Merge branch 'develop' into merge/JAL-3127

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

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 74b6bf0..cf5974c 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -59,7 +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 @@ 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 @@ public class Jalview2XML
   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 @@ 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<>();
 
@@ -760,7 +770,12 @@ 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";
@@ -2882,16 +2897,7 @@ public class Jalview2XML
       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)
       {
@@ -3853,7 +3859,7 @@ public class Jalview2XML
           }
           else
           {
-            cs = ColourSchemeProperty.getColourScheme(al,
+            cs = ColourSchemeProperty.getColourScheme(null, al,
                     jGroup.getColour());
           }
         }
@@ -4967,25 +4973,27 @@ public class Jalview2XML
       }
       else
       {
-        cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
+        cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
+                view.getBgColour());
       }
     }
 
+    /*
+     * turn off 'alignment colour applies to all groups'
+     * while restoring global colour scheme
+     */
+    viewport.setColourAppliesToAllGroups(false);
     viewport.setGlobalColourScheme(cs);
     viewport.getResidueShading().setThreshold(pidThreshold,
             view.isIgnoreGapsinConsensus());
     viewport.getResidueShading()
             .setConsensus(viewport.getSequenceConsensusHash());
-    viewport.setColourAppliesToAllGroups(false);
-
     if (safeBoolean(view.isConservationSelected()) && cs != null)
     {
       viewport.getResidueShading()
               .setConservationInc(safeInt(view.getConsThreshold()));
     }
-
     af.changeColour(cs);
-
     viewport.setColourAppliesToAllGroups(true);
 
     viewport
@@ -5061,7 +5069,8 @@ public class Jalview2XML
           float min = safeFloat(safeFloat(setting.getMin()));
           float max = setting.getMax() == null ? 1f
                   : setting.getMax().floatValue();
-          FeatureColourI gc = new FeatureColour(minColour, maxColour,
+          FeatureColourI gc = new FeatureColour(maxColour, minColour,
+                  maxColour,
                   noValueColour, min, max);
           if (setting.getAttributeName().size() > 0)
           {
@@ -5263,7 +5272,7 @@ public class Jalview2XML
     else
     {
       cs = new AnnotationColourGradient(matchedAnnotation,
-              ColourSchemeProperty.getColourScheme(al,
+              ColourSchemeProperty.getColourScheme(af.getViewport(), al,
                       viewAnnColour.getColourScheme()),
               safeInt(viewAnnColour.getAboveThreshold()));
     }
@@ -5829,15 +5838,16 @@ public class Jalview2XML
     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));
@@ -5847,9 +5857,9 @@ public class Jalview2XML
         frefedSequence.add(newMappingRef(dsfor, jmap));
       }
     }
-    else
+    else if (m.getSequence() != null)
     {
-      /**
+      /*
        * local sequence definition
        */
       Sequence ms = m.getSequence();
@@ -6555,7 +6565,7 @@ public class Jalview2XML
         noValueColour = maxcol;
       }
   
-      colour = new FeatureColour(mincol, maxcol, noValueColour,
+      colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
               safeFloat(colourModel.getMin()),
               safeFloat(colourModel.getMax()));
       final List<String> attributeName = colourModel.getAttributeName();