Merge branch 'develop' into feature/JAL-2422ChimeraX

[jalview.git] / src / jalview / project / Jalview2XML.java

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 5b1c0a3..df4a93e 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -2110,7 +2110,7 @@ public class Jalview2XML
           final String viewId = viewFrame.getViewId();
           state.setViewId(viewId);
           state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
-          state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
+          state.setColourwithAlignPanel(viewFrame.isUsedForColourBy(ap));
           state.setColourByJmol(viewFrame.isColouredByViewer());
           state.setType(viewFrame.getViewerType().toString());
           // pdb.addStructureState(state);
@@ -3163,25 +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
     {
@@ -3336,8 +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
@@ -4447,7 +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();