From 9645fa36888a246dc905404d0c758d783db70d7f Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 26 May 2005 10:21:52 +0000
Subject: [PATCH] bug fix in jpred client. TreeViewer display state and gui
 consistency improved (treecanvas/Treepanel state exchange
 functions).

---
 src/jalview/gui/AlignFrame.java |    3 ++-
 src/jalview/gui/TreePanel.java  |   39 ++++++++++++++++++++++++++++-----------
 src/jalview/ws/JPredClient.java |    1 +
 3 files changed, 31 insertions(+), 12 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1f04fa3..1183cd8 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1069,7 +1069,8 @@ public class AlignFrame extends GAlignFrame
     if(!viewport.alignment.isAligned())
     {
       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.\n"
-                                   +"Try using the Pad function in the edit menu.",
+                                   +"Try using the Pad function in the edit menu,\n"
+                                  +"or one of the multiple sequence alignment web services.",
                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
       return;
     }
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
     }
 
 
diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 0940be6..bb91119 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -27,6 +27,7 @@ public class JPredClient extends WSClient
   }
   public JPredClient(String title, SequenceI[] msf)
   {
+    setWebService();
     wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceReference);
     SequenceI seq = msf[0];
     altitle = "JNet prediction on "+seq.getName()+" using alignment from "+title;
-- 
1.7.10.2