X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureMapping.java;h=cbc2c0070952de38a27c2357fe712d74b9327982;hb=9a47b82e8b3b647773c1c0df94b6ce6b477587e4;hp=06e6bc3507f528ac69d7430b6552bd81f773a78d;hpb=6905363d02254a557f93f66a2b69d85aa0b23696;p=jalview.git

diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index 06e6bc3..cbc2c00 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -1,100 +1,147 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.structure;
-
-import jalview.datamodel.*;
-
-public class StructureMapping
-{
-  String mappingDetails;
-  SequenceI sequence;
-  String pdbfile;
-  String pdbid;
-  String pdbchain;
-
-  //Mapping index 0 is resNum, index 1 is atomNo
-  int[][] mapping;
-
-  public StructureMapping(SequenceI seq,
-                          String pdbfile,
-                          String pdbid,
-                          String chain,
-                          int[][] mapping,
-                          String mappingDetails)
-  {
-    sequence = seq;
-    this.pdbfile = pdbfile;
-    this.pdbid = pdbid;
-    this.pdbchain = chain;
-    this.mapping = mapping;
-    this.mappingDetails = mappingDetails;
-  }
-
-  public SequenceI getSequence()
-  {
-    return sequence;
-  }
-
-  public String getChain()
-  {
-    return pdbchain;
-  }
-
-  public String getPdbId()
-  {
-    return pdbid;
-  }
-
-  public int getAtomNum(int seqpos)
-  {
-    if (mapping.length > seqpos)
-    {
-      return mapping[seqpos][1];
-    }
-    else
-    {
-      return 0;
-    }
-  }
-
-  public int getPDBResNum(int seqpos)
-  {
-    if (mapping.length > seqpos)
-    {
-      return mapping[seqpos][0];
-    }
-    else
-    {
-      return 0;
-    }
-  }
-
-  public int getSeqPos(int pdbResNum)
-  {
-    for (int i = 0; i < mapping.length; i++)
-    {
-      if (mapping[i][0] == pdbResNum)
-      {
-        return i;
-      }
-    }
-    return -1;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.structure;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+
+public class StructureMapping
+{
+  String mappingDetails;
+
+  SequenceI sequence;
+
+  String pdbfile;
+
+  String pdbid;
+
+  String pdbchain;
+
+  // Mapping index 0 is resNum, index 1 is atomNo
+  int[][] mapping;
+
+  public StructureMapping(SequenceI seq, String pdbfile, String pdbid,
+          String chain, int[][] mapping, String mappingDetails)
+  {
+    sequence = seq;
+    this.pdbfile = pdbfile;
+    this.pdbid = pdbid;
+    this.pdbchain = chain;
+    this.mapping = mapping;
+    this.mappingDetails = mappingDetails;
+  }
+
+  public SequenceI getSequence()
+  {
+    return sequence;
+  }
+
+  public String getChain()
+  {
+    return pdbchain;
+  }
+
+  public String getPdbId()
+  {
+    return pdbid;
+  }
+
+  /**
+   * 
+   * @param seqpos
+   * @return 0 or corresponding atom number for the sequence position
+   */
+  public int getAtomNum(int seqpos)
+  {
+    if (mapping.length > seqpos)
+    {
+      return mapping[seqpos][1];
+    }
+    else
+    {
+      return 0;
+    }
+  }
+
+  /**
+   * 
+   * @param seqpos
+   * @return 0 or the corresponding residue number for the sequence position
+   */
+  public int getPDBResNum(int seqpos)
+  {
+    if (mapping.length > seqpos)
+    {
+      return mapping[seqpos][0];
+    }
+    else
+    {
+      return 0;
+    }
+  }
+
+  /**
+   * 
+   * @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++)
+    {
+      if (mapping[i][0] == pdbResNum)
+      {
+        return i;
+      }
+    }
+    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();
+    }
+    ala_copy.remap(ds, mapping, 0, -1, 1);
+    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;
+  }
+}