Merge branch 'develop' into releases/Release_2_10_2_Branch

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

diff --git a/src/jalview/structure/AtomSpec.java b/src/jalview/structure/AtomSpec.java
index d3e8d42..f20cd31 100644 (file)
--- a/src/jalview/structure/AtomSpec.java
+++ b/src/jalview/structure/AtomSpec.java
@@ -1,16 +1,36 @@
+/*
+ * 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.
+ *  
+ * 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;
 
 /**
- * Java bean representing an atom in a PDB (or similar) structure model.
+ * Java bean representing an atom in a PDB (or similar) structure model or
+ * viewer
  * 
  * @author gmcarstairs
  *
  */
 public class AtomSpec
 {
-  // TODO clarify do we want pdbFile here, or pdbId?
-  // compare highlightAtom in 2.8.2 for JalviewJmolBinding and
-  // javascript.MouseOverStructureListener
+  int modelNo;
+
   private String pdbFile;
 
   private String chain;
@@ -20,6 +40,60 @@ public class AtomSpec
   private int atomIndex;
 
   /**
+   * Parses a Chimera atomspec e.g. #1:12.A to construct an AtomSpec model (with
+   * null pdb file name)
+   * 
+   * @param spec
+   * @return
+   * @throw IllegalArgumentException if the spec cannot be parsed, or represents
+   *        more than one residue
+   */
+  public static AtomSpec fromChimeraAtomspec(String spec)
+  {
+    int colonPos = spec.indexOf(":");
+    if (colonPos == -1)
+    {
+      throw new IllegalArgumentException(spec);
+    }
+
+    int hashPos = spec.indexOf("#");
+    if (hashPos == -1 && colonPos != 0)
+    {
+      // # is missing but something precedes : - reject
+      throw new IllegalArgumentException(spec);
+    }
+
+    String modelSubmodel = spec.substring(hashPos + 1, colonPos);
+    int dotPos = modelSubmodel.indexOf(".");
+    int modelId = 0;
+    try
+    {
+      modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
+              : modelSubmodel.substring(0, dotPos));
+    } catch (NumberFormatException e)
+    {
+      // ignore, default to model 0
+    }
+
+    String residueChain = spec.substring(colonPos + 1);
+    dotPos = residueChain.indexOf(".");
+    int resNum = 0;
+    try
+    {
+      resNum = Integer.parseInt(dotPos == -1 ? residueChain
+              : residueChain.substring(0, dotPos));
+    } catch (NumberFormatException e)
+    {
+      // could be a range e.g. #1:4-7.B
+      throw new IllegalArgumentException(spec);
+    }
+
+    String chainId = dotPos == -1 ? "" : residueChain.substring(dotPos + 1);
+
+    return new AtomSpec(modelId, chainId, resNum, 0);
+  }
+
+  /**
    * Constructor
    * 
    * @param pdbFile
@@ -35,6 +109,22 @@ public class AtomSpec
     this.atomIndex = atomNo;
   }
 
+  /**
+   * Constructor
+   * 
+   * @param modelId
+   * @param chainId
+   * @param resNo
+   * @param atomNo
+   */
+  public AtomSpec(int modelId, String chainId, int resNo, int atomNo)
+  {
+    this.modelNo = modelId;
+    this.chain = chainId;
+    this.pdbResNum = resNo;
+    this.atomIndex = atomNo;
+  }
+
   public String getPdbFile()
   {
     return pdbFile;
@@ -55,6 +145,16 @@ public class AtomSpec
     return atomIndex;
   }
 
+  public int getModelNumber()
+  {
+    return modelNo;
+  }
+
+  public void setPdbFile(String file)
+  {
+    pdbFile = file;
+  }
+
   @Override
   public String toString()
   {