X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FBackupFilesTest.java;h=c62ccfb4771aa50c2fdc39f3b2d110b7000a9d91;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=045b5899da4e7ca0b29c4b538add15b2aedd96cb;hpb=27c2e79ddd7e9913b385325798f2ed8a8b084dca;p=jalview.git

diff --git a/test/jalview/io/BackupFilesTest.java b/test/jalview/io/BackupFilesTest.java
index 045b589..c62ccfb 100644
--- a/test/jalview/io/BackupFilesTest.java
+++ b/test/jalview/io/BackupFilesTest.java
@@ -1,12 +1,25 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.JvOptionPane;
-
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
@@ -24,6 +37,13 @@ import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+
 public class BackupFilesTest
 {
   @BeforeClass(alwaysRun = true)
@@ -34,7 +54,8 @@ public class BackupFilesTest
   }
 
   private static boolean actuallyDeleteTmpFiles = true;
-  private static String testDir = "examples";
+
+  private static String testDir = "test/jalview/io";
 
   private static String testBasename = "backupfilestest";
 
@@ -42,7 +63,6 @@ public class BackupFilesTest
 
   private static String testFilename = testBasename + testExt;
 
-
   private static String testFile = testDir + File.separatorChar
           + testFilename;
 
@@ -87,6 +107,33 @@ public class BackupFilesTest
     Assert.assertTrue(backupFiles.length == 0);
   }
 
+  // save with no numbers in the backup file names
+  @Test(groups = { "Functional" })
+  public void backupsEnabledSingleFileBackupTest() throws Exception
+  {
+    // Enable BackupFiles and set noMax so all backupfiles get kept
+    String mysuffix = "~";
+    BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(mysuffix, 1,
+            false, true, 1, false);
+    setBackupFilesOptions(true, false, true,
+            "test/jalview/io/testProps_singlefilebackup.jvprops", bfpe);
+
+    // init the newFile and backups (i.e. make sure newFile exists on its own
+    // and has no backups)
+    initNewFileForTesting();
+    HashMap<Integer, String> correctindexmap = new HashMap<>();
+    correctindexmap.put(0, "backupfilestestTemp.fa~");
+
+    save();
+    Assert.assertTrue(checkBackupFiles(correctindexmap, newFile, "~", 1));
+
+    // and a second time -- see JAL-3628
+    save();
+    Assert.assertTrue(checkBackupFiles(correctindexmap, newFile, "~", 1));
+
+    cleanupTmpFiles(newFile, "~", 1);
+  }
+
   // save keeping all backup files
   @Test(groups = { "Functional" })
   public void backupsEnabledNoRollMaxTest() throws Exception
@@ -207,28 +254,34 @@ public class BackupFilesTest
   private void setBackupFilesOptions(boolean enabled, boolean reverse,
           boolean noMax)
   {
-    Cache.loadProperties("test/jalview/io/testProps.jvprops");
-
     BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
             reverse, noMax, rollMax, false);
+    setBackupFilesOptions(enabled, reverse, noMax,
+            "test/jalview/io/testProps.jvprops", bfpe);
+  }
+
+  private void setBackupFilesOptions(boolean enabled, boolean reverse,
+          boolean noMax, String propsFile, BackupFilesPresetEntry bfpe)
+  {
+    Cache.loadProperties(propsFile);
 
-    Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
+    Cache.setPropertyNoSave(BackupFiles.ENABLED,
             Boolean.toString(enabled));
-    Cache.applicationProperties.setProperty(
+    Cache.setPropertyNoSave(
             BackupFilesPresetEntry.SAVEDCONFIG, bfpe.toString());
     /*
-    Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
+    Cache.setPropertyNoSave(BackupFiles.ENABLED,
             Boolean.toString(enabled));
-    Cache.applicationProperties.setProperty(BackupFiles.SUFFIX, suffix);
-    Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
+    Cache.setPropertyNoSave(BackupFiles.SUFFIX, suffix);
+    Cache.setPropertyNoSave(BackupFiles.SUFFIX_DIGITS,
             Integer.toString(digits));
-    Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
+    Cache.setPropertyNoSave(BackupFiles.REVERSE_ORDER,
             Boolean.toString(reverse));
-    Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
+    Cache.setPropertyNoSave(BackupFiles.NO_MAX,
             Boolean.toString(noMax));
-    Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
+    Cache.setPropertyNoSave(BackupFiles.ROLL_MAX,
             Integer.toString(rollMax));
-    Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
+    Cache.setPropertyNoSave(BackupFiles.CONFIRM_DELETE_OLD,
             "false");
             */
   }
@@ -237,7 +290,7 @@ public class BackupFilesTest
   {
     if (af != null)
     {
-    af.saveAlignment(newFile, jalview.io.FileFormat.Fasta);
+      af.saveAlignment(newFile, jalview.io.FileFormat.Fasta);
     }
   }
 
