From eee8dfa05eeea5b7cc295ba020647842502efe63 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 10 Jul 2015 06:17:34 +0100 Subject: [PATCH] JAL-1807 explicit imports (jalview.workers) --- src/jalview/workers/ConservationThread.java | 3 ++- src/jalview/workers/StrucConsensusThread.java | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java index 236bccf..32e13f2 100644 --- a/src/jalview/workers/ConservationThread.java +++ b/src/jalview/workers/ConservationThread.java @@ -26,6 +26,7 @@ import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.schemes.ResidueProperties; import java.util.ArrayList; import java.util.List; @@ -97,7 +98,7 @@ public class ConservationThread extends AlignCalcWorker implements 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) diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java index 4471b6e..c64521f 100644 --- a/src/jalview/workers/StrucConsensusThread.java +++ b/src/jalview/workers/StrucConsensusThread.java @@ -116,7 +116,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements { final SequenceI[] arr = alignment.getSequencesArray(); nseq = arr.length; - jalview.analysis.StructureFrequency.calculate(arr, 0, + StructureFrequency.calculate(arr, 0, alignment.getWidth(), hStrucConsensus, true, rnaStruc); } catch (ArrayIndexOutOfBoundsException x) { -- 1.7.10.2