X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=bbf1b4515595fdc5837e1384a47cb046259237e1;hb=c6018dc0dc12720e13b75850a5303279ac7094b7;hp=2110632457bf3f136b600662d1518ad4f3378897;hpb=ee8d9bad4fcb0109fd38dc362b77076d3046fec4;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 2110632..bbf1b45 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -20,6 +20,14 @@
  */
 package jalview.datamodel;
 
+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;
+
 import jalview.datamodel.features.FeatureAttributeType;
 import jalview.datamodel.features.FeatureAttributes;
 import jalview.datamodel.features.FeatureLocationI;
@@ -27,12 +35,6 @@ import jalview.datamodel.features.FeatureSourceI;
 import jalview.datamodel.features.FeatureSources;
 import jalview.util.StringUtils;
 
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.TreeMap;
-import java.util.Vector;
-
 /**
  * A class that models a single contiguous feature on a sequence. If flag
  * 'contactFeature' is true, the start and end positions are interpreted instead
@@ -48,10 +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";
@@ -59,24 +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
@@ -184,19 +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);
     }
   }
 
@@ -355,11 +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))
@@ -394,18 +377,25 @@ 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();
   }
 
@@ -438,7 +428,10 @@ 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);
@@ -463,8 +456,8 @@ public class SequenceFeature implements FeatureLocationI
               .getAttributeName(key);
     }
 
-    FeatureAttributes.getInstance().addAttribute(this.type, key, attDesc,
-            value.toString());
+    FeatureAttributes.getInstance().addAttribute(this.type, attDesc, value,
+            key);
   }
 
   /*
@@ -481,16 +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
@@ -603,11 +586,17 @@ public class SequenceFeature implements FeatureLocationI
   }
 
   /**
-   * Answers an html-formatted report of feature details
+   * Answers an html-formatted report of feature details. If parameter
+   * {@code mf} is not null, the feature is a virtual linked feature, and
+   * details included both the original location and the mapped location
+   * (CDS/peptide).
+   * 
+   * @param seqName
+   * @param mf
    * 
    * @return
    */
-  public String getDetailsReport()
+  public String getDetailsReport(String seqName, MappedFeatures mf)
   {
     FeatureSourceI metadata = FeatureSources.getInstance()
             .getSource(source);
@@ -615,9 +604,26 @@ public class SequenceFeature implements FeatureLocationI
     StringBuilder sb = new StringBuilder(128);
     sb.append("<br>");
     sb.append("<table>");
+    String name = mf == null ? seqName : mf.getLinkedSequenceName();
+    sb.append(String.format(ROW_DATA, "Location", name,
+            begin == end ? begin
+                    : begin + (isContactFeature() ? ":" : "-") + end));
+
+    String consequence = "";
+    if (mf != null)
+    {
+      int[] localRange = mf.getMappedPositions(begin, end);
+      int from = localRange[0];
+      int to = localRange[localRange.length - 1];
+      String s = mf.isFromCds() ? "Peptide Location" : "Coding location";
+      sb.append(String.format(ROW_DATA, s, seqName, from == to ? from
+              : from + (isContactFeature() ? ":" : "-") + to));
+      if (mf.isFromCds())
+      {
+        consequence = mf.findProteinVariants(this);
+      }
+    }
     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)
@@ -629,6 +635,12 @@ public class SequenceFeature implements FeatureLocationI
       sb.append(String.format(ROW_DATA, "Group", featureGroup, ""));
     }
 
+    if (!consequence.isEmpty())
+    {
+      sb.append(String.format(ROW_DATA, "Consequence",
+              "<i>Translated by Jalview</i>", consequence));
+    }
+
     if (otherDetails != null)
     {
       TreeMap<String, Object> ordered = new TreeMap<>(
@@ -638,34 +650,37 @@ 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));
           }
         }
       }
@@ -733,3 +748,21 @@ 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();
+  }
+}