X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=7f07a209d5802d185f3f920380381baccec7148a;hb=3bb8cfd24aeaea364b7aad2a238d6412e1c639c7;hp=42760f38e44ce3ad0204f263e07e257bb9a1a151;hpb=ac5f0c912a1c7819530456bab13942ad3734460b;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 42760f3..7f07a20 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1155,7 +1155,7 @@ public class Jalview2XML
               tree.setXpos(tp.getX());
               tree.setYpos(tp.getY());
               tree.setId(makeHashCode(tp, null));
-              tree.setLinkToAllViews(tp.treeCanvas.applyToAllViews);
+              tree.setLinkToAllViews(tp.getTreeCanvas().applyToAllViews);
               jms.addTree(tree);
             }
           }
@@ -1570,27 +1570,27 @@ public class Jalview2XML
       viewer.setXpos(panel.getX());
       viewer.setYpos(panel.getY());
       viewer.setTitle(panel.getTitle());
-      PCAModel pcaModel = panel.pcaModel;
+      PCAModel pcaModel = panel.getPcaModel();
       viewer.setScoreModelName(pcaModel.getScoreModelName());
       viewer.setXDim(panel.getSelectedDimensionIndex(X));
       viewer.setYDim(panel.getSelectedDimensionIndex(Y));
       viewer.setZDim(panel.getSelectedDimensionIndex(Z));
-      viewer.setBgColour(panel.rc.getBackgroundColour().getRGB());
-      viewer.setScaleFactor(panel.rc.scaleFactor);
-      float[] spMin = panel.rc.getSeqMin();
+      viewer.setBgColour(panel.getRotatableCanvas().getBackgroundColour().getRGB());
+      viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
+      float[] spMin = panel.getRotatableCanvas().getSeqMin();
       SeqPointMin spmin = new SeqPointMin();
       spmin.setXPos(spMin[0]);
       spmin.setYPos(spMin[1]);
       spmin.setZPos(spMin[2]);
       viewer.setSeqPointMin(spmin);
-      float[] spMax = panel.rc.getSeqMax();
+      float[] spMax = panel.getRotatableCanvas().getSeqMax();
       SeqPointMax spmax = new SeqPointMax();
       spmax.setXPos(spMax[0]);
       spmax.setYPos(spMax[1]);
       spmax.setZPos(spMax[2]);
       viewer.setSeqPointMax(spmax);
-      viewer.setShowLabels(panel.rc.showLabels);
-      viewer.setLinkToAllViews(panel.rc.applyToAllViews);
+      viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
+      viewer.setLinkToAllViews(panel.getRotatableCanvas().isApplyToAllViews());
       SimilarityParamsI sp = pcaModel.getSimilarityParameters();
       viewer.setIncludeGaps(sp.includeGaps());
       viewer.setMatchGaps(sp.matchGaps());
@@ -1614,7 +1614,7 @@ public class Jalview2XML
       /*
        * (end points of) axes on display
        */
-      for (Point p : panel.rc.axisEndPoints)
+      for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
       {
         Axis axis = new Axis();
         axis.setXPos(p.x);
@@ -4020,7 +4020,7 @@ public class Jalview2XML
         tp.showDistances(tree.getShowDistances());
 
         tp.getTreeCanvas().setThreshold(tree.getThreshold());
-        tp.treeCanvas.applyToAllViews = tree.isLinkToAllViews();
+        tp.getTreeCanvas().applyToAllViews = tree.isLinkToAllViews();
 
         if (tree.getCurrentTree())
         {
@@ -5984,9 +5984,9 @@ public class Jalview2XML
   
         boolean showLabels = viewer.isShowLabels();
         panel.setShowLabels(showLabels);
-        panel.rc.showLabels = showLabels;
-        panel.rc.bgColour = new Color(viewer.getBgColour());
-        panel.rc.applyToAllViews = viewer.isLinkToAllViews();
+        panel.getRotatableCanvas().setShowLabels(showLabels);
+        panel.getRotatableCanvas().setBgColour(new Color(viewer.getBgColour()));
+        panel.getRotatableCanvas().setApplyToAllViews(viewer.isLinkToAllViews());
 
         /*
          * load PCA output data
@@ -6005,7 +6005,7 @@ public class Jalview2XML
         MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
         pca.setEigenmatrix(result);
 
-        panel.pcaModel.setPCA(pca);
+        panel.getPcaModel().setPCA(pca);
 
         /*
          * we haven't saved the input data! (JAL-2647 to do)
@@ -6030,30 +6030,30 @@ public class Jalview2XML
                   seq, pt);
           seqPoints.add(seqPoint);
         }
-        panel.rc.setPoints(seqPoints, seqPoints.size());
+        panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
 
         /*
          * set min-max ranges and scale after setPoints (which recomputes them)
          */
-        panel.rc.scaleFactor = viewer.getScaleFactor();
+        panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
         SeqPointMin spMin = viewer.getSeqPointMin();
         float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
             spMin.getZPos() };
         SeqPointMax spMax = viewer.getSeqPointMax();
         float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
             spMax.getZPos() };
-        panel.rc.setSeqMinMax(min, max);
+        panel.getRotatableCanvas().setSeqMinMax(min, max);
 
         // todo: hold points list in PCAModel only
-        panel.pcaModel.setSequencePoints(seqPoints);
+        panel.getPcaModel().setSequencePoints(seqPoints);
 
         panel.setSelectedDimensionIndex(viewer.getXDim(), X);
         panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
         panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
 
         // is this duplication needed?
-        panel.top = seqPoints.size() - 1;
-        panel.pcaModel.setTop(seqPoints.size() - 1);
+        panel.setTop(seqPoints.size() - 1);
+        panel.getPcaModel().setTop(seqPoints.size() - 1);
 
         /*
          * add the axes' end points for the display
@@ -6061,7 +6061,7 @@ public class Jalview2XML
         for (int i = 0; i < 3; i++)
         {
           Axis axis = viewer.getAxis(i);
-          panel.rc.axisEndPoints[i] = new Point(axis.getXPos(),
+          panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(axis.getXPos(),
                   axis.getYPos(), axis.getZPos());
         }