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JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first...
[jalview.git]
/
src
/
jalview
/
ws
/
jws2
/
AbstractJabaCalcWorker.java
diff --git
a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
index
f2795d2
..
b972ab8
100644
(file)
--- a/
src/jalview/ws/jws2/AbstractJabaCalcWorker.java
+++ b/
src/jalview/ws/jws2/AbstractJabaCalcWorker.java
@@
-78,8
+78,10
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
getCalcId(),
new AAConSettings(true, service, this.preset,
((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
getCalcId(),
new AAConSettings(true, service, this.preset,
- (arguments != null) ? JabaParamStore
- .getJwsArgsfromJaba(arguments) : null), true);
+ (arguments != null)
+ ? JabaParamStore.getJwsArgsfromJaba(arguments)
+ : null),
+ true);
}
}
}
}
@@
-164,8
+166,8
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
super(alignViewport, alignPanel);
}
super(alignViewport, alignPanel);
}
- public AbstractJabaCalcWorker(Jws2Instance service,
- AlignFrame alignFrame, WsParamSetI preset, List<Argument> paramset)
+ public AbstractJabaCalcWorker(Jws2Instance service, AlignFrame alignFrame,
+ WsParamSetI preset, List<Argument> paramset)
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
this.guiProgress = alignFrame;
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
this.guiProgress = alignFrame;
@@
-322,9
+324,8
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
}
if (collectAnnotationResultsFor(rslt))
{
}
if (collectAnnotationResultsFor(rslt))
{
- jalview.bin.Cache.log
- .debug("Updating result annotation from Job " + rslt
- + " at " + service.getUri());
+ jalview.bin.Cache.log.debug("Updating result annotation from Job "
+ + rslt + " at " + service.getUri());
updateResultAnnotation(true);
ap.adjustAnnotationHeight();
}
updateResultAnnotation(true);
ap.adjustAnnotationHeight();
}
@@
-334,8
+335,8
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
catch (JobSubmissionException x)
{
catch (JobSubmissionException x)
{
- System.err.println("submission error with " + getServiceActionText()
- + " :");
+ System.err.println(
+ "submission error with " + getServiceActionText() + " :");
x.printStackTrace();
calcMan.disableWorker(this);
} catch (ResultNotAvailableException x)
x.printStackTrace();
calcMan.disableWorker(this);
} catch (ResultNotAvailableException x)
@@
-371,7
+372,8
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
{
guiProgress.setProgressBar("", progressId);
}
{
guiProgress.setProgressBar("", progressId);
}
- ap.paintAlignment(true);
+ // TODO: may not need to paintAlignment again !
+ ap.paintAlignment(false, false);
}
if (msg.length() > 0)
{
}
if (msg.length() > 0)
{
@@
-444,8
+446,9
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
AnnotatedCollectionI inputSeqs)
{
if (alignment == null || alignment.getWidth() <= 0
AnnotatedCollectionI inputSeqs)
{
if (alignment == null || alignment.getWidth() <= 0
- || alignment.getSequences() == null || alignment.isNucleotide() ? !nucleotidesAllowed
- : !proteinAllowed)
+ || alignment.getSequences() == null || alignment.isNucleotide()
+ ? !nucleotidesAllowed
+ : !proteinAllowed)
{
return null;
}
{
return null;
}
@@
-470,9
+473,10
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
for (SequenceI sq : (inputSeqs.getSequences()))
{
for (SequenceI sq : (inputSeqs.getSequences()))
{
- if (bySequence ? sq.findPosition(end + 1)
- - sq.findPosition(start + 1) > minlen - 1 : sq.getEnd()
- - sq.getStart() > minlen - 1)
+ if (bySequence
+ ? sq.findPosition(end + 1)
+ - sq.findPosition(start + 1) > minlen - 1
+ : sq.getEnd() - sq.getStart() > minlen - 1)
{
String newname = SeqsetUtils.unique_name(seqs.size() + 1);
// make new input sequence with or without gaps
{
String newname = SeqsetUtils.unique_name(seqs.size() + 1);
// make new input sequence with or without gaps
@@
-537,8
+541,8
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
FastaSequence sq = seqs.get(p);
int l = sq.getSequence().length();
// strip gapped columns
FastaSequence sq = seqs.get(p);
int l = sq.getSequence().length();
// strip gapped columns
- char[] padded = new char[realw], orig = sq.getSequence()
- .toCharArray();
+ char[] padded = new char[realw],
+ orig = sq.getSequence().toCharArray();
for (int i = 0, pp = 0; i < realw; pp++)
{
if (gapMap[pp])
for (int i = 0, pp = 0; i < realw; pp++)
{
if (gapMap[pp])
@@
-579,7
+583,7
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
protected boolean checkDone()
{
calcMan.notifyStart(this);
protected boolean checkDone()
{
calcMan.notifyStart(this);
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
while (!calcMan.notifyWorking(this))
{
if (calcMan.isWorking(this))
while (!calcMan.notifyWorking(this))
{
if (calcMan.isWorking(this))
@@
-590,7
+594,7
@@
public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
{
if (ap != null)
{
{
if (ap != null)
{
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
Thread.sleep(200);
}
Thread.sleep(200);