@@ -276,12 +329,18 @@ public class BackupFilesTest
   @AfterClass(alwaysRun = true)
   private void cleanupTmpFiles()
   {
-    File newfile = new File(newFile);
+    cleanupTmpFiles(newFile, suffix, digits);
+  }
+
+  protected static void cleanupTmpFiles(String file, String mysuffix,
+          int mydigits)
+  {
+    File newfile = new File(file);
     if (newfile.exists())
     {
       newfile.delete();
     }
-    File[] tmpFiles = getBackupFiles(newFile, suffix, digits);
+    File[] tmpFiles = getBackupFiles(file, mysuffix, mydigits);
     for (int i = 0; i < tmpFiles.length; i++)
     {
       if (actuallyDeleteTmpFiles)
@@ -297,8 +356,8 @@ public class BackupFilesTest
 
   private static File[] getBackupFiles(String f, String s, int i)
   {
-    TreeMap<Integer, File> bfTreeMap = BackupFiles.getBackupFilesAsTreeMap(f,
-            s, i);
+    TreeMap<Integer, File> bfTreeMap = BackupFiles
+            .getBackupFilesAsTreeMap(f, s, i);
     File[] backupFiles = new File[bfTreeMap.size()];
     bfTreeMap.values().toArray(backupFiles);
     return backupFiles;
@@ -312,8 +371,14 @@ public class BackupFilesTest
   private static boolean checkBackupFiles(HashMap<Integer, String> indexmap)
           throws IOException
   {
-    TreeMap<Integer, File> map = BackupFiles.getBackupFilesAsTreeMap(newFile,
-            suffix, digits);
+    return checkBackupFiles(indexmap, newFile, suffix, digits);
+  }
+
+  private static boolean checkBackupFiles(HashMap<Integer, String> indexmap,
+          String file, String mysuffix, int mydigits) throws IOException
+  {
+    TreeMap<Integer, File> map = BackupFiles.getBackupFilesAsTreeMap(file,
+            mysuffix, mydigits);
     Enumeration<Integer> indexesenum = Collections
             .enumeration(indexmap.keySet());
     while (indexesenum.hasMoreElements())
@@ -350,8 +415,8 @@ public class BackupFilesTest
 
   private static boolean checkBackupFiles(int[] indexes) throws IOException
   {
-    TreeMap<Integer, File> map = BackupFiles.getBackupFilesAsTreeMap(newFile,
-            suffix, digits);
+    TreeMap<Integer, File> map = BackupFiles
+            .getBackupFilesAsTreeMap(newFile, suffix, digits);
     for (int m = 0; m < indexes.length; m++)
     {
       int i = indexes[m];
@@ -369,7 +434,8 @@ public class BackupFilesTest
       {
         return false;
       }
-      // check the filename -- although this uses the same code to forumulate the filename so not much of a test!
+      // check the filename -- although this uses the same code to forumulate
+      // the filename so not much of a test!
       String filename = BackupFilenameParts.getBackupFilename(i,
               newBasename + testExt, suffix, digits);
       if (!filename.equals(f.getName()))
@@ -399,10 +465,14 @@ public class BackupFilesTest
     return filenames;
   }
 
-  public static boolean sequencesEqual(SequenceI s1, SequenceI s2) {
-    if (s1 == null && s2 == null) {
+  public static boolean sequencesEqual(SequenceI s1, SequenceI s2)
+  {
+    if (s1 == null && s2 == null)
+    {
       return true;
-    } else if (s1 == null || s2 == null) {
+    }
+    else if (s1 == null || s2 == null)
+    {
       return false;
     }
     return (s1.getName().equals(s2.getName())