JAL-1605 merge commit

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 08fd306..aa2ae7a 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1127,7 +1127,7 @@ public class Jalview2XML
       view.setShowBoxes(av.getShowBoxes());
       view.setShowColourText(av.getColourText());
       view.setShowFullId(av.getShowJVSuffix());
-      view.setRightAlignIds(av.rightAlignIds);
+      view.setRightAlignIds(av.isRightAlignIds());
       view.setShowSequenceFeatures(av.showSequenceFeatures);
       view.setShowText(av.getShowText());
       view.setShowUnconserved(av.getShowUnconserved());
@@ -1149,7 +1149,7 @@ public class Jalview2XML
       {
         jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
 
-        String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+        String[] renderOrder = ap.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder;
 
         Vector settingsAdded = new Vector();
         Object gstyle = null;
@@ -1158,7 +1158,7 @@ public class Jalview2XML
         {
           for (int ro = 0; ro < renderOrder.length; ro++)
           {
-            gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
+            gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                     .getFeatureStyle(renderOrder[ro]);
             Setting setting = new Setting();
             setting.setType(renderOrder[ro]);
@@ -1176,13 +1176,13 @@ public class Jalview2XML
             }
             else
             {
-              setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+              setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                       .getColour(renderOrder[ro]).getRGB());
             }
 
             setting.setDisplay(av.getFeaturesDisplayed()
                     .containsKey(renderOrder[ro]));
-            float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+            float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                     .getOrder(renderOrder[ro]);
             if (rorder > -1)
             {
@@ -1194,7 +1194,7 @@ public class Jalview2XML
         }
 
         // Make sure we save none displayed feature settings
-        Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
+        Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureColours
                 .keySet().iterator();
         while (en.hasNext())
         {
@@ -1206,11 +1206,11 @@ public class Jalview2XML
 
           Setting setting = new Setting();
           setting.setType(key);
-          setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+          setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                   .getColour(key).getRGB());
 
           setting.setDisplay(false);
-          float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+          float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                   .getOrder(key);
           if (rorder > -1)
           {
@@ -1219,7 +1219,7 @@ public class Jalview2XML
           fs.addSetting(setting);
           settingsAdded.addElement(key);
         }
-        en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
+        en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups
                 .keySet().iterator();
         Vector groupsAdded = new Vector();
         while (en.hasNext())
@@ -1231,7 +1231,7 @@ public class Jalview2XML
           }
           Group g = new Group();
           g.setName(grp);
-          g.setDisplay(((Boolean) ap.seqPanel.seqCanvas
+          g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
                   .getFeatureRenderer().featureGroups.get(grp))
                   .booleanValue());
           fs.addGroup(g);
@@ -3474,7 +3474,7 @@ public class Jalview2XML
 
     af.viewport.setConservationSelected(view.getConservationSelected());
     af.viewport.setShowJVSuffix(view.getShowFullId());
-    af.viewport.rightAlignIds = view.getRightAlignIds();
+    af.viewport.setRightAlignIds(view.getRightAlignIds());
     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
             .getFontStyle(), view.getFontSize()));
     af.alignPanel.fontChanged();
@@ -3635,24 +3635,24 @@ public class Jalview2XML
             gc.setColourByLabel(setting.getColourByLabel());
           }
           // and put in the feature colour table.
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+          af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour(
                   setting.getType(), gc);
         }
         else
         {
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+          af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour(
                   setting.getType(),
                   new java.awt.Color(setting.getColour()));
         }
         renderOrder[fs] = setting.getType();
         if (setting.hasOrder())
         {
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+          af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder(
                   setting.getType(), setting.getOrder());
         }
         else
         {
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+          af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder(
                   setting.getType(),
                   fs / jms.getFeatureSettings().getSettingCount());
         }
@@ -3662,9 +3662,9 @@ public class Jalview2XML
                   setting.getColour()));
         }
       }
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
       Hashtable fgtable;
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
+      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
       for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
       {
         Group grp = jms.getFeatureSettings().getGroup(gs);