Merge branch 'develop' into releases/Release_2_11_Branch

[jalview.git] / src / jalview / datamodel / SequenceFeature.java

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index ffbd497..7052f34 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -27,9 +27,11 @@ import jalview.datamodel.features.FeatureSourceI;
 import jalview.datamodel.features.FeatureSources;
 import jalview.util.StringUtils;
 
+import java.util.Comparator;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.SortedMap;
 import java.util.TreeMap;
 import java.util.Vector;
 
@@ -59,18 +61,6 @@ public class SequenceFeature implements FeatureLocationI
   private static final String ROW_DATA = "<tr><td>%s</td><td>%s</td><td>%s</td></tr>";
 
   /*
-   * map of otherDetails special keys, and their value fields' delimiter
-   */
-  private static final Map<String, String> INFO_KEYS = new HashMap<>();
-
-  static
-  {
-    INFO_KEYS.put("CSQ", ",");
-    // todo capture second level metadata (CSQ FORMAT)
-    // and delimiter "|" so as to report in a table within a table?
-  }
-
-  /*
    * ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
    * name1=value1;name2=value2,value3;...etc
    */
@@ -184,7 +174,7 @@ public class SequenceFeature implements FeatureLocationI
 
     if (sf.otherDetails != null)
     {
-      otherDetails = new HashMap<String, Object>();
+      otherDetails = new HashMap<>();
       for (Entry<String, Object> entry : sf.otherDetails.entrySet())
       {
         otherDetails.put(entry.getKey(), entry.getValue());
@@ -192,7 +182,7 @@ public class SequenceFeature implements FeatureLocationI
     }
     if (sf.links != null && sf.links.size() > 0)
     {
-      links = new Vector<String>();
+      links = new Vector<>();
       for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
       {
         links.addElement(sf.links.elementAt(i));
@@ -359,7 +349,7 @@ public class SequenceFeature implements FeatureLocationI
   {
     if (links == null)
     {
-      links = new Vector<String>();
+      links = new Vector<>();
     }
 
     if (!links.contains(labelLink))
@@ -394,18 +384,25 @@ public class SequenceFeature implements FeatureLocationI
 
   /**
    * Answers the value of the specified attribute as string, or null if no such
-   * value
+   * value. If more than one attribute name is provided, tries to resolve as keys
+   * to nested maps. For example, if attribute "CSQ" holds a map of key-value
+   * pairs, then getValueAsString("CSQ", "Allele") returns the value of "Allele"
+   * in that map.
    * 
    * @param key
    * @return
    */
-  public String getValueAsString(String key)
+  public String getValueAsString(String... key)
   {
     if (otherDetails == null)
     {
       return null;
     }
-    Object value = otherDetails.get(key);
+    Object value = otherDetails.get(key[0]);
+    if (key.length > 1 && value instanceof Map<?, ?>)
+    {
+      value = ((Map) value).get(key[1]);
+    }
     return value == null ? null : value.toString();
   }
 
@@ -438,14 +435,35 @@ public class SequenceFeature implements FeatureLocationI
     {
       if (otherDetails == null)
       {
-        otherDetails = new HashMap<String, Object>();
+        otherDetails = new HashMap<>();
       }
 
       otherDetails.put(key, value);
-      FeatureAttributes.getInstance().addAttribute(this.type, key);
+      recordAttribute(key, value);
     }
   }
 
+  /**
+   * Notifies the addition of a feature attribute. This lets us keep track of
+   * which attributes are present on each feature type, and also the range of
+   * numerical-valued attributes.
+   * 
+   * @param key
+   * @param value
+   */
+  protected void recordAttribute(String key, Object value)
+  {
+    String attDesc = null;
+    if (source != null)
+    {
+      attDesc = FeatureSources.getInstance().getSource(source)
+              .getAttributeName(key);
+    }
+
+    FeatureAttributes.getInstance().addAttribute(this.type, attDesc, value,
+            key);
+  }
+
   /*
    * The following methods are added to maintain the castor Uniprot mapping file
    * for the moment.
@@ -621,30 +639,37 @@ public class SequenceFeature implements FeatureLocationI
         {
           continue; // to avoid double reporting
         }
-        if (INFO_KEYS.containsKey(key))
+
+        Object value = entry.getValue();
+        if (value instanceof Map<?, ?>)
         {
           /*
-           * split selected INFO data by delimiter over multiple lines
+           * expand values in a Map attribute across separate lines
+           * copy to a TreeMap for alphabetical ordering
            */
-          String delimiter = INFO_KEYS.get(key);
-          String[] values = entry.getValue().toString().split(delimiter);
-          for (String value : values)
+          Map<String, Object> values = (Map<String, Object>) value;
+          SortedMap<String, Object> sm = new TreeMap<>(
+                  String.CASE_INSENSITIVE_ORDER);
+          sm.putAll(values);
+          for (Entry<?, ?> e : sm.entrySet())
           {
-            sb.append(String.format(ROW_DATA, key, "", value));
+            sb.append(String.format(ROW_DATA, key, e.getKey().toString(), e
+                    .getValue().toString()));
           }
         }
         else
-        { // tried <td title="key"> but it failed to provide a tooltip :-(
+        {
+          // tried <td title="key"> but it failed to provide a tooltip :-(
           String attDesc = null;
           if (metadata != null)
           {
             attDesc = metadata.getAttributeName(key);
           }
-          String value = entry.getValue().toString();
-          if (isValueInteresting(key, value, metadata))
+          String s = entry.getValue().toString();
+          if (isValueInteresting(key, s, metadata))
           {
             sb.append(String.format(ROW_DATA, key, attDesc == null ? ""
-                    : attDesc, value));
+                    : attDesc, s));
           }
         }
       }
@@ -712,3 +737,21 @@ public class SequenceFeature implements FeatureLocationI
     source = theSource;
   }
 }
+
+class SFSortByEnd implements Comparator<SequenceFeature>
+{
+  @Override
+  public int compare(SequenceFeature a, SequenceFeature b)
+  {
+    return a.getEnd() - b.getEnd();
+  }
+}
+
+class SFSortByBegin implements Comparator<SequenceFeature>
+{
+  @Override
+  public int compare(SequenceFeature a, SequenceFeature b)
+  {
+    return a.getBegin() - b.getBegin();
+  }
+}