From: amwaterhouse Date: Thu, 26 Oct 2006 12:18:52 +0000 (+0000) Subject: showConservation, quality, identity not used X-Git-Tag: Release_2_2~215 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e3a5770d5844eb5cf183424643605611d3545726;p=jalview.git showConservation, quality, identity not used --- diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index f9f32e4..c0e9dc9 100755 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -51,9 +51,6 @@ public class AlignViewport boolean renderGaps = true; boolean showSequenceFeatures = false; boolean showAnnotation = true; - boolean showConservation = true; - boolean showQuality = true; - boolean showIdentity = true; boolean colourAppliesToAllGroups = true; ColourSchemeI globalColourScheme = null; boolean conservationColourSelected = false; @@ -155,10 +152,6 @@ public class AlignViewport showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true); showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true); - showConservation = Cache.getDefault("SHOW_CONSERVATION", true); - - showQuality = Cache.getDefault("SHOW_QUALITY", true); - showIdentity = Cache.getDefault("SHOW_IDENTITY", true); autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); @@ -199,12 +192,13 @@ public class AlignViewport AlignmentAnnotation.BAR_GRAPH); conservation.hasText = true; - if (showConservation) + + if (Cache.getDefault("SHOW_CONSERVATION", true)) { alignment.addAnnotation(conservation); } - if (showQuality) + if (Cache.getDefault("SHOW_QUALITY", true)) { quality = new AlignmentAnnotation("Quality", "Alignment Quality based on Blosum62 scores", @@ -223,7 +217,7 @@ public class AlignViewport AlignmentAnnotation.BAR_GRAPH); consensus.hasText = true; - if (showIdentity) + if (Cache.getDefault("SHOW_IDENTITY", true)) { alignment.addAnnotation(consensus); } @@ -504,6 +498,8 @@ public class AlignViewport } catch (OutOfMemoryError error) { + consensus = null; + hconsensus = null; javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 056555a..fef8a83 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -1338,10 +1338,6 @@ public class Jalview2XML af.viewport.setStartRes(view.getStartRes()); af.viewport.setStartSeq(view.getStartSeq()); af.viewport.setShowAnnotation(view.getShowAnnotation()); - af.viewport.showConservation = !hideConservation; - af.viewport.showQuality = !hideQuality; - af.viewport.showIdentity = !hideConsensus; - af.viewport.setAbovePIDThreshold(view.getPidSelected()); af.abovePIDThreshold.setSelected(view.getPidSelected()); af.viewport.setColourText(view.getShowColourText());