colSel != null && colSel.hasHiddenColumns())
+ HiddenColumns hidden = alignment.getHiddenColumns();
+ if (hidden != null && hidden.hasHiddenColumns())
{
if (start == 0)
{
- start = colSel.adjustForHiddenColumns(start);
+ start = hidden.adjustForHiddenColumns(start);
}
- end = colSel.getHiddenBoundaryRight(start);
+ end = hidden.getHiddenBoundaryRight(start);
if (start == end)
{
end = max;
regions.add(new int[] { start, end });
- if (colSel != null && colSel.hasHiddenColumns())
+ if (hidden != null && hidden.hasHiddenColumns())
{
- start = colSel.adjustForHiddenColumns(end);
- start = colSel.getHiddenBoundaryLeft(start) + 1;
+ start = hidden.adjustForHiddenColumns(end);
+ start = hidden.getHiddenBoundaryLeft(start) + 1;
}
} while (end < max);
public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
boolean selectedOnly)
{
- ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
+ ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
AlignmentAnnotation[] aa;
if ((aa = alignment.getAlignmentAnnotation()) != null)
{
AlignmentAnnotation clone = new AlignmentAnnotation(annot);
if (selectedOnly && selectionGroup != null)
{
- colSel.makeVisibleAnnotation(selectionGroup.getStartRes(),
+ alignment.getHiddenColumns().makeVisibleAnnotation(
+ selectionGroup.getStartRes(),
selectionGroup.getEndRes(), clone);
}
else
{
- colSel.makeVisibleAnnotation(clone);
+ alignment.getHiddenColumns().makeVisibleAnnotation(clone);
}
ala.add(clone);
}
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", 3,
+ rs.setConservation(Conservation.calculateConservation("All",
alignment.getSequences(), 0, alignment.getWidth(), false,
getConsPercGaps(), false));
}
{
initRNAStructure();
}
- consensus = new AlignmentAnnotation("Consensus", "PID",
+ consensus = new AlignmentAnnotation("Consensus",
+ MessageManager.getString("label.consensus_descr"),
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())
{
if (doConsensus)
{
complementConsensus = new AlignmentAnnotation("cDNA Consensus",
- "PID for cDNA", new Annotation[1], 0f, 100f,
+ MessageManager
+ .getString("label.complement_consensus_descr"),
+ 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",
+ MessageManager.getString("label.occupancy_descr"),
+ 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)
if (conservation == null)
{
conservation = new AlignmentAnnotation("Conservation",
- "Conservation of total alignment less than "
- + getConsPercGaps() + "% gaps", new Annotation[1],
+ MessageManager.formatMessage("label.conservation_descr",
+ getConsPercGaps()), new Annotation[1],
0f, 11f, AlignmentAnnotation.BAR_GRAPH);
conservation.hasText = true;
conservation.autoCalculated = true;
if (quality == null)
{
quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
+ MessageManager.getString("label.quality_descr"),
new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
quality.hasText = true;
quality.autoCalculated = true;
{
if (alignment.hasRNAStructure() && strucConsensus == null)
{
- strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+ strucConsensus = new AlignmentAnnotation("StrucConsensus",
+ MessageManager.getString("label.strucconsensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
strucConsensus.hasText = true;
strucConsensus.autoCalculated = true;
// intersect alignment annotation with alignment groups
AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
- List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
+ List<SequenceGroup> oldrfs = new ArrayList<>();
if (aan != null)
{
for (int an = 0; an < aan.length; an++)
public void setViewStyle(ViewStyleI settingsForView)
{
viewStyle = new ViewStyle(settingsForView);
+ if (residueShading != null)
+ {
+ residueShading.setConservationApplied(settingsForView
+ .isConservationColourSelected());
+ }
}
@Override
viewStyle.setScaleProteinAsCdna(b);
}
+ @Override
+ public boolean isProteinFontAsCdna()
+ {
+ return viewStyle.isProteinFontAsCdna();
+ }
+
+ @Override
+ public void setProteinFontAsCdna(boolean b)
+ {
+ viewStyle.setProteinFontAsCdna(b);
+ }
+
/**
* @return true if view should scroll to show the highlighted region of a
* sequence
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()
+ public ViewportRanges getRanges()
{
- return endSeq;
+ return ranges;
}
/**
* 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();
*/
int lastSeq = alignment.getHeight() - 1;
List<AlignedCodonFrame> seqMappings = null;
- for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+ for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
{
sequence = getAlignment().getSequenceAt(seqNo);
if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
selectionIsDefinedGroup = gps.contains(selectionGroup);
}
}
- return selectionGroup.getContext() == alignment
- || selectionIsDefinedGroup;
+ return selectionGroup.isDefined() || 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;
+ }
+
+ /**
+ * get the consensus sequence as displayed under the PID consensus annotation
+ * row.
+ *
+ * @return consensus sequence as a new sequence object
+ */
+ public SequenceI getConsensusSeq()
+ {
+ if (consensus == null)
+ {
+ updateConsensus(null);
+ }
+ if (consensus == null)
+ {
+ return null;
+ }
+ StringBuffer seqs = new StringBuffer();
+ for (int i = 0; i < consensus.annotations.length; i++)
+ {
+ Annotation annotation = consensus.annotations[i];
+ if (annotation != null)
+ {
+ String description = annotation.description;
+ if (description != null && description.startsWith("["))
+ {
+ // consensus is a tie - just pick the first one
+ seqs.append(description.charAt(1));
+ }
+ else
+ {
+ seqs.append(annotation.displayCharacter);
+ }
+ }
+ }
+
+ SequenceI sq = new Sequence("Consensus", seqs.toString());
+ sq.setDescription("Percentage Identity Consensus "
+ + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+ return sq;
}
}
git://source.jalview.org / jalview.git / blobdiff