reconciled with develop

diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java
index c3887ff..f6b47c3 100644 (file)
--- a/src/jalview/gui/FeatureTypeSettings.java
+++ b/src/jalview/gui/FeatureTypeSettings.java
@@ -186,12 +186,12 @@ public class FeatureTypeSettings extends JalviewDialog
   /*
    * choice of what to colour by text (Label or attribute)
    */
-  private JComboBox<String> colourByTextCombo;
+  private JComboBox<Object> colourByTextCombo;
 
   /*
    * choice of what to colour by range (Score or attribute)
    */
-  private JComboBox<String> colourByRangeCombo;
+  private JComboBox<Object> colourByRangeCombo;
 
   private JRadioButton andFilters;
 
@@ -1121,10 +1121,10 @@ public class FeatureTypeSettings extends JalviewDialog
    * @param withRange
    * @param withText
    */
-  protected JComboBox<String> populateAttributesDropdown(
+  protected JComboBox<Object> populateAttributesDropdown(
           List<String[]> attNames, boolean withRange, boolean withText)
   {
-    List<String> displayAtts = new ArrayList<>();
+    List<Object> displayAtts = new ArrayList<>();
     List<String> tooltips = new ArrayList<>();
 
     if (withText)
@@ -1160,7 +1160,7 @@ public class FeatureTypeSettings extends JalviewDialog
       tooltips.add(desc == null ? "" : desc);
     }
 
-    JComboBox<String> attCombo = JvSwingUtils
+    JComboBox<Object> attCombo = JvSwingUtils
             .buildComboWithTooltips(displayAtts, tooltips);
 
     return attCombo;
@@ -1340,7 +1340,7 @@ public class FeatureTypeSettings extends JalviewDialog
      * drop-down choice of attribute, with description as a tooltip 
      * if we can obtain it
      */
-    JComboBox<String> attCombo = populateAttributesDropdown(attNames, true,
+    JComboBox<Object> attCombo = populateAttributesDropdown(attNames, true,
             true);
     String filterBy = setSelectedAttribute(attCombo, filter);
 
@@ -1478,7 +1478,7 @@ public class FeatureTypeSettings extends JalviewDialog
    * @param attCombo
    * @param filter
    */
-  private String setSelectedAttribute(JComboBox<String> attCombo,
+  private String setSelectedAttribute(JComboBox<Object> attCombo,
           FeatureMatcherI filter)
   {
     String item = null;
@@ -1695,7 +1695,7 @@ public class FeatureTypeSettings extends JalviewDialog
    * @param valueField
    * @param filterIndex
    */
-  protected boolean updateFilter(JComboBox<String> attCombo,
+  protected boolean updateFilter(JComboBox<Object> attCombo,
           JComboBox<Condition> condCombo, JTextField valueField,
           int filterIndex)
   {

diff --git a/src/jalview/io/BackupFilenameParts.java b/src/jalview/io/BackupFilenameParts.java
index 4f93ece..1504404 100644 (file)
--- a/src/jalview/io/BackupFilenameParts.java
+++ b/src/jalview/io/BackupFilenameParts.java
@@ -1,7 +1,5 @@
 package jalview.io;
 
-import jalview.bin.Cache;
-
 import java.io.File;
 
 public class BackupFilenameParts
@@ -113,7 +111,9 @@ public class BackupFilenameParts
           String filename, String base, boolean extensionMatch)
   {
     BackupFilenameParts bfp = new BackupFilenameParts();
-    String template = Cache.getDefault(BackupFiles.SUFFIX, null);
+    BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+            .getSavedBackupEntry();
+    String template = bfpe.suffix;
     if (template == null)
     {
       return bfp;
@@ -121,8 +121,7 @@ public class BackupFilenameParts
     int digits;
     try
     {
-      digits = Integer
-              .parseInt(Cache.getDefault(BackupFiles.SUFFIX_DIGITS, null));
+      digits = bfpe.digits;
     } catch (Exception e)
     {
       return bfp;

diff --git a/test/jalview/io/BackupFilesTest.java b/test/jalview/io/BackupFilesTest.java
index bb59f28..c84285a 100644 (file)
--- a/test/jalview/io/BackupFilesTest.java
+++ b/test/jalview/io/BackupFilesTest.java
@@ -34,7 +34,8 @@ 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";
 
@@ -61,7 +62,7 @@ public class BackupFilesTest
 
   private static String suffix = "_BACKUPTEST-%n";
 
-  private static int digits = 8;
+  private static int digits = 6;
 
   private static int rollMax = 2;
 
