JAL-2738 copy to spikes/mungo

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

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index ba7412c..0352918 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -25,6 +25,7 @@ import jalview.datamodel.features.FeatureLocationI;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.TreeMap;
 import java.util.Vector;
 
 /**
@@ -52,6 +53,16 @@ public class SequenceFeature implements FeatureLocationI
   private static final String LOCATION = "!Location";
 
   /*
+   * 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", ",");
+  }
+
+  /*
    * ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
    * name1=value1;name2=value2,value3;...etc
    */
@@ -233,8 +244,8 @@ public class SequenceFeature implements FeatureLocationI
       return false;
     }
 
-    if (!(type + description + featureGroup + getPhase()).equals(sf.type
-            + sf.description + sf.featureGroup + sf.getPhase()))
+    if (!(type + description + featureGroup + getPhase()).equals(
+            sf.type + sf.description + sf.featureGroup + sf.getPhase()))
     {
       return false;
     }
@@ -535,4 +546,59 @@ public class SequenceFeature implements FeatureLocationI
   {
     return begin == 0 && end == 0;
   }
+
+  /**
+   * Answers a formatted text report of feature details
+   * 
+   * @return
+   */
+  public String getDetailsReport()
+  {
+    StringBuilder sb = new StringBuilder(128);
+    if (begin == end)
+    {
+      sb.append(String.format("%s %d %s", type, begin, description));
+    }
+    else
+    {
+      sb.append(String.format("%s %d-%d %s", type, begin, end, description));
+    }
+    if (featureGroup != null)
+    {
+      sb.append(" (").append(featureGroup).append(")");
+    }
+    sb.append("\n\n");
+
+    if (otherDetails != null)
+    {
+      TreeMap<String, Object> ordered = new TreeMap<>(
+              String.CASE_INSENSITIVE_ORDER);
+      ordered.putAll(otherDetails);
+
+      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))
+        {
+          /*
+           * split selected INFO data by delimiter over multiple lines
+           */
+          sb.append(key).append("=\n  ");
+          String delimiter = INFO_KEYS.get(key);
+          String value = entry.getValue().toString();
+          sb.append(value.replace(delimiter, "\n  "));
+        }
+        else
+        {
+          sb.append(key + "=" + entry.getValue().toString() + "\n");
+        }
+      }
+    }
+    String text = sb.toString();
+    return text;
+  }
 }