/*
- * 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, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import java.awt.*;
import jalview.analysis.*;
+import jalview.api.AlignViewportI;
import jalview.bin.*;
import jalview.datamodel.*;
import jalview.schemes.*;
import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
-public class AlignViewport implements SelectionSource
+public class AlignViewport implements AlignViewportI, 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();
- }
+ showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix);
- param = applet.getParameter("showAnnotation");
- if (param != null)
- {
- showAnnotation = Boolean.valueOf(param).booleanValue();
- }
-
- param = applet.getParameter("showConservation");
- if (param != null)
- {
- showConservation = Boolean.valueOf(param).booleanValue();
- }
-
- 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);
+ normaliseSequenceLogo = applet.getDefaultParameter("normaliseSequenceLogo", normaliseSequenceLogo);
+
+ showGroupConsensus = applet.getDefaultParameter("showGroupConsensus", showGroupConsensus);
+
+ showGroupConservation = applet.getDefaultParameter("showGroupConservation", showGroupConservation);
+
+ showConsensusHistogram = applet.getDefaultParameter("showConsensusHistogram", showConsensusHistogram);
+
}
if (applet != null)
ConservationThread conservationThread;
ConsensusThread consensusThread;
+
+// StrucConsensusThread strucConsensusThread;
+
boolean consUpdateNeeded = false;
static boolean UPDATING_CONSENSUS = false;
+ static boolean UPDATING_STRUC_CONSENSUS = false;
+
static boolean UPDATING_CONSERVATION = false;
boolean updatingConsensus = false;
+ boolean updatingStrucConsensus = false;
+
boolean updatingConservation = false;
/**
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();
}
}
- public boolean followHighlight = false;
+ public boolean followHighlight = true;
public boolean getFollowHighlight()
{
}
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;
+ /**
+ * should consensus profile be rendered normalised to row height
+ */
+ public boolean normaliseSequenceLogo = false;
/**
* should consensus histograms be rendered by default
/**
* @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;
}
/**
}
}
}
- public void sendSelection()
+
+ @Override
+ public boolean hasHiddenColumns()
{
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().sendSelection(
- new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()), this);
+ return hasHiddenColumns;
+ }
+
+ public boolean isNormaliseSequenceLogo()
+ {
+ return normaliseSequenceLogo;
+ }
+
+ public void setNormaliseSequenceLogo(boolean state)
+ {
+ normaliseSequenceLogo = state;
+ }
+
+ public boolean isCalcInProgress()
+ {
+ // TODO generalise to iterate over all calculators associated with av
+ return updatingConsensus || updatingConservation || updatingStrucConsensus;
+ }
+
+ public boolean isCalculationInProgress(
+ AlignmentAnnotation alignmentAnnotation)
+ {
+ if (!alignmentAnnotation.autoCalculated)
+ return false;
+ if ((updatingConsensus && consensus==alignmentAnnotation)
+ || (updatingConservation && (conservation==alignmentAnnotation || quality==alignmentAnnotation))
+ // || (updatingStrucConsensus && strucConsensus==alignmentAnnotation)
+ )
+ {
+ return true;
+ }
+ return false;
}
+ /**
+ *
+ * @return true if alignment characters should be displayed
+ */
+ public boolean isValidCharWidth()
+ {
+ return validCharWidth;
+ }
+ @Override
+ public Hashtable[] getSequenceConsensusHash()
+ {
+ return hconsensus;
+ }
+
+ @Override
+ public Hashtable[] getRnaStructureConsensusHash()
+ {
+ return null; // TODO: JAL-891 port to jvlite : refactor and introduce hStrucConsensus;
+ }
}
git://source.jalview.org / jalview.git / blobdiff