JAL-3446 post-merge unit test fixes, formatting

diff --git a/src/jalview/datamodel/features/FeatureAttributes.java b/src/jalview/datamodel/features/FeatureAttributes.java
index 655d1eb..a57fd55 100644 (file)
--- a/src/jalview/datamodel/features/FeatureAttributes.java
+++ b/src/jalview/datamodel/features/FeatureAttributes.java
@@ -132,12 +132,17 @@ public class FeatureAttributes implements ApplicationSingletonI
       if (value != null)
       {
         value = value.trim();
+        if (value.isEmpty())
+        {
+          return;
+        }
 
         /*
          * Parse numeric value unless we have previously
          * seen text data for this attribute type
          */
-        if (type == null && couldBeNumber(value) || type == Datatype.Number)
+        if ((type == null && couldBeNumber(value))
+                || type == Datatype.Number)
         {
           try
           {
@@ -161,11 +166,23 @@ public class FeatureAttributes implements ApplicationSingletonI
             hasValue = false;
           }
         }
+        else
+        {
+          /*
+           * if not a number, and not seen before...
+           */
+          type = Datatype.Character;
+          min = 0f;
+          max = 0f;
+          hasValue = false;
+        }
       }
     }
 
     /**
-     * Answers the description of the attribute, if recorded and unique, or null if either no, or more than description is recorded
+     * Answers the description of the attribute, if recorded and unique, or null
+     * if either no, or more than description is recorded
+     * 
      * @return
      */
     public String getDescription()
@@ -224,24 +241,31 @@ public class FeatureAttributes implements ApplicationSingletonI
   }
 
   /**
-   * This quick check will save significant time avoiding numerous NumberFormatExceptions.
+   * A partial check that the string is numeric - only checks the first
+   * character. Returns true if the first character is a digit, or if it is '.',
+   * '+' or '-' and not the only character. Otherwise returns false (including
+   * for an empty string). Note this is not a complete check as it returns true
+   * for (e.g.) "1A".
    * 
    * @param f
    * @return
    */
-  public boolean couldBeNumber(String f)
+  public static boolean couldBeNumber(String f)
   {
     int len = f.length();
     if (len == 0)
+    {
       return false;
+    }
     char ch = f.charAt(0);
-    switch (ch) {
+    switch (ch)
+    {
     case '.':
     case '+':
     case '-':
       return len > 1;
     }
-    return (ch <= '9' &&  ch >= '0');
+    return (ch <= '9' && ch >= '0');
   }
 
   /**
@@ -372,7 +396,7 @@ public class FeatureAttributes implements ApplicationSingletonI
     {
       return;
     }
-  
+
     Map<String[], AttributeData> atts = attributes.get(featureType);
     if (atts == null)
     {

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index ce3c29d..4030afa 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -809,8 +809,8 @@ public class Preferences extends GPreferences
             Boolean.toString(structFromPdb.isSelected()));
     if (!Platform.isJS())
     {
-    Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
-            structViewer.getSelectedItem().toString());
+      Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
+              structViewer.getSelectedItem().toString());
     }
     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
     Cache.setPropertyNoSave("MAP_WITH_SIFTS",

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index bb1bb94..0f8157b 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1275,35 +1275,35 @@ public class StructureSelectionManager implements ApplicationSingletonI
   {
     if (mappings != null)
     {
-    mappings.clear();
+      mappings.clear();
     }
     if (seqmappings != null)
     {
-    seqmappings.clear();
+      seqmappings.clear();
     }
     if (sel_listeners != null)
     {
-    sel_listeners.clear();
+      sel_listeners.clear();
     }
     if (listeners != null)
     {
-    listeners.clear();
+      listeners.clear();
     }
     if (commandListeners != null)
     {
-    commandListeners.clear();
+      commandListeners.clear();
     }
     if (view_listeners != null)
     {
-    view_listeners.clear();
+      view_listeners.clear();
     }
     if (pdbFileNameId != null)
     {
-    pdbFileNameId.clear();
+      pdbFileNameId.clear();
     }
     if (pdbIdFileName != null)
     {
-    pdbIdFileName.clear();
+      pdbIdFileName.clear();
     }
   }
 

