/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import jalview.bin.*;
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
-public class AlignViewport
+public class AlignViewport implements SelectionSource, VamsasSource
{
int startRes;
boolean ignoreGapsInConsensusCalculation = false;
- jalview.bin.JalviewLite applet;
+ public jalview.bin.JalviewLite applet;
Hashtable sequenceColours;
String sequenceSetID;
Hashtable hiddenRepSequences;
+
+ public void finalize() {
+ applet=null;
+ quality=null;
+ alignment=null;
+ colSel=null;
+ }
public AlignViewport(AlignmentI al, JalviewLite applet)
{
if (applet != null)
{
- String param = applet.getParameter("showFullId");
- if (param != null)
- {
- showJVSuffix = Boolean.valueOf(param).booleanValue();
- }
-
- param = applet.getParameter("showAnnotation");
- if (param != null)
- {
- showAnnotation = Boolean.valueOf(param).booleanValue();
- }
-
- param = applet.getParameter("showConservation");
- if (param != null)
- {
- showConservation = Boolean.valueOf(param).booleanValue();
- }
+ showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix);
- param = applet.getParameter("showQuality");
- if (param != null)
- {
- showQuality = Boolean.valueOf(param).booleanValue();
- }
+ showAnnotation = applet.getDefaultParameter("showAnnotation", showAnnotation);
+
+ showConservation = applet.getDefaultParameter("showConservation", showConservation);
+
+ showQuality = applet.getDefaultParameter("showQuality", showQuality);
- param = applet.getParameter("showConsensus");
- if (param != null)
- {
- showConsensus = Boolean.valueOf(param).booleanValue();
- }
+ showConsensus = applet.getDefaultParameter("showConsensus", showConsensus);
- param = applet.getParameter("showUnconserved");
- if (param != null)
- {
- this.showUnconserved = Boolean.valueOf(param).booleanValue();
- }
+ showUnconserved = applet.getDefaultParameter("showUnconserved", showUnconserved);
- param = applet.getParameter("upperCase");
+ String param = applet.getParameter("upperCase");
if (param != null)
{
if (param.equalsIgnoreCase("bold"))
upperCasebold = true;
}
}
- param = applet.getParameter("sortByTree");
- if (param != null)
- {
- sortByTree = Boolean.valueOf(param).booleanValue();
- }
-
+ sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
+
+ followHighlight = applet.getDefaultParameter("automaticScrolling",followHighlight);
+ followSelection = followHighlight;
+
+ showSequenceLogo = applet.getDefaultParameter("showSequenceLogo", showSequenceLogo);
+
+ showGroupConsensus = applet.getDefaultParameter("showGroupConsensus", showGroupConsensus);
+
+ showGroupConservation = applet.getDefaultParameter("showGroupConservation", showGroupConservation);
+
+ showConsensusHistogram = applet.getDefaultParameter("showConsensusHistogram", showConsensusHistogram);
+
}
if (applet != null)
AAFrequency.calculate(alignment.getSequencesArray(), 0,
alignment.getWidth(), hconsensus, true); // always calculate the
// full profile
- AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth,
- ignoreGapsInConsensusCalculation,
- includeAllConsensusSymbols);
-
+ updateAnnotation(true);
+ //AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth,
+ // ignoreGapsInConsensusCalculation,
+ // true);
+
if (globalColourScheme != null)
{
globalColourScheme.setConsensus(hconsensus);
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);
+ }
+ }
}
/**
{
if (consensus == null)
{
+ updateConsensus(null);
+ }
+ if (consensus == null)
+ {
return null;
}
StringBuffer seqs = new StringBuffer();
firePropertyChange("alignment", null, alignment.getSequences());
}
}
+ public void showSequence(int index)
+ {
+ Vector tmp = alignment.getHiddenSequences().showSequence(index,
+ hiddenRepSequences);
+ if (tmp.size() > 0)
+ {
+ if (selectionGroup == null)
+ {
+ selectionGroup = new SequenceGroup();
+ selectionGroup.setEndRes(alignment.getWidth() - 1);
+ }
+ for (int t = 0; t < tmp.size(); t++)
+ {
+ selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+ }
+ firePropertyChange("alignment", null, alignment.getSequences());
+ sendSelection();
+ }
+
+ if (alignment.getHiddenSequences().getSize() < 1)
+ {
+ hasHiddenRows = false;
+ }
+ }
public void showColumn(int col)
