X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=ca0423b218f8e970e44dd9e2dc1401e1197418e6;hb=31bbef5af00068ef84bf56f8b8d1d7a29da84bd3;hp=9a303e24604f612890de935d5f4385a4bf287dd0;hpb=b2eb64f196223039a95348a4026f0453693ee0e7;p=jalview.git

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 9a303e2..ca0423b 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -1501,6 +1501,9 @@ public class Jalview2XML
       view.setFollowHighlight(av.isFollowHighlight());
       view.setFollowSelection(av.followSelection);
       view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
+      view.setShowComplementFeatures(av.isShowComplementFeatures());
+      view.setShowComplementFeaturesOnTop(
+              av.isShowComplementFeaturesOnTop());
       if (av.getFeaturesDisplayed() != null)
       {
         FeatureSettings fs = new FeatureSettings();
@@ -3160,25 +3163,25 @@ public class Jalview2XML
    * @param prefix
    *          a prefix for the temporary file name, must be at least three
    *          characters long
-   * @param origFile
+   * @param suffixModel
    *          null or original file - so new file can be given the same suffix
    *          as the old one
    * @return
    */
   protected String copyJarEntry(jarInputStreamProvider jprovider,
-          String jarEntryName, String prefix, String origFile)
+          String jarEntryName, String prefix, String suffixModel)
   {
     BufferedReader in = null;
     PrintWriter out = null;
     String suffix = ".tmp";
-    if (origFile == null)
+    if (suffixModel == null)
     {
-      origFile = jarEntryName;
+      suffixModel = jarEntryName;
     }
-    int sfpos = origFile.lastIndexOf(".");
-    if (sfpos > -1 && sfpos < (origFile.length() - 3))
+    int sfpos = suffixModel.lastIndexOf(".");
+    if (sfpos > -1 && sfpos < (suffixModel.length() - 1))
     {
-      suffix = "." + origFile.substring(sfpos + 1);
+      suffix = "." + suffixModel.substring(sfpos + 1);
     }
     try
     {
@@ -3333,8 +3336,10 @@ public class Jalview2XML
                   || tmpSeq.getEnd() != jseq.getEnd())
           {
             System.err.println(
-                    "Warning JAL-2154 regression: updating start/end for sequence "
-                            + tmpSeq.toString() + " to " + jseq);
+                    String.format("Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
+                            tmpSeq.getName(), tmpSeq.getStart(),
+                            tmpSeq.getEnd(), jseq.getStart(),
+                            jseq.getEnd()));
           }
         }
         else
@@ -4444,7 +4449,7 @@ public class Jalview2XML
      */
     String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
     chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
-            "chimera", null);
+            "chimera", ".py");
 
     Set<Entry<File, StructureData>> fileData = data.getFileData()
             .entrySet();
@@ -5019,6 +5024,9 @@ public class Jalview2XML
     viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
     viewport.setShowGroupConsensus(view.isShowGroupConsensus());
     viewport.setShowGroupConservation(view.isShowGroupConservation());
+    viewport.setShowComplementFeatures(view.isShowComplementFeatures());
+    viewport.setShowComplementFeaturesOnTop(
+            view.isShowComplementFeaturesOnTop());
 
     // recover feature settings
     if (jm.getFeatureSettings() != null)