JAL-1925 update source version in license

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index cf60490..688762f 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -70,13 +70,7 @@ public class StructureSelectionManager
   /*
    * Set of any registered mappings between (dataset) sequences.
    */
-  Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
-
-  /*
-   * Reference counters for the above mappings. Remove mappings when ref count
-   * goes to zero.
-   */
-  private Map<AlignedCodonFrame, Integer> seqMappingRefCounts = new HashMap<AlignedCodonFrame, Integer>();
+  public Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
 
   private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
 
@@ -518,8 +512,13 @@ public class StructureSelectionManager
         if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
         {
           resNum = tmp.resNumber;
-          mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
-          mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
+          if (tmp.alignmentMapping >= -1)
+          {
+            // TODO (JAL-1836) address root cause: negative residue no in PDB
+            // file
+            mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
+            mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
+          }
         }
 
         index++;
@@ -721,7 +720,7 @@ public class StructureSelectionManager
               {
                 results = MappingUtils.buildSearchResults(seq, index,
                         seqmappings);
-               }
+              }
               if (handlingVamsasMo)
               {
                 results.addResult(seq, index, index);
@@ -911,83 +910,48 @@ public class StructureSelectionManager
   }
 
   /**
-   * Decrement the reference counter for each of the given mappings, and remove
-   * it entirely if its reference counter reduces to zero.
-   * 
-   * @param set
-   */
-  public void removeMappings(Set<AlignedCodonFrame> set)
-  {
-    if (set != null)
-    {
-      for (AlignedCodonFrame acf : set)
-      {
-        removeMapping(acf);
-      }
-    }
-  }
-
-  /**
-   * Decrement the reference counter for the given mapping, and remove it
-   * entirely if its reference counter reduces to zero.
+   * Remove the given mapping
    * 
    * @param acf
    */
-  public void removeMapping(AlignedCodonFrame acf)
+  public void deregisterMapping(AlignedCodonFrame acf)
   {
-    if (acf != null && seqmappings.contains(acf))
+    if (acf != null)
     {
-      int count = seqMappingRefCounts.get(acf);
-      count--;
-      if (count > 0)
-      {
-        seqMappingRefCounts.put(acf, count);
-      }
-      else
-      {
-        seqmappings.remove(acf);
-        seqMappingRefCounts.remove(acf);
-        if (seqmappings.isEmpty())
-        { // debug
-          System.out.println("All mappings removed");
-        }
+      boolean removed = seqmappings.remove(acf);
+      if (removed && seqmappings.isEmpty())
+      { // debug
+        System.out.println("All mappings removed");
       }
     }
   }
 
   /**
-   * Add each of the given codonFrames to the stored set. If not aready present,
-   * increments its reference count instead.
+   * Add each of the given codonFrames to the stored set, if not aready present.
    * 
    * @param set
    */
-  public void addMappings(Set<AlignedCodonFrame> set)
+  public void registerMappings(Set<AlignedCodonFrame> set)
   {
     if (set != null)
     {
       for (AlignedCodonFrame acf : set)
       {
-        addMapping(acf);
+        registerMapping(acf);
       }
     }
   }
 
   /**
-   * Add the given mapping to the stored set, or if already stored, increment
-   * its reference counter.
+   * Add the given mapping to the stored set, unless already stored.
    */
-  public void addMapping(AlignedCodonFrame acf)
+  public void registerMapping(AlignedCodonFrame acf)
   {
     if (acf != null)
     {
-      if (seqmappings.contains(acf))
-      {
-        seqMappingRefCounts.put(acf, seqMappingRefCounts.get(acf) + 1);
-      }
-      else
+      if (!seqmappings.contains(acf))
       {
         seqmappings.add(acf);
-        seqMappingRefCounts.put(acf, 1);
       }
     }
   }
@@ -1006,10 +970,6 @@ public class StructureSelectionManager
     {
       seqmappings.clear();
     }
-    if (seqMappingRefCounts != null)
-    {
-      seqMappingRefCounts.clear();
-    }
     if (sel_listeners != null)
     {
       sel_listeners.clear();
@@ -1187,20 +1147,4 @@ public class StructureSelectionManager
     }
     return null;
   }
-
-  /**
-   * Returns the reference count for a mapping
-   * 
-   * @param acf
-   * @return
-   */
-  protected int getMappingReferenceCount(AlignedCodonFrame acf)
-  {
-    if (seqMappingRefCounts == null)
-    {
-      return 0;
-    }
-    Integer count = seqMappingRefCounts.get(acf);
-    return (count == null ? 0 : count.intValue());
-  }
 }