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showQuality may be updated during archive file load
author
amwaterhouse
<Andrew Waterhouse>
Thu, 12 Oct 2006 17:15:45 +0000
(17:15 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Thu, 12 Oct 2006 17:15:45 +0000
(17:15 +0000)
src/jalview/gui/AlignViewport.java
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diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
7d02e14
..
9a7df7f
100755
(executable)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-212,6
+212,7
@@
public class AlignViewport
0f,
11f,
AlignmentAnnotation.BAR_GRAPH);
0f,
11f,
AlignmentAnnotation.BAR_GRAPH);
+ quality.hasText = true;
alignment.addAnnotation(quality);
}
alignment.addAnnotation(quality);
}
@@
-278,8
+279,6
@@
public class AlignViewport
{
try
{
{
try
{
- long t = System.currentTimeMillis();
-
int alWidth = alignment.getWidth();
Conservation cons = new jalview.analysis.Conservation("All",
int alWidth = alignment.getWidth();
Conservation cons = new jalview.analysis.Conservation("All",
@@
-289,14
+288,11
@@
public class AlignViewport
cons.calculate();
cons.verdict(false, ConsPercGaps);
cons.calculate();
cons.verdict(false, ConsPercGaps);
- if (showQuality)
+ if (quality!=null)
{
cons.findQuality();
}
{
cons.findQuality();
}
- System.out.println("Conservation took " + (System.currentTimeMillis() - t) +
- "ms");
-
String sequence = cons.getConsSequence().getSequence();
float minR;
String sequence = cons.getConsSequence().getSequence();
float minR;
@@
-321,8
+317,9
@@
public class AlignViewport
conservation.annotations = new Annotation[alWidth];
conservation.annotations = new Annotation[alWidth];
- if (showQuality)
+ if (quality!=null)
{
{
+ quality.graphMax = cons.qualityRange[1].floatValue();
quality.annotations = new Annotation[alWidth];
qmin = cons.qualityRange[0].floatValue();
qmax = cons.qualityRange[1].floatValue();
quality.annotations = new Annotation[alWidth];
qmin = cons.qualityRange[0].floatValue();
qmax = cons.qualityRange[1].floatValue();
@@
-351,7
+348,7
@@
public class AlignViewport
minB + (maxB * vprop)));
// Quality calc
minB + (maxB * vprop)));
// Quality calc
- if (showQuality)
+ if (quality!=null)
{
value = ( (Double) cons.quality.get(i)).floatValue();
vprop = value - qmin;
{
value = ( (Double) cons.quality.get(i)).floatValue();
vprop = value - qmin;
@@
-363,11
+360,6
@@
public class AlignViewport
minB + (maxB * vprop)));
}
}
minB + (maxB * vprop)));
}
}
-
- if (quality != null)
- {
- quality.graphMax = cons.qualityRange[1].floatValue();
- }
}
catch (OutOfMemoryError error)
{
}
catch (OutOfMemoryError error)
{
@@
-466,16
+458,13
@@
public class AlignViewport
consensus.annotations = null;
consensus.annotations = new Annotation[aWidth];
consensus.annotations = null;
consensus.annotations = new Annotation[aWidth];
- long t = System.currentTimeMillis();
+
hconsensus = new Hashtable[aWidth];
AAFrequency.calculate(alignment.getSequencesArray(),
0,
alignment.getWidth(),
hconsensus);
hconsensus = new Hashtable[aWidth];
AAFrequency.calculate(alignment.getSequencesArray(),
0,
alignment.getWidth(),
hconsensus);
- System.out.println("Consensus took " +
- (System.currentTimeMillis() - t) + "ms");
-
for (int i = 0; i < aWidth; i++)
{
float value = 0;
for (int i = 0; i < aWidth; i++)
{
float value = 0;