diff --git a/test/jalview/datamodel/features/FeatureAttributesTest.java b/test/jalview/datamodel/features/FeatureAttributesTest.java
index 0846ec2..d9efa23 100644 (file)
--- a/test/jalview/datamodel/features/FeatureAttributesTest.java
+++ b/test/jalview/datamodel/features/FeatureAttributesTest.java
@@ -44,7 +44,7 @@ public class FeatureAttributesTest
    * Test the method that keeps attribute names in non-case-sensitive order,
    * including handling of 'compound' names
    */
-  @Test(groups="Functional")
+  @Test(groups = "Functional")
   public void testAttributeNameComparator()
   {
     FeatureAttributes fa = FeatureAttributes.getInstance();
@@ -52,19 +52,24 @@ public class FeatureAttributesTest
             "comparator");
 
     assertEquals(
-            comp.compare(new String[] { "CSQ" }, new String[] { "csq" }), 0);
+            comp.compare(new String[]
+            { "CSQ" }, new String[] { "csq" }), 0);
 
-    assertTrue(comp.compare(new String[] { "CSQ", "a" },
-            new String[] { "csq" }) > 0);
+    assertTrue(
+            comp.compare(new String[]
+            { "CSQ", "a" }, new String[] { "csq" }) > 0);
 
-    assertTrue(comp.compare(new String[] { "CSQ" }, new String[] { "csq",
-        "b" }) < 0);
+    assertTrue(
+            comp.compare(new String[]
+            { "CSQ" }, new String[] { "csq", "b" }) < 0);
 
-    assertTrue(comp.compare(new String[] { "CSQ", "AF" }, new String[] {
-        "csq", "ac" }) > 0);
+    assertTrue(
+            comp.compare(new String[]
+            { "CSQ", "AF" }, new String[] { "csq", "ac" }) > 0);
 
-    assertTrue(comp.compare(new String[] { "CSQ", "ac" }, new String[] {
-        "csq", "AF" }) < 0);
+    assertTrue(
+            comp.compare(new String[]
+            { "CSQ", "ac" }, new String[] { "csq", "AF" }) < 0);
   }
 
   @Test(groups = "Functional")
@@ -124,10 +129,13 @@ public class FeatureAttributesTest
             "group");
     sf.setValue("kd", "-1");
     sf.setValue("domain", "Metal");
+    sf.setValue("foo", " ");
     sf.setValue("phase", "1");
-    sf.setValue("phase", "reverse");
+    sf.setValue("phase", "1reverse");
     assertEquals(fa.getDatatype("Pfam", "kd"), Datatype.Number);
     assertEquals(fa.getDatatype("Pfam", "domain"), Datatype.Character);
     assertEquals(fa.getDatatype("Pfam", "phase"), Datatype.Mixed);
+    assertNull(fa.getDatatype("Pfam", "unobserved"));
+    assertNull(fa.getDatatype("Pfam", "foo"));// empty values are ignored
   }
 }

diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index 8108cd8..044cbc7 100644 (file)
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -81,6 +81,7 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
   {
     StructureImportSettings.setShowSeqFeatures(true);
     ssm = StructureSelectionManager.getStructureSelectionManager(null);
+    ssm.resetAll();
   }
 
   @Test(groups = { "Functional" })
@@ -139,10 +140,11 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
     ssm.registerMappings(set2);
     ssm.registerMappings(set2);
 
-    assertEquals(3, ssm.getSequenceMappings().size());
-    assertTrue(ssm.getSequenceMappings().contains(acf1));
-    assertTrue(ssm.getSequenceMappings().contains(acf2));
-    assertTrue(ssm.getSequenceMappings().contains(acf3));
+    List<AlignedCodonFrame> mappings = ssm.getSequenceMappings();
+    assertEquals(3, mappings.size());
+    assertTrue(mappings.contains(acf1));
+    assertTrue(mappings.contains(acf2));
+    assertTrue(mappings.contains(acf3));
   }
 
   /**