X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=2dd9cf0d44442e12b3822fed20e61ee1b10f65fe;hb=6635c2d0807d44d4d2f7464c920fc65b50d976b9;hp=8f82a1afd7d4b9853be493ff9b88075ae100fef9;hpb=14193747f3831242bc7dfac12394eb20eb0ba480;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 8f82a1a..2dd9cf0 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -21,14 +21,17 @@
 package jalview.datamodel;
 
 import jalview.datamodel.features.FeatureAttributeType;
+import jalview.datamodel.features.FeatureAttributes;
 import jalview.datamodel.features.FeatureLocationI;
 import jalview.datamodel.features.FeatureSourceI;
 import jalview.datamodel.features.FeatureSources;
 import jalview.util.StringUtils;
 
-import java.util.HashMap;
+import java.util.Comparator;
+import java.util.LinkedHashMap;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.SortedMap;
 import java.util.TreeMap;
 import java.util.Vector;
 
@@ -47,10 +50,10 @@ public class SequenceFeature implements FeatureLocationI
 
   private static final String STATUS = "status";
 
-  private static final String STRAND = "STRAND";
+  public static final String STRAND = "STRAND";
 
-  // private key for Phase designed not to conflict with real GFF data
-  private static final String PHASE = "!Phase";
+  // key for Phase designed not to conflict with real GFF data
+  public static final String PHASE = "!Phase";
 
   // private key for ENA location designed not to conflict with real GFF data
   private static final String LOCATION = "!Location";
@@ -58,24 +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
-   */
-  private static final String ATTRIBUTES = "ATTRIBUTES";
-
-  /*
    * type, begin, end, featureGroup, score and contactFeature are final 
    * to ensure that the integrity of SequenceFeatures data store 
    * can't be broken by direct update of these fields
@@ -183,19 +168,13 @@ public class SequenceFeature implements FeatureLocationI
 
     if (sf.otherDetails != null)
     {
-      otherDetails = new HashMap<String, Object>();
-      for (Entry<String, Object> entry : sf.otherDetails.entrySet())
-      {
-        otherDetails.put(entry.getKey(), entry.getValue());
-      }
+      otherDetails = new LinkedHashMap<>();
+      otherDetails.putAll(sf.otherDetails);
     }
     if (sf.links != null && sf.links.size() > 0)
     {
-      links = new Vector<String>();
-      for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
-      {
-        links.addElement(sf.links.elementAt(i));
-      }
+      links = new Vector<>();
+      links.addAll(sf.links);
     }
   }
 
@@ -354,11 +333,16 @@ public class SequenceFeature implements FeatureLocationI
     return featureGroup;
   }
 
+  /**
+   * Adds a hyperlink for the feature. This should have the format label|url.
+   * 
+   * @param labelLink
+   */
   public void addLink(String labelLink)
   {
     if (links == null)
     {
-      links = new Vector<String>();
+      links = new Vector<>();
     }
 
     if (!links.contains(labelLink))
@@ -392,6 +376,30 @@ public class SequenceFeature implements FeatureLocationI
   }
 
   /**
+   * Answers the value of the specified attribute as string, or null if no such
+   * 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)
+  {
+    if (otherDetails == null)
+    {
+      return null;
+    }
+    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();
+  }
+
+  /**
    * Returns a property value for the given key if known, else the specified
    * default value
    * 
@@ -420,11 +428,36 @@ public class SequenceFeature implements FeatureLocationI
     {
       if (otherDetails == null)
       {
-        otherDetails = new HashMap<String, Object>();
+        /*
+         * LinkedHashMap preserves insertion order of attributes
+         */
+        otherDetails = new LinkedHashMap<>();
       }
 
       otherDetails.put(key, value);
+      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);
   }
 
   /*
@@ -441,16 +474,6 @@ public class SequenceFeature implements FeatureLocationI
     return (String) getValue(STATUS);
   }
 
-  public void setAttributes(String attr)
-  {
-    setValue(ATTRIBUTES, attr);
-  }
-
-  public String getAttributes()
-  {
-    return (String) getValue(ATTRIBUTES);
-  }
-
   /**
    * Return 1 for forward strand ('+' in GFF), -1 for reverse strand ('-' in
    * GFF), and 0 for unknown or not (validly) specified
@@ -565,9 +588,11 @@ public class SequenceFeature implements FeatureLocationI
   /**
    * Answers an html-formatted report of feature details
    * 
+   * @param seqName
+   * 
    * @return
    */
-  public String getDetailsReport()
+  public String getDetailsReport(String seqName)
   {
     FeatureSourceI metadata = FeatureSources.getInstance()
             .getSource(source);
@@ -575,9 +600,10 @@ public class SequenceFeature implements FeatureLocationI
     StringBuilder sb = new StringBuilder(128);
     sb.append("<br>");
     sb.append("<table>");
+    sb.append(String.format(ROW_DATA, "Location", seqName,
+            begin == end ? begin
+                    : begin + (isContactFeature() ? ":" : "-") + end));
     sb.append(String.format(ROW_DATA, "Type", type, ""));
-    sb.append(String.format(ROW_DATA, "Start/end", begin == end ? begin
-            : begin + (isContactFeature() ? ":" : "-") + end, ""));
     String desc = StringUtils.stripHtmlTags(description);
     sb.append(String.format(ROW_DATA, "Description", desc, ""));
     if (!Float.isNaN(score) && score != 0f)
@@ -598,34 +624,37 @@ public class SequenceFeature implements FeatureLocationI
       for (Entry<String, Object> entry : ordered.entrySet())
       {
         String key = entry.getKey();
-        if (ATTRIBUTES.equals(key))
-        {
-          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));
           }
         }
       }
@@ -693,3 +722,21 @@ 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();
+  }
+}