/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
import jalview.schemes.*;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class AlignViewport implements SelectionSource
+public class AlignViewport implements SelectionSource, VamsasSource
{
private static final int RIGHT_JUSTIFY = 1;
showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED",
false);
sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false);
+ followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS",
+ true);
}
/**
private boolean shownpfeats;
/**
- * consensus annotation includes all percentage for all symbols in column
- */
- private boolean includeAllConsensusSymbols = true;
-
- /**
* trigger update of conservation annotation
*/
public void updateConservation(final AlignmentPanel ap)
try
{
- int aWidth = (alignment != null) ? alignment.getWidth() : 0; // null
+ int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null
// pointer
// possibility
// here.
- if (aWidth < 0)
+ if (aWidth <= 0)
{
+ updatingConsensus = false;
+ UPDATING_CONSENSUS = false;
return;
}
consensus.annotations = new Annotation[aWidth];
hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
- .getWidth(), hconsensus, includeAllConsensusSymbols);
- AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth,
- ignoreGapsInConsensusCalculation,
- includeAllConsensusSymbols);
+ AAFrequency.calculate(alignment.getSequencesArray(), 0,
+ alignment.getWidth(), hconsensus, true);
+ updateAnnotation(true);
if (globalColourScheme != null)
{
ap.paintAlignment(true);
}
}
+
+ /**
+ * update the consensus annotation from the sequence profile data using
+ * current visualization settings.
+ */
+ public void updateAnnotation()
+ {
+ updateAnnotation(false);
+ }
+
+ protected void updateAnnotation(boolean immediate)
+ {
+ // TODO: make calls thread-safe, so if another thread calls this method,
+ // it will either return or wait until one calculation is finished.
+ if (immediate
+ || (!updatingConsensus && consensus != null && hconsensus != null))
+ {
+ AAFrequency.completeConsensus(consensus, hconsensus, 0,
+ hconsensus.length, ignoreGapsInConsensusCalculation,
+ showSequenceLogo);
+ }
+ }
}
/**
public jalview.datamodel.CigarArray getViewAsCigars(
boolean selectedRegionOnly)
{
- CigarArray selection = null;
- SequenceI[] seqs = null;
- int i, iSize;
- int start = 0, end = 0;
- if (selectedRegionOnly && selectionGroup != null)
- {
- iSize = selectionGroup.getSize();
- seqs = selectionGroup.getSequencesInOrder(alignment);
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes(); // inclusive for start and end in
- // SeqCigar constructor
- }
- else
- {
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth() - 1;
- }
- SeqCigar[] selseqs = new SeqCigar[iSize];
- for (i = 0; i < iSize; i++)
- {
- selseqs[i] = new SeqCigar(seqs[i], start, end);
- }
- selection = new CigarArray(selseqs);
- // now construct the CigarArray operations
- if (hasHiddenColumns)
- {
- Vector regions = colSel.getHiddenColumns();
- int[] region;
- int hideStart, hideEnd;
- int last = start;
- for (int j = 0; last < end & j < regions.size(); j++)
- {
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
- // edit hidden regions to selection range
- if (hideStart < last)
- {
- if (hideEnd > last)
- {
- hideStart = last;
- }
- else
- {
- continue;
- }
- }
-
- if (hideStart > end)
- {
- break;
- }
-
- if (hideEnd > end)
- {
- hideEnd = end;
- }
-
- if (hideStart > hideEnd)
- {
- break;
- }
- /**
- * form operations...
- */
- if (last < hideStart)
- {
- selection.addOperation(CigarArray.M, hideStart - last);
- }
- selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart);
- last = hideEnd + 1;
- }
- // Final match if necessary.
- if (last < end)
- {
- selection.addOperation(CigarArray.M, end - last + 1);
- }
- }
- else
- {
- selection.addOperation(CigarArray.M, end - start + 1);
- }
- return selection;
+ return new jalview.datamodel.CigarArray(alignment, (hasHiddenColumns ? colSel : null), (selectedRegionOnly ? selectionGroup : null));
}
/**
* boolean true to just return the selected view
* @return AlignmentView
*/
- jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
+ public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
{
- // JBPNote:
- // this is here because the AlignmentView constructor modifies the
- // CigarArray
- // object. Refactoring of Cigar and alignment view representation should
- // be done to remove redundancy.
- CigarArray aligview = getViewAsCigars(selectedOnly);
- if (aligview != null)
- {
- return new AlignmentView(aligview,
- (selectedOnly && selectionGroup != null) ? selectionGroup
- .getStartRes() : 0);
- }
- return null;
+ return getAlignmentView(selectedOnly, false);
+ }
+
+ /**
+ * return a compact representation of the current alignment selection to pass
+ * to an analysis function
+ *
+ * @param selectedOnly
+ * boolean true to just return the selected view
+ * @param markGroups
+ * boolean true to annotate the alignment view with groups on the alignment (and intersecting with selected region if selectedOnly is true)
+ * @return AlignmentView
+ */
+ public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups)
+ {
+ return new AlignmentView(alignment, colSel, selectionGroup, hasHiddenColumns, selectedOnly, markGroups);
}
/**
{
Alignment al = (Alignment) alignment;
Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0, al
- .getWidth() - 1);
+ ResidueProperties.propHash, 3, al.getSequences(), 0,
+ al.getWidth() - 1);
c.calculate();
c.verdict(false, ConsPercGaps);
SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
{
- ((ClustalxColourScheme) sg.cs).resetClustalX(sg
- .getSequences(hiddenRepSequences), sg.getWidth());
+ ((ClustalxColourScheme) sg.cs).resetClustalX(
+ sg.getSequences(hiddenRepSequences), sg.getWidth());
}
sg.recalcConservation();
}
*/
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;
+ if (consensusThread != null)
+ {
+ consensusThread.updateAnnotation();
+ }
+ }
this.showSequenceLogo = showSequenceLogo;
}
}
/**
- * @return the includeAllConsensusSymbols
- */
- public boolean isIncludeAllConsensusSymbols()
- {
- return includeAllConsensusSymbols;
- }
-
- /**
- * @param includeAllConsensusSymbols
- * the includeAllConsensusSymbols to set
- */
- public void setIncludeAllConsensusSymbols(
- boolean includeAllConsensusSymbols)
- {
- this.includeAllConsensusSymbols = includeAllConsensusSymbols;
- }
-
- /**
*
* @return flag to indicate if the consensus histogram should be rendered by
* default
git://source.jalview.org / jalview.git / blobdiff