JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index a76b2f2..147cc07 100644 (file)
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -1,23 +1,27 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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;
 
 public class StructureMapping
 {
@@ -60,6 +64,11 @@ 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)
@@ -72,6 +81,11 @@ public class StructureMapping
     }
   }
 
+  /**
+   * 
+   * @param seqpos
+   * @return 0 or the corresponding residue number for the sequence position
+   */
   public int getPDBResNum(int seqpos)
   {
     if (mapping.length > seqpos)
@@ -84,6 +98,11 @@ public class StructureMapping
     }
   }
 
+  /**
+   * 
+   * @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++)
@@ -95,4 +114,37 @@ public class StructureMapping
     }
     return -1;
   }
+
+  /**
+   * 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;
+  }
 }