X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=4116c3b49aa94211708088b8ed4258d8ff6eeef9;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=536f76722459a14a585174bbd7dd333f0d4e454d;hpb=d4ec118f86b5c9dee801e743c46aaacc7bb521d1;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 536f767..4116c3b 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -605,10 +605,30 @@ public abstract class AlignmentViewport protected ColumnSelection colSel = new ColumnSelection(); - public boolean autoCalculateConsensus = true; + protected boolean autoCalculateConsensusAndConservation = true; + + public boolean getAutoCalculateConsensusAndConservation() + { // BH 2019.07.24 + return autoCalculateConsensusAndConservation; + } + + public void setAutoCalculateConsensusAndConservation(boolean b) + { + autoCalculateConsensusAndConservation = b; + } protected boolean autoCalculateStrucConsensus = true; + public boolean getAutoCalculateStrucConsensus() + { // BH 2019.07.24 + return autoCalculateStrucConsensus; + } + + public void setAutoCalculateStrucConsensus(boolean b) + { + autoCalculateStrucConsensus = b; + } + protected boolean ignoreGapsInConsensusCalculation = false; protected ResidueShaderI residueShading = new ResidueShader(); @@ -824,7 +844,7 @@ public abstract class AlignmentViewport // see note in mantis : issue number 8585 if (alignment.isNucleotide() || (conservation == null && quality == null) - || !autoCalculateConsensus) + || !autoCalculateConsensusAndConservation) { return; } @@ -842,7 +862,7 @@ public abstract class AlignmentViewport public void updateConsensus(final AlignmentViewPanel ap) { // see note in mantis : issue number 8585 - if (consensus == null || !autoCalculateConsensus) + if (consensus == null || !autoCalculateConsensusAndConservation) { return; } @@ -1859,11 +1879,11 @@ public abstract class AlignmentViewport { alignment.padGaps(); } - if (autoCalculateConsensus) + if (autoCalculateConsensusAndConservation) { updateConsensus(ap); } - if (hconsensus != null && autoCalculateConsensus) + if (hconsensus != null && autoCalculateConsensusAndConservation) { updateConservation(ap); }