X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureMapping.java;h=3fcb5e9dda64cf2b8413bb4ffabecb24ce559501;hb=4ff572f7cf17f5ca9c23f82bbe41005af8af55cc;hp=b706f1702d20fd8e2194480be355a2da253c97d6;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index b706f17..3fcb5e9 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -1,23 +1,29 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.structure;
 
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+
+import java.util.HashMap;
 
 public class StructureMapping
 {
@@ -31,11 +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;
@@ -60,39 +74,89 @@ 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;
+  }
+
+  /**
+   * transfer a copy of an alignment annotation row in the PDB chain coordinate
+   * system onto the mapped sequence
+   * 
+   * @param ana
+   * @return the copy that was remapped to the mapped sequence
+   * @note this method will create a copy and add it to the dataset sequence for
+   *       the mapped sequence as well as the mapped sequence (if it is not a
+   *       dataset sequence).
+   */
+  public AlignmentAnnotation transfer(AlignmentAnnotation ana)
+  {
+    AlignmentAnnotation ala_copy = new AlignmentAnnotation(ana);
+    SequenceI ds = sequence;
+    while (ds.getDatasetSequence() != null)
+    {
+      ds = ds.getDatasetSequence();
+    }
+    // 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)
+    {
+      // mapping wasn't to an original dataset sequence, so we make a copy on
+      // the mapped sequence too
+      ala_copy = new AlignmentAnnotation(ala_copy);
+      sequence.addAlignmentAnnotation(ala_copy);
+    }
+    return ala_copy;
   }
 }