3253-omnibus save

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

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 1f2e639..2dd9cf0 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -28,7 +28,7 @@ import jalview.datamodel.features.FeatureSources;
 import jalview.util.StringUtils;
 
 import java.util.Comparator;
-import java.util.HashMap;
+import java.util.LinkedHashMap;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.SortedMap;
@@ -50,10 +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";
@@ -61,12 +61,6 @@ public class SequenceFeature implements FeatureLocationI
   private static final String ROW_DATA = "<tr><td>%s</td><td>%s</td><td>%s</td></tr>";
 
   /*
-   * 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
@@ -174,19 +168,13 @@ public class SequenceFeature implements FeatureLocationI
 
     if (sf.otherDetails != null)
     {
-      otherDetails = new HashMap<>();
-      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<>();
-      for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
-      {
-        links.addElement(sf.links.elementAt(i));
-      }
+      links.addAll(sf.links);
     }
   }
 
@@ -217,8 +205,7 @@ public class SequenceFeature implements FeatureLocationI
   @Override
   public boolean equals(Object o)
   {
-    return (o instanceof SequenceFeature
-            && equals((SequenceFeature) o, false));
+    return equals(o, false);
   }
 
   /**
@@ -231,19 +218,47 @@ public class SequenceFeature implements FeatureLocationI
    * @param ignoreParent
    * @return
    */
-  public boolean equals(SequenceFeature sf, boolean ignoreParent)
+  public boolean equals(Object o, boolean ignoreParent)
   {
-    return (begin == sf.begin && end == sf.end
-            && getStrand() == sf.getStrand()
-            && (Float.isNaN(score) ? Float.isNaN(sf.score)
-                    : score == sf.score)
-            && (type + description + featureGroup + getPhase())
-                    .equals(sf.type + sf.description + sf.featureGroup
-                            + sf.getPhase())
-            && equalAttribute(getValue("ID"), sf.getValue("ID"))
-            && equalAttribute(getValue("Name"), sf.getValue("Name"))
-            && (ignoreParent || equalAttribute(getValue("Parent"),
-                    sf.getValue("Parent"))));
+    if (o == null || !(o instanceof SequenceFeature))
+    {
+      return false;
+    }
+
+    SequenceFeature sf = (SequenceFeature) o;
+    boolean sameScore = Float.isNaN(score) ? Float.isNaN(sf.score)
+            : score == sf.score;
+    if (begin != sf.begin || end != sf.end || !sameScore)
+    {
+      return false;
+    }
+
+    if (getStrand() != sf.getStrand())
+    {
+      return false;
+    }
+
+    if (!(type + description + featureGroup + getPhase()).equals(
+            sf.type + sf.description + sf.featureGroup + sf.getPhase()))
+    {
+      return false;
+    }
+    if (!equalAttribute(getValue("ID"), sf.getValue("ID")))
+    {
+      return false;
+    }
+    if (!equalAttribute(getValue("Name"), sf.getValue("Name")))
+    {
+      return false;
+    }
+    if (!ignoreParent)
+    {
+      if (!equalAttribute(getValue("Parent"), sf.getValue("Parent")))
+      {
+        return false;
+      }
+    }
+    return true;
   }
 
   /**
@@ -318,6 +333,11 @@ 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)
@@ -408,7 +428,10 @@ public class SequenceFeature implements FeatureLocationI
     {
       if (otherDetails == null)
       {
-        otherDetails = new HashMap<>();
+        /*
+         * LinkedHashMap preserves insertion order of attributes
+         */
+        otherDetails = new LinkedHashMap<>();
       }
 
       otherDetails.put(key, value);
@@ -451,16 +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
@@ -575,9 +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);
@@ -585,9 +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)
@@ -608,10 +624,6 @@ 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
-        }
 
         Object value = entry.getValue();
         if (value instanceof Map<?, ?>)
@@ -709,8 +721,6 @@ public class SequenceFeature implements FeatureLocationI
   {
     source = theSource;
   }
-
- 
 }
 
 class SFSortByEnd implements Comparator<SequenceFeature>