X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureAttributes.java;h=d2745115de84f688bc6d0342ece596351b535d13;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=3dc4f191950acf6428282e5b5d6437f4b90a424b;hpb=9feb54a4d32293b760afcdc29672fb6a880c6cbb;p=jalview.git

diff --git a/src/jalview/datamodel/features/FeatureAttributes.java b/src/jalview/datamodel/features/FeatureAttributes.java
index 3dc4f19..d274511 100644
--- a/src/jalview/datamodel/features/FeatureAttributes.java
+++ b/src/jalview/datamodel/features/FeatureAttributes.java
@@ -1,10 +1,32 @@
+/*
+ * 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;
 import java.util.Collections;
+import java.util.Comparator;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.TreeMap;
 
 /**
@@ -12,9 +34,52 @@ import java.util.TreeMap;
  */
 public class FeatureAttributes
 {
+  public enum Datatype
+  {
+    Character, Number, Mixed
+  }
+
   private static FeatureAttributes instance = new FeatureAttributes();
 
-  private Map<String, Map<String, AttributeData>> attributes;
+  /*
+   * map, by feature type, of a map, by attribute name, of
+   * attribute description and min-max range (if known)
+   */
+  private Map<String, Map<String[], AttributeData>> attributes;
+
+  /*
+   * a case-insensitive comparator so that attributes are ordered e.g.
+   * AC
+   * af
+   * CSQ:AFR_MAF
+   * CSQ:Allele
+   */
+  private Comparator<String[]> comparator = new Comparator<String[]>()
+  {
+    @Override
+    public int compare(String[] o1, String[] o2)
+    {
+      int i = 0;
+      while (i < o1.length || i < o2.length)
+      {
+        if (o2.length <= i)
+        {
+          return o1.length <= i ? 0 : 1;
+        }
+        if (o1.length <= i)
+        {
+          return -1;
+        }
+        int comp = String.CASE_INSENSITIVE_ORDER.compare(o1[i], o2[i]);
+        if (comp != 0)
+        {
+          return comp;
+        }
+        i++;
+      }
+      return 0; // same length and all matched
+    }
+  };
 
   private class AttributeData
   {
@@ -39,9 +104,11 @@ public class FeatureAttributes
      */
     boolean hasValue = false;
 
+    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
@@ -52,21 +119,43 @@ public class FeatureAttributes
 
       if (value != null)
       {
-        try
-        {
-          float f = Float.valueOf(value);
-          min = Float.min(min, f);
-          max = Float.max(max, f);
-          hasValue = true;
-        } 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)
         {
-          // ok, wasn't a number, ignore for min-max purposes
+          try
+          {
+            float f = Float.valueOf(value);
+            min = hasValue ? Math.min(min, f) : f;
+            max = hasValue ? Math.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;
+          }
         }
       }
     }
 
     /**
-     * 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()
@@ -78,6 +167,11 @@ public class FeatureAttributes
       return null;
     }
 
+    public Datatype getType()
+    {
+      return type;
+    }
+
     /**
      * Adds the given description to the list of known descriptions (without
      * duplication)
@@ -116,17 +210,19 @@ public class FeatureAttributes
   }
 
   /**
-   * Answers the attributes known for the given feature type, in alphabetical
-   * order (not case sensitive), or an empty set if no attributes are known
+   * Answers the attribute names known for the given feature type, in
+   * alphabetical order (not case sensitive), or an empty set if no attributes
+   * are known. An attribute name is typically 'simple' e.g. "AC", but may be
+   * 'compound' e.g. {"CSQ", "Allele"} where a feature has map-valued attributes
    * 
    * @param featureType
    * @return
    */
-  public List<String> getAttributes(String featureType)
+  public List<String[]> getAttributes(String featureType)
   {
     if (!attributes.containsKey(featureType))
     {
-      return Collections.<String> emptyList();
+      return Collections.<String[]> emptyList();
     }
 
     return new ArrayList<>(attributes.get(featureType).keySet());
@@ -156,23 +252,39 @@ public class FeatureAttributes
    * type, and updates the min-max for any numeric value
    * 
    * @param featureType
-   * @param attName
    * @param description
    * @param value
+   * @param attName
    */
-  public void addAttribute(String featureType, String attName,
-          String description, String value)
+  public void addAttribute(String featureType, String description,
+          Object value, String... attName)
   {
     if (featureType == null || attName == null)
     {
       return;
     }
 
