JAL-3141 Forgot this file, sorry!

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index fdc2847..553c4fa 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -43,6 +43,7 @@ import jalview.datamodel.features.FeatureMatcherSet;
 import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.ext.varna.RnaModel;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.BackupFiles;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.renderer.ResidueShaderI;
@@ -52,7 +53,6 @@ import jalview.schemabinding.version2.Annotation;
 import jalview.schemabinding.version2.AnnotationColours;
 import jalview.schemabinding.version2.AnnotationElement;
 import jalview.schemabinding.version2.CalcIdParam;
-import jalview.schemabinding.version2.Colour;
 import jalview.schemabinding.version2.CompoundMatcher;
 import jalview.schemabinding.version2.DBRef;
 import jalview.schemabinding.version2.Features;
@@ -463,7 +463,9 @@ public class Jalview2XML
     FileOutputStream fos = null;
     try
     {
+
       fos = new FileOutputStream(statefile);
+
       JarOutputStream jout = new JarOutputStream(fos);
       saveState(jout);
 
@@ -647,7 +649,11 @@ public class Jalview2XML
   {
     try
     {
-      FileOutputStream fos = new FileOutputStream(jarFile);
+      // create backupfiles object and get new temp filename destination
+      BackupFiles backupfiles = new BackupFiles(jarFile);
+      FileOutputStream fos = new FileOutputStream(
+              backupfiles.getTempFilePath());
+
       JarOutputStream jout = new JarOutputStream(fos);
       List<AlignFrame> frames = new ArrayList<>();
 
@@ -669,7 +675,12 @@ public class Jalview2XML
       }
       ;
       jout.close();
-      return true;
+      boolean success = true;
+
+      backupfiles.setWriteSuccess(success);
+      success = backupfiles.rollBackupsAndRenameTempFile();
+
+      return success;
     } catch (Exception ex)
     {
       errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
@@ -1450,9 +1461,10 @@ public class Jalview2XML
         }
         else
         {
-          ArrayList<int[]> hiddenRegions = hidden.getHiddenColumnsCopy();
-          for (int[] region : hiddenRegions)
+          Iterator<int[]> hiddenRegions = hidden.iterator();
+          while (hiddenRegions.hasNext())
           {
+            int[] region = hiddenRegions.next();
             HiddenColumns hc = new HiddenColumns();
             hc.setStart(region[0]);
             hc.setEnd(region[1]);