Merge branch 'documentation/JAL-3407_2.11.1_release' into releases/Release_2_11_1_Branch

[jalview.git] / src / jalview / datamodel / features / FeatureAttributes.java

diff --git a/src/jalview/datamodel/features/FeatureAttributes.java b/src/jalview/datamodel/features/FeatureAttributes.java
index e359b62..c15650d 100644 (file)
--- a/src/jalview/datamodel/features/FeatureAttributes.java
+++ b/src/jalview/datamodel/features/FeatureAttributes.java
@@ -1,3 +1,23 @@
+/*
+ * 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.datamodel.features;
 
 import java.util.ArrayList;
@@ -87,8 +107,8 @@ public class FeatureAttributes
     Datatype type;
 
     /**
-     * Note one instance of this attribute, recording unique, non-null names,
-     * and the min/max of any numerical values
+     * Note one instance of this attribute, recording unique, non-null
+     * descriptions, and the min/max of any numerical values
      * 
      * @param desc
      * @param value
@@ -99,20 +119,35 @@ public class FeatureAttributes
 
       if (value != null)
       {
-        try
-        {
-          float f = Float.valueOf(value);
-          min = hasValue ? Float.min(min, f) : f;
-          max = hasValue ? Float.max(max, f) : f;
-          hasValue = true;
-          type = (type == null || type == Datatype.Number) ? Datatype.Number
-                  : Datatype.Mixed;
-        } catch (NumberFormatException e)
+        value = value.trim();
+
+        /*
+         * Parse numeric value unless we have previously
+         * seen text data for this attribute type
+         */
+        if (type == null || type == Datatype.Number)
         {
-          // not a number, ignore for min-max purposes
-          type = (type == null || type == Datatype.Character)
-                  ? Datatype.Character
-                  : Datatype.Mixed;
+          try
+          {
+            float f = Float.valueOf(value);
+            min = hasValue ? Float.min(min, f) : f;
+            max = hasValue ? Float.max(max, f) : f;
+            hasValue = true;
+            type = (type == null || type == Datatype.Number)
+                    ? Datatype.Number
+                    : Datatype.Mixed;
+          } catch (NumberFormatException e)
+          {
+            /*
+             * non-numeric data: treat attribute as Character (or Mixed)
+             */
+            type = (type == null || type == Datatype.Character)
+                    ? Datatype.Character
+                    : Datatype.Mixed;
+            min = 0f;
+            max = 0f;
+            hasValue = false;
+          }
         }
       }
     }
@@ -284,9 +319,8 @@ public class FeatureAttributes
 
   /**
    * Answers the [min, max] value range of the given attribute for the given
-   * feature type, if known, else null. Attributes which only have text values
-   * would normally return null, however text values which happen to be numeric
-   * could result in a 'min-max' range.
+   * feature type, if known, else null. Attributes with a mixture of text and
+   * numeric values are considered text (do not return a min-max range).
    * 
    * @param featureType
    * @param attName
@@ -357,4 +391,27 @@ public class FeatureAttributes
     }
     return null;
   }
+
+  /**
+   * Resets all attribute metadata
+   */
+  public void clear()
+  {
+    attributes.clear();
+  }
+
+  /**
+   * Resets attribute metadata for one feature type
+   * 
+   * @param featureType
+   */
+  public void clear(String featureType)
+  {
+    Map<String[], AttributeData> map = attributes.get(featureType);
+    if (map != null)
+    {
+      map.clear();
+    }
+
+  }
 }