JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index e4749c9..78634e0 100644 (file)
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,6 +23,8 @@ package jalview.structure;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
 
+import java.util.HashMap;
+
 public class StructureMapping
 {
   String mappingDetails;
@@ -35,11 +37,19 @@ public class StructureMapping
 
   String pdbchain;
 
-  // Mapping index 0 is resNum, index 1 is atomNo
-  int[][] mapping;
+  public static final int UNASSIGNED_VALUE = -1;
+
+  private static final int PDB_RES_NUM_INDEX = 0;
+
+  private static final int PDB_ATOM_NUM_INDEX = 1;
+
+  // Mapping key is residue index while value is an array containing PDB resNum,
+  // and atomNo
+  HashMap<Integer, int[]> mapping;
 
   public StructureMapping(SequenceI seq, String pdbfile, String pdbid,
-          String chain, int[][] mapping, String mappingDetails)
+          String chain, HashMap<Integer, int[]> mapping,
+          String mappingDetails)
   {
     sequence = seq;
     this.pdbfile = pdbfile;
@@ -64,40 +74,57 @@ public class StructureMapping
     return pdbid;
   }
 
+  /**
+   * 
+   * @param seqpos
+   * @return 0 or corresponding atom number for the sequence position
+   */
   public int getAtomNum(int seqpos)
   {
-    if (mapping.length > seqpos)
+    int[] resNumAtomMap = mapping.get(seqpos);
+    if (resNumAtomMap != null)
     {
-      return mapping[seqpos][1];
+      return resNumAtomMap[PDB_ATOM_NUM_INDEX];
     }
     else
     {
-      return 0;
+      return UNASSIGNED_VALUE;
     }
   }
 
+  /**
+   * 
+   * @param seqpos
+   * @return 0 or the corresponding residue number for the sequence position
+   */
   public int getPDBResNum(int seqpos)
   {
-    if (mapping.length > seqpos)
+    int[] resNumAtomMap = mapping.get(seqpos);
+    if (resNumAtomMap != null)
     {
-      return mapping[seqpos][0];
+      return resNumAtomMap[PDB_RES_NUM_INDEX];
     }
     else
     {
-      return 0;
+      return UNASSIGNED_VALUE;
     }
   }
 
+  /**
+   * 
+   * @param pdbResNum
+   * @return -1 or the corresponding sequence position for a pdb residue number
+   */
   public int getSeqPos(int pdbResNum)
   {
-    for (int i = 0; i < mapping.length; i++)
+    for (Integer seqPos : mapping.keySet())
     {
-      if (mapping[i][0] == pdbResNum)
+      if (pdbResNum == getPDBResNum(seqPos))
       {
-        return i;
+        return seqPos;
       }
     }
-    return -1;
+    return UNASSIGNED_VALUE;
   }
 
   /**
@@ -118,7 +145,10 @@ public class StructureMapping
     {
       ds = ds.getDatasetSequence();
     }
-    ala_copy.remap(ds, mapping, 0, -1, 1);
+    // need to relocate annotation from pdb coordinates to local sequence
+    // -1,-1 doesn't look at pdbresnum but fails to remap sequence positions...
+
+    ala_copy.remap(ds, mapping, -1, -1, 0);
     ds.addAlignmentAnnotation(ala_copy);
     if (ds != sequence)
     {
@@ -129,4 +159,14 @@ public class StructureMapping
     }
     return ala_copy;
   }
+
+  public String getMappingDetailsOutput()
+  {
+    return mappingDetails;
+  }
+
+  public HashMap<Integer, int[]> getMapping()
+  {
+    return mapping;
+  }
 }