Merge remote-tracking branch 'origin/feature/JAL-3141_backupfiles_for211' into merge...

diff --combined src/jalview/gui/AlignFrame.java
index 936e714,bf9569b..36db248
--- 1/src/jalview/gui/AlignFrame.java
--- 2/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -64,6 -64,7 +64,7 @@@ import jalview.gui.ColourMenuHelper.Col
  import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  import jalview.io.AlignmentProperties;
  import jalview.io.AnnotationFile;
+ import jalview.io.BackupFiles;
  import jalview.io.BioJsHTMLOutput;
  import jalview.io.DataSourceType;
  import jalview.io.FileFormat;
@@@ -1187,9 -1188,13 +1188,13 @@@ public class AlignFrame extends GAlignF
        }
        else
        {
+         // create backupfiles object and get new temp filename destination
+         BackupFiles backupfiles = new BackupFiles(file);
+ 
          try
          {
-           PrintWriter out = new PrintWriter(new FileWriter(file));
+           PrintWriter out = new PrintWriter(
+                   new FileWriter(backupfiles.getTempFilePath()));
  
            out.print(output);
            out.close();
@@@ -1202,6 -1207,11 +1207,11 @@@
            success = false;
            ex.printStackTrace();
          }
+ 
+         backupfiles.setWriteSuccess(success);
+         // do the backup file roll and rename the temp file to actual file
+         success = backupfiles.rollBackupsAndRenameTempFile();
+ 
        }
      }
  
@@@ -2398,8 -2408,12 +2408,8 @@@
    @Override
    public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
    {
 -    SequenceGroup sg = new SequenceGroup();
 -
 -    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
 -    {
 -      sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
 -    }
 +    SequenceGroup sg = new SequenceGroup(
 +            viewport.getAlignment().getSequences());
  
      sg.setEndRes(viewport.getAlignment().getWidth() - 1);
      viewport.setSelectionGroup(sg);
@@@ -2886,7 -2900,7 +2896,7 @@@
      viewport.setFollowHighlight(state);
      if (state)
      {
 -      alignPanel.scrollToPosition(viewport.getSearchResults(), false);
 +      alignPanel.scrollToPosition(viewport.getSearchResults());
      }
    }
  

diff --combined src/jalview/project/Jalview2XML.java
index e57dd01,7b23c8d..f772cf5
--- 1/src/jalview/project/Jalview2XML.java
--- 2/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@@ -59,7 -59,6 +59,6 @@@ import jalview.gui.AppVarna
  import jalview.gui.ChimeraViewFrame;
  import jalview.gui.Desktop;
  import jalview.gui.FeatureRenderer;
- import jalview.gui.Jalview2XML_V1;
  import jalview.gui.JvOptionPane;
  import jalview.gui.OOMWarning;
  import jalview.gui.PCAPanel;
@@@ -69,6 -68,7 +68,7 @@@ import jalview.gui.StructureViewer
  import jalview.gui.StructureViewer.ViewerType;
  import jalview.gui.StructureViewerBase;
  import jalview.gui.TreePanel;
+ import jalview.io.BackupFiles;
  import jalview.io.DataSourceType;
  import jalview.io.FileFormat;
  import jalview.io.NewickFile;
@@@ -551,24 -551,30 +551,30 @@@ public class Jalview2XM
    public void saveState(File statefile)
    {
      FileOutputStream fos = null;
+ 
      try
      {
+ 
        fos = new FileOutputStream(statefile);
+ 
        JarOutputStream jout = new JarOutputStream(fos);
        saveState(jout);
+       fos.close();
  
      } catch (Exception e)
      {
+       Cache.log.error("Couln't write Jalview state to " + statefile, e);
        // TODO: inform user of the problem - they need to know if their data was
        // not saved !
        if (errorMessage == null)
        {
-         errorMessage = "Couldn't write Jalview Archive to output file '"
+         errorMessage = "Did't write Jalview Archive to output file '"
                  + statefile + "' - See console error log for details";
        }
        else
        {
-         errorMessage += "(output file was '" + statefile + "')";
+         errorMessage += "(Didn't write Jalview Archive to output file '"
+                 + statefile + ")";
        }
        e.printStackTrace();
      } finally
@@@ -738,7 -744,11 +744,11 @@@
    {
      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<>();
  
@@@ -760,7 -770,12 +770,12 @@@
        }
        ;
        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";
@@@ -2882,16 -2897,7 +2897,7 @@@
        ex.printStackTrace(System.err);
        if (attemptversion1parse)
        {
-         // Is Version 1 Jar file?
-         try
-         {
-           af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
-         } catch (Exception ex2)
-         {
-           System.err.println("Exception whilst loading as jalviewXMLV1:");
-           ex2.printStackTrace();
-           af = null;
-         }
+         // used to attempt to parse as V1 castor-generated xml
        }
        if (Desktop.instance != null)
        {
@@@ -5829,16 -5835,15 +5835,16 @@@
      jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
              fto, m.getMapFromUnit().intValue(),
              m.getMapToUnit().intValue());
 -    // if (m.getMappingChoice() != null)
 -    // {
 -    // MappingChoice mc = m.getMappingChoice();
 +
 +    /*
 +     * (optional) choice of dseqFor or Sequence
 +     */
      if (m.getDseqFor() != null)
      {
        String dsfor = m.getDseqFor();
        if (seqRefIds.containsKey(dsfor))
        {
 -        /**
 +        /*
           * recover from hash
           */
          jmap.setTo(seqRefIds.get(dsfor));
@@@ -5848,9 -5853,9 +5854,9 @@@
          frefedSequence.add(newMappingRef(dsfor, jmap));
        }
      }
 -    else
 +    else if (m.getSequence() != null)
      {
 -      /**
 +      /*
         * local sequence definition
         */
        Sequence ms = m.getSequence();