JAL-2314 Tidy up

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index cda08c6..e8b832d 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -39,6 +39,7 @@ import jalview.ext.varna.RnaModel;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
+import jalview.renderer.ResidueShaderI;
 import jalview.schemabinding.version2.AlcodMap;
 import jalview.schemabinding.version2.AlcodonFrame;
 import jalview.schemabinding.version2.Annotation;
@@ -73,7 +74,6 @@ import jalview.schemabinding.version2.Tree;
 import jalview.schemabinding.version2.UserColours;
 import jalview.schemabinding.version2.Viewport;
 import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.CollectionColourSchemeI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.FeatureColour;
@@ -87,6 +87,7 @@ import jalview.util.Platform;
 import jalview.util.StringUtils;
 import jalview.util.jarInputStreamProvider;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -755,6 +756,7 @@ public class Jalview2XML
     List<UserColourScheme> userColours = new ArrayList<UserColourScheme>();
 
     AlignViewport av = ap.av;
+    ViewportRanges vpRanges = av.getRanges();
 
     JalviewModel object = new JalviewModel();
     object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
@@ -1178,7 +1180,7 @@ public class Jalview2XML
         ColourSchemeI colourScheme = sg.getColourScheme();
         if (colourScheme != null)
         {
-          CollectionColourSchemeI groupColourScheme = sg
+          ResidueShaderI groupColourScheme = sg
                   .getGroupColourScheme();
           if (groupColourScheme.conservationApplied())
           {
@@ -1270,8 +1272,8 @@ public class Jalview2XML
       view.setWidth(size.width);
       view.setHeight(size.height);
 
-      view.setStartRes(av.startRes);
-      view.setStartSeq(av.startSeq);
+      view.setStartRes(vpRanges.getStartRes());
+      view.setStartSeq(vpRanges.getStartSeq());
 
       if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
       {
@@ -1294,7 +1296,7 @@ public class Jalview2XML
                 .getGlobalColourScheme()));
       }
 
-      CollectionColourSchemeI vcs = av.getViewportColourScheme();
+      ResidueShaderI vcs = av.getResidueShading();
       ColourSchemeI cs = av.getGlobalColourScheme();
 
       if (cs != null)
@@ -3373,6 +3375,7 @@ public class Jalview2XML
                 jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
                 jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
         sg.getGroupColourScheme().setThreshold(pidThreshold, true);
+        sg.getGroupColourScheme().setConservationInc(jGroup.getConsThreshold());
         sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
 
         sg.textColour = new java.awt.Color(jGroup.getTextCol1());
@@ -4418,10 +4421,12 @@ public class Jalview2XML
 
     af.viewport.setShowAnnotation(view.getShowAnnotation());
     af.viewport.setAbovePIDThreshold(view.getPidSelected());
+    af.viewport.setThreshold(view.getPidThreshold());
 
     af.viewport.setColourText(view.getShowColourText());
 
     af.viewport.setConservationSelected(view.getConservationSelected());
+    af.viewport.setIncrement(view.getConsThreshold());
     af.viewport.setShowJVSuffix(view.getShowFullId());
     af.viewport.setRightAlignIds(view.getRightAlignIds());
     af.viewport.setFont(
@@ -4445,8 +4450,8 @@ public class Jalview2XML
     af.viewport.setThresholdTextColour(view.getTextColThreshold());
     af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
             .isShowUnconserved() : false);
-    af.viewport.setStartRes(view.getStartRes());
-    af.viewport.setStartSeq(view.getStartSeq());
+    af.viewport.getRanges().setStartRes(view.getStartRes());
+    af.viewport.getRanges().setStartSeq(view.getStartSeq());
     af.alignPanel.updateLayout();
     ColourSchemeI cs = null;
     // apply colourschemes
@@ -4468,24 +4473,18 @@ public class Jalview2XML
       {
         cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
       }
-
-      // if (cs != null)
-      // {
-      // cs.setThreshold(view.getPidThreshold(), true);
-      // cs.setConsensus(af.viewport.getSequenceConsensusHash());
-      // }
     }
 
     af.viewport.setGlobalColourScheme(cs);
-    af.viewport.getViewportColourScheme().setThreshold(
+    af.viewport.getResidueShading().setThreshold(
             view.getPidThreshold(), true);
-    af.viewport.getViewportColourScheme().setConsensus(
+    af.viewport.getResidueShading().setConsensus(
             af.viewport.getSequenceConsensusHash());
     af.viewport.setColourAppliesToAllGroups(false);
 
     if (view.getConservationSelected() && cs != null)
     {
-      af.viewport.getViewportColourScheme().setConservationInc(
+      af.viewport.getResidueShading().setConservationInc(
               view.getConsThreshold());
     }