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Merge branch 'j2s/develop-toc' into j2s/develop
[jalview.git]
/
src
/
jalview
/
workers
/
ConservationThread.java
diff --git
a/src/jalview/workers/ConservationThread.java
b/src/jalview/workers/ConservationThread.java
index
a8bc268
..
32e13f2
100644
(file)
--- a/
src/jalview/workers/ConservationThread.java
+++ b/
src/jalview/workers/ConservationThread.java
@@
-1,32
+1,35
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.workers;
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.workers;
-import java.util.ArrayList;
-import java.util.List;
-
import jalview.analysis.Conservation;
import jalview.api.AlignCalcWorkerI;
import jalview.analysis.Conservation;
import jalview.api.AlignCalcWorkerI;
-import jalview.api.AlignmentViewPanel;
import jalview.api.AlignViewportI;
import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.schemes.ResidueProperties;
+
+import java.util.ArrayList;
+import java.util.List;
public class ConservationThread extends AlignCalcWorker implements
AlignCalcWorkerI
public class ConservationThread extends AlignCalcWorker implements
AlignCalcWorkerI
@@
-72,6
+75,7
@@
public class ConservationThread extends AlignCalcWorker implements
if (alignViewport.isClosed())
{
abortAndDestroy();
if (alignViewport.isClosed())
{
abortAndDestroy();
+ return;
}
List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
AlignmentI alignment = alignViewport.getAlignment();
}
List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
AlignmentI alignment = alignViewport.getAlignment();
@@
-94,7
+98,7
@@
public class ConservationThread extends AlignCalcWorker implements
try
{
cons = Conservation.calculateConservation("All",
try
{
cons = Conservation.calculateConservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
+ ResidueProperties.propHash, 3,
alignment.getSequences(), 0, alWidth - 1, false,
ConsPercGaps, quality != null);
} catch (IndexOutOfBoundsException x)
alignment.getSequences(), 0, alWidth - 1, false,
ConsPercGaps, quality != null);
} catch (IndexOutOfBoundsException x)