Merge remote-tracking branch 'origin/merge/JAL-845_JAL-1640' into

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 917b6d9..e1d1925 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1043,14 +1043,15 @@ public class Jalview2XML
               av.getSequenceSetId()));
       view.setId(av.getViewId());
       view.setViewName(av.viewName);
-      view.setGatheredViews(av.gatherViewsHere);
+      view.setGatheredViews(av.isGatherViewsHere());
 
-      if (ap.av.explodedPosition != null)
+      Rectangle position = ap.av.getExplodedGeometry();
+      if (position != null)
       {
-        view.setXpos(av.explodedPosition.x);
-        view.setYpos(av.explodedPosition.y);
-        view.setWidth(av.explodedPosition.width);
-        view.setHeight(av.explodedPosition.height);
+        view.setXpos(position.x);
+        view.setYpos(position.y);
+        view.setWidth(position.width);
+        view.setHeight(position.height);
       }
       else
       {
@@ -1108,7 +1109,7 @@ public class Jalview2XML
       view.setFontName(av.font.getName());
       view.setFontSize(av.font.getSize());
       view.setFontStyle(av.font.getStyle());
-      view.setRenderGaps(av.renderGaps);
+      view.setRenderGaps(av.isRenderGaps());
       view.setShowAnnotation(av.isShowAnnotation());
       view.setShowBoxes(av.getShowBoxes());
       view.setShowColourText(av.getColourText());
@@ -1118,19 +1119,19 @@ public class Jalview2XML
       view.setShowText(av.getShowText());
       view.setShowUnconserved(av.getShowUnconserved());
       view.setWrapAlignment(av.getWrapAlignment());
-      view.setTextCol1(av.textColour.getRGB());
-      view.setTextCol2(av.textColour2.getRGB());
-      view.setTextColThreshold(av.thresholdTextColour);
+      view.setTextCol1(av.getTextColour().getRGB());
+      view.setTextCol2(av.getTextColour2().getRGB());
+      view.setTextColThreshold(av.getThresholdTextColour());
       view.setShowConsensusHistogram(av.isShowConsensusHistogram());
       view.setShowSequenceLogo(av.isShowSequenceLogo());
       view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
       view.setShowGroupConsensus(av.isShowGroupConsensus());
       view.setShowGroupConservation(av.isShowGroupConservation());
-      view.setShowNPfeatureTooltip(av.isShowNpFeats());
-      view.setShowDbRefTooltip(av.isShowDbRefs());
+      view.setShowNPfeatureTooltip(av.isShowNPFeats());
+      view.setShowDbRefTooltip(av.isShowDBRefs());
       view.setFollowHighlight(av.followHighlight);
       view.setFollowSelection(av.followSelection);
-      view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
+      view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
       if (av.getFeaturesDisplayed() != null)
       {
         jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
@@ -2078,7 +2079,7 @@ public class Jalview2XML
             if (object.getJalviewModelSequence().getViewportCount() > 0)
             {
               af = _af;
-              if (af.viewport.gatherViewsHere)
+              if (af.viewport.isGatherViewsHere())
               {
                 gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
               }
@@ -3599,7 +3600,7 @@ public class Jalview2XML
               .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
     }
 
-    af.viewport.gatherViewsHere = view.getGatheredViews();
+    af.viewport.setGatherViewsHere(view.getGatheredViews());
 
     if (view.getSequenceSetId() != null)
     {
@@ -3664,27 +3665,27 @@ public class Jalview2XML
     af.viewport.setConservationSelected(view.getConservationSelected());
     af.viewport.setShowJVSuffix(view.getShowFullId());
     af.viewport.setRightAlignIds(view.getRightAlignIds());
-    af.viewport.setFont(new java.awt.Font(view.getFontName(), view
-            .getFontStyle(), view.getFontSize()));
-    af.alignPanel.fontChanged();
+    af.viewport.setFont(
+            new java.awt.Font(view.getFontName(), view.getFontStyle(), view
+                    .getFontSize()), true);
+    // TODO: allow custom charWidth/Heights to be restored by updating them
+    // after setting font - which means set above to false
     af.viewport.setRenderGaps(view.getRenderGaps());
     af.viewport.setWrapAlignment(view.getWrapAlignment());
-    af.alignPanel.setWrapAlignment(view.getWrapAlignment());
     af.viewport.setShowAnnotation(view.getShowAnnotation());
-    af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
 
     af.viewport.setShowBoxes(view.getShowBoxes());
 
     af.viewport.setShowText(view.getShowText());
 
-    af.viewport.textColour = new java.awt.Color(view.getTextCol1());
-    af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
-    af.viewport.thresholdTextColour = view.getTextColThreshold();
+    af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
+    af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
+    af.viewport.setThresholdTextColour(view.getTextColThreshold());
     af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
             .isShowUnconserved() : false);
     af.viewport.setStartRes(view.getStartRes());
     af.viewport.setStartSeq(view.getStartSeq());
-
+    af.alignPanel.updateLayout();
     ColourSchemeI cs = null;
     // apply colourschemes
     if (view.getBgColour() != null)
@@ -3767,11 +3768,11 @@ public class Jalview2XML
     }
     if (view.hasShowDbRefTooltip())
     {
-      af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
+      af.viewport.setShowDBRefs(view.getShowDbRefTooltip());
     }
     if (view.hasShowNPfeatureTooltip())
     {
-      af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip());
+      af.viewport.setShowNPFeats(view.hasShowNPfeatureTooltip());
     }
     if (view.hasShowGroupConsensus())
     {