From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 26 May 2016 15:42:58 +0000 (+0100)
Subject: Merge branch 'develop' of http://source.jalview.org/git/jalview into develop
X-Git-Tag: Release_2_10_0~212^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=26d6b93c65eb33be2892f90d632d7cbfc026e07e;hp=b92809e042da3d7445392119c159ef8730b8a136;p=jalview.git

Merge branch 'develop' of source.jalview.org/git/jalview into develop
---

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index 4201f43..c0c7c46 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -199,8 +199,9 @@ public class ChimeraManager
       return null;
     }
 
-    List<ChimeraModel> newModelList = getModelList();
-    for (ChimeraModel newModel : newModelList)
+    // patch for Jalview - set model name in Chimera
+    // TODO: find a variant that works for sub-models
+    for (ChimeraModel newModel : getModelList())
     {
       if (!modelList.contains(newModel))
       {
@@ -209,15 +210,12 @@ public class ChimeraManager
                 "setattr M name " + modelName + " #"
                         + newModel.getModelNumber(), false);
         modelList.add(newModel);
-
       }
     }
 
     // assign color and residues to open models
     for (ChimeraModel chimeraModel : modelList)
     {
-      // // patch for Jalview - set model name in Chimera
-      // // TODO: find a variant that works for sub-models
       // get model color
       Color modelColor = getModelColor(chimeraModel);
       if (modelColor != null)
@@ -731,7 +729,7 @@ public class ChimeraManager
    */
   public List<String> sendChimeraCommand(String command, boolean reply)
   {
-    // System.out.println("chimeradebug>> " + command);
+   // System.out.println("chimeradebug>> " + command);
     if (!isChimeraLaunched() || command == null
             || "".equals(command.trim()))
     {
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8ae74d4..d9d5f27 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -6062,9 +6062,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     try
     {
       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
-
       al = dna.reverseCdna(complement);
       viewport.addAlignment(al, "");
+      addHistoryItem(new EditCommand(
+              MessageManager.getString("label.add_sequences"),
+              Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
+              viewport.getAlignment()));
     } catch (Exception ex)
     {
       System.err.println(ex.getMessage());
diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index 3bd175b..00af242 100644
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -124,8 +124,7 @@ public class HtmlSvgOutput
         }
       }
 
-      if (renderStyle.equalsIgnoreCase(MessageManager
-              .getString("label.lineart")))
+      if (renderStyle.equalsIgnoreCase("Lineart"))
       {
         g1.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
                 SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
diff --git a/src/jalview/util/ImageMaker.java b/src/jalview/util/ImageMaker.java
index 9bc732b..72fa605 100755
--- a/src/jalview/util/ImageMaker.java
+++ b/src/jalview/util/ImageMaker.java
@@ -272,8 +272,7 @@ MessageManager.formatMessage(
       }
     }
 
-    if (renderStyle.equalsIgnoreCase(MessageManager
-            .getString("label.lineart")))
+    if (renderStyle.equalsIgnoreCase("Lineart"))
     {
       ig2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
               SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);