JAL-2388 Make startRes,startSeq,endRes,endSeq private with get/setters

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 7057c2a..55d29d5 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;
@@ -1174,38 +1175,43 @@ public class Jalview2XML
           // group has references so set its ID field
           jGroup.setId(groupRefs.get(sg));
         }
-        if (sg.cs != null)
+        ColourSchemeI colourScheme = sg.getColourScheme();
+        if (colourScheme != null)
         {
-          if (sg.cs.conservationApplied())
+          ResidueShaderI groupColourScheme = sg
+                  .getGroupColourScheme();
+          if (groupColourScheme.conservationApplied())
           {
-            jGroup.setConsThreshold(sg.cs.getConservationInc());
+            jGroup.setConsThreshold(groupColourScheme.getConservationInc());
 
-            if (sg.cs instanceof jalview.schemes.UserColourScheme)
+            if (colourScheme instanceof jalview.schemes.UserColourScheme)
             {
-              jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
+              jGroup.setColour(setUserColourScheme(colourScheme,
+                      userColours, jms));
             }
             else
             {
-              jGroup.setColour(sg.cs.getSchemeName());
+              jGroup.setColour(colourScheme.getSchemeName());
             }
           }
-          else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
+          else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
           {
             jGroup.setColour("AnnotationColourGradient");
             jGroup.setAnnotationColours(constructAnnotationColours(
-                    (jalview.schemes.AnnotationColourGradient) sg.cs,
+                    (jalview.schemes.AnnotationColourGradient) colourScheme,
                     userColours, jms));
           }
-          else if (sg.cs instanceof jalview.schemes.UserColourScheme)
+          else if (colourScheme instanceof jalview.schemes.UserColourScheme)
           {
-            jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
+            jGroup.setColour(setUserColourScheme(colourScheme,
+                    userColours, jms));
           }
           else
           {
-            jGroup.setColour(sg.cs.getSchemeName());
+            jGroup.setColour(colourScheme.getSchemeName());
           }
 
-          jGroup.setPidThreshold(sg.cs.getThreshold());
+          jGroup.setPidThreshold(groupColourScheme.getThreshold());
         }
 
         jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
@@ -1264,8 +1270,8 @@ public class Jalview2XML
       view.setWidth(size.width);
       view.setHeight(size.height);
 
-      view.setStartRes(av.startRes);
-      view.setStartSeq(av.startSeq);
+      view.setStartRes(av.getStartRes());
+      view.setStartSeq(av.getStartSeq());
 
       if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
       {
@@ -1288,23 +1294,20 @@ public class Jalview2XML
                 .getGlobalColourScheme()));
       }
 
+      ResidueShaderI vcs = av.getResidueShading();
       ColourSchemeI cs = av.getGlobalColourScheme();
 
       if (cs != null)
       {
-        if (cs.conservationApplied())
+        if (vcs.conservationApplied())
         {
-          view.setConsThreshold(cs.getConservationInc());
+          view.setConsThreshold(vcs.getConservationInc());
           if (cs instanceof jalview.schemes.UserColourScheme)
           {
             view.setBgColour(setUserColourScheme(cs, userColours, jms));
           }
         }
-
-        if (cs instanceof ResidueColourScheme)
-        {
-          view.setPidThreshold(cs.getThreshold());
-        }
+        view.setPidThreshold(vcs.getThreshold());
       }
 
       view.setConservationSelected(av.getConservationSelected());
@@ -3340,18 +3343,13 @@ public class Jalview2XML
                   && jGroup.getAnnotationColours() != null)
           {
             addAnnotSchemeGroup = true;
-            cs = null;
           }
           else
           {
             cs = ColourSchemeProperty.getColourScheme(al, jGroup.getColour());
           }
-
-          if (cs != null)
-          {
-            cs.setThreshold(jGroup.getPidThreshold(), true);
-          }
         }
+        int pidThreshold = jGroup.getPidThreshold();
 
         Vector<SequenceI> seqs = new Vector<SequenceI>();
 
@@ -3374,7 +3372,8 @@ public class Jalview2XML
         SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
                 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());
@@ -3440,8 +3439,8 @@ public class Jalview2XML
         if (addAnnotSchemeGroup)
         {
           // reconstruct the annotation colourscheme
-          sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(),
-                  null, al, jms, false);
+          sg.setColourScheme(constructAnnotationColour(
+                  jGroup.getAnnotationColours(), null, al, jms, false));
         }
       }
     }
@@ -4472,19 +4471,19 @@ public class Jalview2XML
       {
         cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
       }
-
-      if (cs != null)
-      {
-        cs.setConsensus(af.viewport.getSequenceConsensusHash());
-      }
     }
 
     af.viewport.setGlobalColourScheme(cs);
+    af.viewport.getResidueShading().setThreshold(
+            view.getPidThreshold(), true);
+    af.viewport.getResidueShading().setConsensus(
+            af.viewport.getSequenceConsensusHash());
     af.viewport.setColourAppliesToAllGroups(false);
 
     if (view.getConservationSelected() && cs != null)
     {
-      cs.setConservationInc(view.getConsThreshold());
+      af.viewport.getResidueShading().setConservationInc(
+              view.getConsThreshold());
     }
 
     af.changeColour(cs);
@@ -4705,7 +4704,7 @@ public class Jalview2XML
       propagateAnnColour = true;
       for (jalview.datamodel.SequenceGroup sg : al.getGroups())
       {
-        if (sg.cs instanceof AnnotationColourGradient)
+        if (sg.getColourScheme() instanceof AnnotationColourGradient)
         {
           propagateAnnColour = false;
         }
@@ -4786,9 +4785,10 @@ public class Jalview2XML
                * viewAnnColour.getAboveThreshold()); } else
                */
               {
-                sg.cs = new AnnotationColourGradient(
-                        annAlignment.getAlignmentAnnotation()[i], sg.cs,
-                        viewAnnColour.getAboveThreshold());
+                sg.setColourScheme(new AnnotationColourGradient(
+                        annAlignment.getAlignmentAnnotation()[i], sg
+                                .getColourScheme(), viewAnnColour
+                                .getAboveThreshold()));
                 if (cs instanceof AnnotationColourGradient)
                 {
                   if (viewAnnColour.hasPerSequence())