-    Map<String, AttributeData> atts = attributes.get(featureType);
+    /*
+     * if attribute value is a map, drill down one more level to
+     * record its sub-fields
+     */
+    if (value instanceof Map<?, ?>)
+    {
+      for (Entry<?, ?> entry : ((Map<?, ?>) value).entrySet())
+      {
+        String[] attNames = new String[attName.length + 1];
+        System.arraycopy(attName, 0, attNames, 0, attName.length);
+        attNames[attName.length] = entry.getKey().toString();
+        addAttribute(featureType, description, entry.getValue(), attNames);
+      }
+      return;
+    }
+
+    String valueAsString = value.toString();
+    Map<String[], AttributeData> atts = attributes.get(featureType);
     if (atts == null)
     {
-      atts = new TreeMap<String, AttributeData>(
-              String.CASE_INSENSITIVE_ORDER);
+      atts = new TreeMap<>(comparator);
       attributes.put(featureType, atts);
     }
     AttributeData attData = atts.get(attName);
@@ -181,7 +293,7 @@ public class FeatureAttributes
       attData = new AttributeData();
       atts.put(attName, attData);
     }
-    attData.addInstance(description, value);
+    attData.addInstance(description, valueAsString);
   }
 
   /**
@@ -192,10 +304,10 @@ public class FeatureAttributes
    * @param attName
    * @return
    */
-  public String getDescription(String featureType, String attName)
+  public String getDescription(String featureType, String... attName)
   {
     String desc = null;
-    Map<String, AttributeData> atts = attributes.get(featureType);
+    Map<String[], AttributeData> atts = attributes.get(featureType);
     if (atts != null)
     {
       AttributeData attData = atts.get(attName);
@@ -209,17 +321,16 @@ 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
    * @return
    */
-  public float[] getMinMax(String featureType, String attName)
+  public float[] getMinMax(String featureType, String... attName)
   {
-    Map<String, AttributeData> atts = attributes.get(featureType);
+    Map<String[], AttributeData> atts = attributes.get(featureType);
     if (atts != null)
     {
       AttributeData attData = atts.get(attName);
@@ -238,19 +349,18 @@ public class FeatureAttributes
    * @param attName
    * @param description
    */
-  public void addDescription(String featureType, String attName,
-          String description)
+  public void addDescription(String featureType, String description,
+          String... attName)
   {
     if (featureType == null || attName == null)
     {
       return;
     }
-  
-    Map<String, AttributeData> atts = attributes.get(featureType);
+
+    Map<String[], AttributeData> atts = attributes.get(featureType);
     if (atts == null)
     {
-      atts = new TreeMap<String, AttributeData>(
-              String.CASE_INSENSITIVE_ORDER);
+      atts = new TreeMap<>(comparator);
       attributes.put(featureType, atts);
     }
     AttributeData attData = atts.get(attName);
@@ -261,4 +371,49 @@ public class FeatureAttributes
     }
     attData.addDescription(description);
   }
+
+  /**
+   * Answers the datatype of the feature, which is one of Character, Number or
+   * Mixed (or null if not known), as discovered from values recorded.
+   * 
+   * @param featureType
+   * @param attName
+   * @return
+   */
+  public Datatype getDatatype(String featureType, String... attName)
+  {
+    Map<String[], AttributeData> atts = attributes.get(featureType);
+    if (atts != null)
+    {
+      AttributeData attData = atts.get(attName);
+      if (attData != null)
+      {
+        return attData.getType();
+      }
+    }
+    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();
+    }
+
+  }
 }