import jalview.bin.*;
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+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;
{
sortByTree = Boolean.valueOf(param).booleanValue();
}
-
+ param = applet.getParameter("automaticScrolling");
+ if (param!=null) {
+ 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();
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();
}
}
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)
{
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().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 showConsensusHistogram
+ * the showConsensusHistogram to set
*/
+ public void setShowConsensusHistogram(boolean showConsensusHistogram)
+ {
+ this.showConsensusHistogram = showConsensusHistogram;
+ }
+
/**
- * @param showGroupConsensus
- * the showGroupConsensus to set
+ * @return the showGroupConservation
*/
- public void setShowGroupConsensus(boolean showGroupConsensus)
+ public boolean isShowGroupConservation()
{
- this.showGroupConsensus = showGroupConsensus;
+ return showGroupConservation;
}
/**
- * @return the includeAllConsensusSymbols
+ * @param showGroupConservation
+ * the showGroupConservation to set
*/
- public boolean isIncludeAllConsensusSymbols()
+ public void setShowGroupConservation(boolean showGroupConservation)
{
- return false;
+ 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;
}
/**
}
}
}
-
}
git://source.jalview.org / jalview.git / blobdiff