X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=78bef801cda4eab910621a740031829d16d70773;hb=c521a798765bb3672e89ea8cda3241a97d6c6e73;hp=047c1d4cc749ca1bd2fafe27f12c3a4f0e599d30;hpb=9ec724cefe52ca1e3fa72d726557b0108a4b043a;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 047c1d4..78bef80 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -53,12 +53,28 @@ public class TreePanel extends GTreePanel
     tree = new NJTree(seq, type, pwtype, start, end);
 
     treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-
+    treeCanvas.setShowDistances(true); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+    setViewStateFromTreeCanvas(treeCanvas);
     tree.reCount(tree.getTopNode());
     tree.findHeight(tree.getTopNode());
     scrollPane.setViewportView(treeCanvas);
 
   }
+  private void setViewStateFromTreeCanvas(TreeCanvas tree) {
+    // update view menu state from treeCanvas render state
+    distanceMenu.setSelected(tree.showDistances);
+    bootstrapMenu.setSelected(tree.showBootstrap);
+    placeholdersMenu.setSelected(tree.markPlaceholders);
+  }
+
+  private void setTreeCanvasFromViewState(TreeCanvas tree) {
+      // update view menu state from treeCanvas render state
+      tree.showDistances = distanceMenu.isSelected();
+      tree.showBootstrap = bootstrapMenu.isSelected();
+      tree.markPlaceholders = placeholdersMenu.isSelected();
+    }
+
+
   public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
                    String type, String pwtype)
     {
@@ -80,11 +96,14 @@ public class TreePanel extends GTreePanel
       tree = new NJTree(seq, newtree);
       // Now have to calculate longest name based on the leaves
       Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());
-
-      for (int i=0;i < leaves.size();i++)
-        if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())
-          longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName();
-
+      boolean has_placeholders = false;
+      for (int i=0;i < leaves.size();i++) {
+        SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+        if (lf.isPlaceholder())
+          has_placeholders = true;
+        if (longestName.length()<((Sequence) lf.element()).getName().length())
+          longestName = TreeCanvas.PLACEHOLDER+((Sequence) lf.element()).getName();
+      }
       tree.reCount(tree.getTopNode());
       tree.findHeight(tree.getTopNode());
 
@@ -92,11 +111,9 @@ public class TreePanel extends GTreePanel
       treeCanvas.setShowBootstrap(newtree.HasBootstrap());
       treeCanvas.setShowDistances(newtree.HasDistances());
       scrollPane.setViewportView(treeCanvas);
-      distanceMenu.setSelected(newtree.HasDistances());
-      bootstrapMenu.setSelected(newtree.HasBootstrap());
-      if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree
-        placeholdersMenu.setSelected(treeCanvas.markPlaceholders);
-
+      treeCanvas.setMarkPlaceholders(has_placeholders);
+      setViewStateFromTreeCanvas(treeCanvas);
+      // JBPNote TODO: preference for always marking placeholders in new associated tree
     }