import jalview.datamodel.*;
import jalview.schemes.*;
import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
-public class AlignViewport implements SelectionSource
+public class AlignViewport implements SelectionSource, VamsasSource
{
int startRes;
followHighlight = Boolean.valueOf(param).booleanValue();
followSelection = followHighlight;
}
+ if ((param=applet.getParameter("showSequenceLogo"))!=null) {
+ showSequenceLogo=Boolean.valueOf(param).booleanValue();
+ }
+ if ((param=applet.getParameter("showGroupConsensus"))!=null) {
+ showGroupConsensus=Boolean.valueOf(param).booleanValue();
+ }
+ if ((param=applet.getParameter("showGroupConservation"))!=null) {
+ showGroupConservation=Boolean.valueOf(param).booleanValue();
+ }
+ if ((param=applet.getParameter("showConsensusHistogram"))!=null) {
+ showConsensusHistogram=Boolean.valueOf(param).booleanValue();
+ }
+
}
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();
}
return false;
}
+ public void sendSelection()
+ {
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager().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;
}
/**
}
}
}
- public void sendSelection()
- {
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().sendSelection(
- new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()), this);
- }
-
-
}