{
colSel.revealHiddenColumns(col);
firePropertyChange("alignment", null, alignment.getSequences());
hasHiddenRows = false;
hiddenRepSequences = null;
+ sendSelection();
}
}
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));
}
/**
* @return AlignmentView
*/
jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
+ {
+ 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)
{
- // 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 new AlignmentView(alignment, colSel, selectionGroup, hasHiddenColumns, selectedOnly, markGroups);
}
-
/**
* This method returns the visible alignment as text, as seen on the GUI, ie
* if columns are hidden they will not be returned in the result. Use this for
return sequenceSetID;
}
+ /**
+ * unique viewId for synchronizing state (e.g. with stored Jalview Project)
+ *
+ */
+ private String viewId = null;
+
+ public String getViewId()
+ {
+ if (viewId == null)
+ {
+ viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
+ }
+ return viewId;
+ }
public void alignmentChanged(AlignmentPanel ap)
{
}
}
- public boolean followHighlight = false;
+ public boolean followHighlight = true;
public boolean getFollowHighlight()
{
return followHighlight;
}
+ public boolean followSelection = true;
+
+ /**
+ * @return true if view selection should always follow the selections
+ * broadcast by other selection sources
+ */
+ public boolean getFollowSelection()
+ {
+ return followSelection;
+ }
+
+ private long sgrouphash = -1, colselhash = -1;
+
+ /**
+ * checks current SelectionGroup against record of last hash value, and
+ * updates record.
+ *
+ * @return true if SelectionGroup changed since last call
+ */
+ boolean isSelectionGroupChanged()
+ {
+ int hc = (selectionGroup == null) ? -1 : selectionGroup.hashCode();
+ if (hc != sgrouphash)
+ {
+ sgrouphash = hc;
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * checks current colsel against record of last hash value, and updates
+ * record.
+ *
+ * @return true if colsel changed since last call
+ */
+ boolean isColSelChanged()
+ {
+ int hc = (colSel == null) ? -1 : colSel.hashCode();
+ if (hc != colselhash)
+ {
+ colselhash = hc;
+ return true;
+ }
+ return false;
+ }
+ public void sendSelection()
+ {
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(applet).sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
+ }
+
+
+
+
/**
* show non-conserved residues only
*/
}
/**
- * consensus annotation includes all percentage for all symbols in column
- * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1
- * compatible)
- */
- private boolean includeAllConsensusSymbols = false;
-
- /**
- * should conservation rows be shown for groups DISABLED FOR 2.5 RELEASE (bug
- * 62446)
+ * should conservation rows be shown for groups
*/
boolean showGroupConservation = false;
/**
- * should consensus rows be shown for groups DISABLED FOR 2.5 RELEASE (bug
- * 62446)
+ * should consensus rows be shown for groups
*/
boolean showGroupConsensus = false;
/**
- * should consensus profile be rendered by default DISABLED FOR 2.5 RELEASE
- * (bug #60064 logo rendering is not AWT 1.1 compatible)
+ * should consensus profile be rendered by default
*/
public boolean showSequenceLogo = false;
/**
* @param showSequenceLogo
- * the new value public void setShowSequenceLogo(boolean
- * showSequenceLogo) { this.showSequenceLogo = 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;
+ if (consensusThread != null)
+ {
+ consensusThread.updateAnnotation();
+ }
+ }
+ this.showSequenceLogo = showSequenceLogo;
+ }
+
/**
- * @param showGroupConsensus
- * the showGroupConsensus to set
+ * @param showConsensusHistogram
+ * the showConsensusHistogram to set
*/
- public void setShowGroupConsensus(boolean showGroupConsensus)
+ public void setShowConsensusHistogram(boolean showConsensusHistogram)
{
- this.showGroupConsensus = showGroupConsensus;
+ this.showConsensusHistogram = showConsensusHistogram;
}
/**
- * @return the includeAllConsensusSymbols
+ * @return the showGroupConservation
*/
- public boolean isIncludeAllConsensusSymbols()
+ public boolean isShowGroupConservation()
{
- return false;
+ 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;
}
/**
}
}
}
-
}