-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
+ * 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.
+ *
+ * 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/>.
*/
package jalview.gui;
*
*/
private AlignViewport alignViewport;
+
AlignmentPanel ap;
public ConservationThread(AlignViewport alignViewport, AlignmentPanel ap)
AlignViewport.UPDATING_CONSERVATION = true;
- int alWidth = this.alignViewport.alignment.getWidth();
- if (alWidth < 0)
+ int alWidth;
+
+ if (alignViewport==null || alignViewport.alignment==null || (alWidth=alignViewport.alignment.getWidth())< 0)
{
+ this.alignViewport.updatingConservation = false;
+ AlignViewport.UPDATING_CONSERVATION = false;
return;
}
Conservation cons = new jalview.analysis.Conservation("All",
- jalview.schemes.ResidueProperties.propHash, 3, this.alignViewport.alignment
- .getSequences(), 0, alWidth - 1);
+ jalview.schemes.ResidueProperties.propHash, 3,
+ this.alignViewport.alignment.getSequences(), 0, alWidth - 1);
cons.calculate();
cons.verdict(false, this.alignViewport.ConsPercGaps);
{
cons.findQuality();
}
- cons.completeAnnotations(alignViewport.conservation,alignViewport.quality, 0, alWidth);
+ cons.completeAnnotations(alignViewport.conservation,
+ alignViewport.quality, 0, alWidth);
} catch (OutOfMemoryError error)
{
new OOMWarning("calculating conservation", error);
}
}
-}
\ No newline at end of file
+}