@@ -107,28 +108,28 @@ public class BackupFilesTest
     }
 
     // check 10 backup files
-    HashMap correctindexmap = new HashMap();
-    correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-00000001");
-    correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-00000002");
-    correctindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-00000003");
-    correctindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-00000004");
-    correctindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-00000005");
-    correctindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-00000006");
-    correctindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-00000007");
-    correctindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-00000008");
-    correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-00000009");
-    correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-00000010");
-    HashMap wrongindexmap = new HashMap();
+    HashMap<Integer, String> correctindexmap = new HashMap<>();
+    correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-000001");
+    correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-000002");
+    correctindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-000003");
+    correctindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-000004");
+    correctindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-000005");
+    correctindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-000006");
+    correctindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-000007");
+    correctindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-000008");
+    correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-000009");
+    correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-000010");
+    HashMap<Integer, String> wrongindexmap = new HashMap<>();
     wrongindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-1");
-    wrongindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-00000002");
-    wrongindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-00000003");
-    wrongindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-00000004");
-    wrongindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-00000005");
-    wrongindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-00000006");
-    wrongindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-00000007");
-    wrongindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-00000008");
-    wrongindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-00000009");
-    wrongindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-00000010");
+    wrongindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-000002");
+    wrongindexmap.put(3, "backupfilestestTemp.fa_BACKUPTEST-000003");
+    wrongindexmap.put(4, "backupfilestestTemp.fa_BACKUPTEST-000004");
+    wrongindexmap.put(5, "backupfilestestTemp.fa_BACKUPTEST-000005");
+    wrongindexmap.put(6, "backupfilestestTemp.fa_BACKUPTEST-000006");
+    wrongindexmap.put(7, "backupfilestestTemp.fa_BACKUPTEST-000007");
+    wrongindexmap.put(8, "backupfilestestTemp.fa_BACKUPTEST-000008");
+    wrongindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-000009");
+    wrongindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-000010");
     int[] indexes2 = { 3, 4, 5, 6, 7, 8, 9, 10 };
     int[] indexes3 = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 };
     Assert.assertTrue(checkBackupFiles(correctindexmap));
@@ -158,9 +159,9 @@ public class BackupFilesTest
 
     // check there are "rollMax" backup files and they are all saved correctly
     // check 10 backup files
-    HashMap correctindexmap = new HashMap();
-    correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-00000009");
-    correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-00000010");
+    HashMap<Integer, String> correctindexmap = new HashMap<>();
+    correctindexmap.put(9, "backupfilestestTemp.fa_BACKUPTEST-000009");
+    correctindexmap.put(10, "backupfilestestTemp.fa_BACKUPTEST-000010");
     int[] indexes2 = { 10 };
     int[] indexes3 = { 8, 9, 10 };
     Assert.assertTrue(checkBackupFiles(correctindexmap));
@@ -189,9 +190,9 @@ public class BackupFilesTest
 
     // check there are "rollMax" backup files and they are all saved correctly
     // check 10 backup files
-    HashMap correctindexmap = new HashMap();
-    correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-00000001");
-    correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-00000002");
+    HashMap<Integer, String> correctindexmap = new HashMap<>();
+    correctindexmap.put(1, "backupfilestestTemp.fa_BACKUPTEST-000001");
+    correctindexmap.put(2, "backupfilestestTemp.fa_BACKUPTEST-000002");
     int[] indexes2 = { 1 };
     int[] indexes3 = { 1, 2, 3 };
     Assert.assertTrue(checkBackupFiles(correctindexmap));
@@ -209,6 +210,14 @@ public class BackupFilesTest
   {
     Cache.loadProperties("test/jalview/io/testProps.jvprops");
 
+    BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
+            reverse, noMax, rollMax, false);
+
+    Cache.setPropertyNoSave(BackupFiles.ENABLED,
+            Boolean.toString(enabled));
+    Cache.setPropertyNoSave(
+            BackupFilesPresetEntry.SAVEDCONFIG, bfpe.toString());
+    /*
     Cache.setPropertyNoSave(BackupFiles.ENABLED,
             Boolean.toString(enabled));
     Cache.setPropertyNoSave(BackupFiles.SUFFIX, suffix);
@@ -222,6 +231,7 @@ public class BackupFilesTest
             Integer.toString(rollMax));
     Cache.setPropertyNoSave(BackupFiles.CONFIRM_DELETE_OLD,
             "false");
+            */
   }
 
   private void save()