import java.awt.*;
import jalview.analysis.*;
+import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.bin.*;
import jalview.datamodel.*;
import jalview.schemes.*;
import jalview.structure.SelectionSource;
import jalview.structure.VamsasSource;
+import jalview.workers.ConservationThread;
-public class AlignViewport implements AlignViewportI, SelectionSource, VamsasSource
+public class AlignViewport extends AlignmentViewport implements AlignViewportI, SelectionSource, VamsasSource
{
int startRes;
boolean autocalculateConsensus = true;
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
this);
Hashtable hiddenRepSequences;
+ AlignCalcManagerI calculator=new jalview.workers.AlignCalcManager();
+
public void finalize() {
applet=null;
quality=null;
if (!alignment.isNucleotide())
{
conservation = new AlignmentAnnotation("Conservation",
- "Conservation of total alignment less than " + ConsPercGaps
+ "Conservation of total alignment less than " + getConsPercGaps()
+ "% gaps", new Annotation[1], 0f, 11f,
AlignmentAnnotation.BAR_GRAPH);
conservation.hasText = true;
return showSequenceFeatures;
}
- class ConservationThread extends Thread
- {
- AlignmentPanel ap;
-
- public ConservationThread(AlignmentPanel ap)
- {
- this.ap = ap;
- }
-
- public void run()
- {
- try
- {
- updatingConservation = true;
-
- while (UPDATING_CONSERVATION)
- {
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(false);
- }
- Thread.sleep(200);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- UPDATING_CONSERVATION = true;
-
- int alWidth = (alignment==null) ? -1 : alignment.getWidth();
- if (alWidth < 0)
- {
- updatingConservation = false;
- UPDATING_CONSERVATION = false;
- return;
- }
-
- Conservation cons = new jalview.analysis.Conservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
- alignment.getSequences(), 0, alWidth - 1);
-
- cons.calculate();
- cons.verdict(false, ConsPercGaps);
-
- if (quality != null)
- {
- cons.findQuality();
- }
-
- char[] sequence = cons.getConsSequence().getSequence();
- float minR;
- float minG;
- float minB;
- float maxR;
- float maxG;
- float maxB;
- minR = 0.3f;
- minG = 0.0f;
- minB = 0f;
- maxR = 1.0f - minR;
- maxG = 0.9f - minG;
- maxB = 0f - minB; // scalable range for colouring both Conservation and
- // Quality
-
- float min = 0f;
- float max = 11f;
- float qmin = 0f;
- float qmax = 0f;
-
- char c;
-
- conservation.annotations = new Annotation[alWidth];
-
- if (quality != null)
- {
- quality.graphMax = cons.qualityRange[1].floatValue();
- quality.annotations = new Annotation[alWidth];
- qmin = cons.qualityRange[0].floatValue();
- qmax = cons.qualityRange[1].floatValue();
- }
-
- for (int i = 0; i < alWidth; i++)
- {
- float value = 0;
-
- c = sequence[i];
-
- if (Character.isDigit(c))
- {
- value = (int) (c - '0');
- }
- else if (c == '*')
- {
- value = 11;
- }
- else if (c == '+')
- {
- value = 10;
- }
- // TODO - refactor to use a graduatedColorScheme to calculate the
- // histogram colors.
- float vprop = value - min;
- vprop /= max;
- conservation.annotations[i] = new Annotation(String.valueOf(c),
- String.valueOf(value), ' ', value, new Color(minR
- + (maxR * vprop), minG + (maxG * vprop), minB
- + (maxB * vprop)));
-
- // Quality calc
- if (quality != null)
- {
- value = ((Double) cons.quality.elementAt(i)).floatValue();
- vprop = value - qmin;
- vprop /= qmax;
- quality.annotations[i] = new Annotation(" ",
- String.valueOf(value), ' ', value, new Color(minR
- + (maxR * vprop), minG + (maxG * vprop), minB
- + (maxB * vprop)));
- }
- }
- } catch (OutOfMemoryError error)
- {
- System.out.println("Out of memory calculating conservation!!");
- conservation = null;
- quality = null;
- System.gc();
- }
-
- UPDATING_CONSERVATION = false;
- updatingConservation = false;
-
- if (ap != null)
- {
- ap.paintAlignment(true);
- }
-
- }
- }
-
- ConservationThread conservationThread;
ConsensusThread consensusThread;
return;
}
- conservationThread = new ConservationThread(ap);
- conservationThread.start();
+ calculator.startWorker(new ConservationThread(this, ap));
}
/**
cs.setConsensus(hconsensus);
if (cs.conservationApplied())
{
- Alignment al = (Alignment) alignment;
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0,
- al.getWidth() - 1);
- c.calculate();
- c.verdict(false, ConsPercGaps);
-
- cs.setConservation(c);
+ cs.setConservation(Conservation.calculateConservation("All",
+ ResidueProperties.propHash, 3, alignment.getSequences(), 0,
+ alignment.getWidth(), false, getConsPercGaps(), false));
}
}
{
return null; // TODO: JAL-891 port to jvlite : refactor and introduce hStrucConsensus;
}
+
+ @Override
+ public AlignmentAnnotation getAlignmentQualityAnnot()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public AlignmentAnnotation getAlignmentConservationAnnotation()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public boolean isClosed()
+ {
+ System.err.println("Alignment is "+alignment==null ? "closed" : "open");
+ return alignment==null;
+ }
+
+ @Override
+ public AlignCalcManagerI getCalcManager()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff