Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855

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

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index d4b2c04..c8f9be6 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -229,6 +229,11 @@ public class Jalview2XML
   private static final String UTF_8 = "UTF-8";
 
   /**
+   * used in decision if quit confirmation should be issued
+   */
+  private static boolean stateSavedUpToDate = false;
+
+  /**
    * prefix for recovering datasets for alignments with multiple views where
    * non-existent dataset IDs were written for some views
    */
@@ -616,6 +621,27 @@ public class Jalview2XML
   {
     AlignFrame[] frames = Desktop.getAlignFrames();
 
+    setStateSavedUpToDate(true);
+
+    if (Cache.getDefault("DEBUG_DELAY_SAVE", false))
+    {
+      int n = debugDelaySave;
+      int i = 0;
+      while (i < n)
+      {
+        Console.debug("***** debugging save sleep " + i + "/" + n);
+        try
+        {
+          Thread.sleep(1000);
+        } catch (InterruptedException e)
+        {
+          // TODO Auto-generated catch block
+          e.printStackTrace();
+        }
+        i++;
+      }
+    }
+
     if (frames == null)
     {
       return;
@@ -763,6 +789,25 @@ public class Jalview2XML
       FileOutputStream fos = new FileOutputStream(
               doBackup ? backupfiles.getTempFilePath() : jarFile);
 
+      if (Cache.getDefault("DEBUG_DELAY_SAVE", false))
+      {
+        int n = debugDelaySave;
+        int i = 0;
+        while (i < n)
+        {
+          Console.debug("***** debugging save sleep " + i + "/" + n);
+          try
+          {
+            Thread.sleep(1000);
+          } catch (InterruptedException e)
+          {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+          }
+          i++;
+        }
+      }
+
       JarOutputStream jout = new JarOutputStream(fos);
       List<AlignFrame> frames = new ArrayList<>();
 
@@ -6537,4 +6582,44 @@ public class Jalview2XML
 
     return colour;
   }
+
+  public static void setStateSavedUpToDate(boolean s)
+  {
+    Console.debug("Setting overall stateSavedUpToDate to " + s);
+    stateSavedUpToDate = s;
+  }
+
+  public static boolean stateSavedUpToDate()
+  {
+    Console.debug("Returning overall stateSavedUpToDate value: "
+            + stateSavedUpToDate);
+    return stateSavedUpToDate;
+  }
+
+  public static boolean allSavedUpToDate()
+  {
+    if (stateSavedUpToDate()) // nothing happened since last project save
+      return true;
+
+    AlignFrame[] frames = Desktop.getAlignFrames();
+    if (frames != null)
+    {
+      for (int i = 0; i < frames.length; i++)
+      {
+        if (frames[i] == null)
+          continue;
+        if (!frames[i].getViewport().savedUpToDate())
+          return false; // at least one alignment is not individually saved
+      }
+    }
+    return true;
+  }
+
+  // used for debugging and tests
+  private static int debugDelaySave = 20;
+
+  public static void setDebugDelaySave(int n)
+  {
+    debugDelaySave = n;
+  }
 }