From: hansonr <hansonr@stolaf.edu>
Date: Tue, 3 Jul 2018 14:15:33 +0000 (+0100)
Subject: JAL-3026 VARNA files
X-Git-Tag: Release_2_11_4_0~45^2~18^2~599
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=41c7bc48046a03ae8247fa8f691f7fe68db8cce2;p=jalview.git

JAL-3026 VARNA files
---

diff --git a/build-zip-varna-BH.xml b/build-zip-varna-BH.xml
new file mode 100644
index 0000000..f9a6b04
--- /dev/null
+++ b/build-zip-varna-BH.xml
@@ -0,0 +1,31 @@
+<?xml version="1.0"?>
+<!--
+ * just a crude unzip of non-Jalview classes for development purposes -BH 2018
+-->
+<project name="jalviewX" default="zipvarna" basedir="."
+ xmlns:if="ant:if"
+    xmlns:unless="ant:unless">
+	
+  <target name="zipvarna">
+	
+  	
+  	<!-- inputs directories -->
+    <property name="resourceDir" value="resources" />  	
+  	<property name="libjsDir" value="libjs"/>
+    <property name="swingjsDir" value="swingjs"/>
+  	
+ 	<!-- inputs zip files -->
+  	<property name="swingjs.zip" value="${swingjsDir}/SwingJS-site.zip" />
+    <property name="varna.zip" value="${libjsDir}/VARNA-site.zip" />
+
+	<!-- output directories -->
+  	<property name="site" value="site"/>
+  	<property name="j2sDir" value="${site}/swingjs/j2s"/>
+
+
+  	<property name="libjsDir" value="libjs"/>
+  	  	
+  	<echo> Zipping up ${varna.zip} </echo>
+  	<zip destfile="${varna.zip}" basedir="site" includes="fr_*,swingjs/j2s/fr/**" />
+</target>
+</project>
diff --git a/libjs/VARNA-site.zip b/libjs/VARNA-site.zip
index 00b7830..53d36df 100644
Binary files a/libjs/VARNA-site.zip and b/libjs/VARNA-site.zip differ
diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index ee4ef79..7430856 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -289,7 +289,8 @@ public class AppVarnaBinding extends JalviewVarnaBinding
                         name += " (Model " + mn++ + ")";
                       }
                       _rnaList.add(varnaPanel.getConfig().clone(), r, name,
-                              true);
+                              true); 
+                      // BH 2018 SwingJS clone of varnaPanel or its config will be the object itself, not a clone
                     }
                   }
                 }
@@ -545,7 +546,7 @@ public class AppVarnaBinding extends JalviewVarnaBinding
    */
   public void addStructure(RNA rna)
   {
-    VARNAConfig config = vp.getConfig().clone();
+    VARNAConfig config = vp.getConfig().clone(); // BH 2018 this will NOT be a clone in SwingJS
     addStructure(rna, config);
   }
 
diff --git a/srcjar/fr/orsay/lri/varna/VARNAPanel.java b/srcjar/fr/orsay/lri/varna/VARNAPanel.java
index 13906af..3ab14b7 100644
--- a/srcjar/fr/orsay/lri/varna/VARNAPanel.java
+++ b/srcjar/fr/orsay/lri/varna/VARNAPanel.java
@@ -2454,6 +2454,8 @@ public class VARNAPanel extends JPanel implements PropertyChangeListener {
 			super.setBackground(new Color(0, 0, 0, 120));
 		}
 
+		// BH 2018 was lt, not lteq here
+		// SwingJS sets the minimum panel size -- probably incorrectly -- to the size for VARNAPanel
 		if (getMinimumSize().height <= getSize().height
 				&& getMinimumSize().width <= getSize().width) {
 			// Draw Title
diff --git a/srcjar/fr/orsay/lri/varna/applications/VARNAEditor.java b/srcjar/fr/orsay/lri/varna/applications/VARNAEditor.java
index 665e9fc..818cfda 100644
--- a/srcjar/fr/orsay/lri/varna/applications/VARNAEditor.java
+++ b/srcjar/fr/orsay/lri/varna/applications/VARNAEditor.java
@@ -193,6 +193,9 @@ public class VARNAEditor extends JFrame implements DropTargetListener, Interface
 		e3.printStackTrace();
 		}
 		_vp.setPreferredSize(new Dimension(400, 400));
+		// 
+		
+		 // BH 2018 this will NOT be a clone in SwingJS
 	    _rnaList.add(_vp.getConfig().clone(),_RNA2,generateDefaultName());
 	    _rnaList.add(_vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
 
diff --git a/srcjar/fr/orsay/lri/varna/applications/VARNAGUI.java b/srcjar/fr/orsay/lri/varna/applications/VARNAGUI.java
index fe468c4..e62503f 100644
--- a/srcjar/fr/orsay/lri/varna/applications/VARNAGUI.java
+++ b/srcjar/fr/orsay/lri/varna/applications/VARNAGUI.java
@@ -271,7 +271,7 @@ public class VARNAGUI extends JFrame implements DropTargetListener, InterfaceVAR
 		});
 		// BH 2018 SwingJS can't clone, as it does not implement serialization 
 		if (/** @j2sNative false && */ true)
-		_duplicateButton.addActionListener(new ActionListener() {
+		  _duplicateButton.addActionListener(new ActionListener() {
 			public void actionPerformed(ActionEvent e) {
 					_rnaList.add((VARNAConfig)_vp.getConfig().clone(),_vp.getRNA().clone(),_vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true); 
 			}});
@@ -279,7 +279,8 @@ public class VARNAGUI extends JFrame implements DropTargetListener, InterfaceVAR
 		JPanel ops = new JPanel();
 		ops.setLayout(new GridLayout(1,2));
 		ops.add(_deleteButton);
-		ops.add(_duplicateButton);
+                if (/** @j2sNative false && */ true)
+                  ops.add(_duplicateButton);
 		
 		JPanel opspanel = new JPanel(new BorderLayout());
 		opspanel.add(ops,BorderLayout.NORTH);