JAL-3438 spotless for 2.11.2.0

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

diff --git a/src/jalview/structure/AtomSpec.java b/src/jalview/structure/AtomSpec.java
index 271bf1d..54aab7f 100644 (file)
--- a/src/jalview/structure/AtomSpec.java
+++ b/src/jalview/structure/AtomSpec.java
@@ -29,6 +29,8 @@ package jalview.structure;
  */
 public class AtomSpec
 {
+  int modelNo;
+
   private String pdbFile;
 
   private String chain;
@@ -38,6 +40,72 @@ 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)
+   * 
+   * <pre>
+   * Chimera format: 
+   *    #1.2:12-20.A     model 1, submodel 2, chain A, atoms 12-20
+   * </pre>
+   * 
+   * @param spec
+   * @return
+   * @throw IllegalArgumentException if the spec cannot be parsed, or represents
+   *        more than one residue
+   * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
+   */
+  public static AtomSpec fromChimeraAtomspec(String spec)
+  {
+    int modelSeparatorPos = spec.indexOf(":");
+    if (modelSeparatorPos == -1)
+    {
+      throw new IllegalArgumentException(spec);
+    }
+
+    int hashPos = spec.indexOf("#");
+    if (hashPos == -1 && modelSeparatorPos != 0)
+    {
+      // # is missing but something precedes : - reject
+      throw new IllegalArgumentException(spec);
+    }
+
+    String modelSubmodel = spec.substring(hashPos + 1, modelSeparatorPos);
+    int modelId = 0;
+    try
+    {
+      int subModelPos = modelSubmodel.indexOf(".");
+      modelId = Integer.valueOf(
+              subModelPos > 0 ? modelSubmodel.substring(0, subModelPos)
+                      : modelSubmodel);
+    } catch (NumberFormatException e)
+    {
+      // ignore, default to model 0
+    }
+
+    /*
+     * now process what follows the model, either
+     * Chimera:  atoms.chain
+     * ChimeraX: chain:atoms
+     */
+    String atomsAndChain = spec.substring(modelSeparatorPos + 1);
+    String[] tokens = atomsAndChain.split("\\.");
+    String atoms = tokens.length == 1 ? atomsAndChain : (tokens[0]);
+    int resNum = 0;
+    try
+    {
+      resNum = Integer.parseInt(atoms);
+    } catch (NumberFormatException e)
+    {
+      // could be a range e.g. #1:4-7.B
+      throw new IllegalArgumentException(spec);
+    }
+
+    String chainId = tokens.length == 1 ? "" : (tokens[1]);
+
+    return new AtomSpec(modelId, chainId, resNum, 0);
+  }
+
+  /**
    * Constructor
    * 
    * @param pdbFile
@@ -53,6 +121,22 @@ 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;
@@ -73,10 +157,86 @@ public class AtomSpec
     return atomIndex;
   }
 
+  public int getModelNumber()
+  {
+    return modelNo;
+  }
+
+  public void setPdbFile(String file)
+  {
+    pdbFile = file;
+  }
+
   @Override
   public String toString()
   {
     return "pdbFile: " + pdbFile + ", chain: " + chain + ", res: "
             + pdbResNum + ", atom: " + atomIndex;
   }
+
+  /**
+   * Parses a ChimeraX atomspec to construct an AtomSpec model (with null pdb
+   * file name)
+   * 
+   * <pre>
+   * ChimeraX format:
+   *    #1.2/A:12-20     model 1, submodel 2, chain A, atoms 12-20
+   * </pre>
+   * 
+   * @param spec
+   * @return
+   * @throw IllegalArgumentException if the spec cannot be parsed, or represents
+   *        more than one residue
+   * @see http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html
+   */
+  public static AtomSpec fromChimeraXAtomspec(String spec)
+  {
+    int modelSeparatorPos = spec.indexOf("/");
+    if (modelSeparatorPos == -1)
+    {
+      throw new IllegalArgumentException(spec);
+    }
+
+    int hashPos = spec.indexOf("#");
+    if (hashPos == -1 && modelSeparatorPos != 0)
+    {
+      // # is missing but something precedes : - reject
+      throw new IllegalArgumentException(spec);
+    }
+
+    String modelSubmodel = spec.substring(hashPos + 1, modelSeparatorPos);
+    int modelId = 0;
+    try
+    {
+      int subModelPos = modelSubmodel.indexOf(".");
+      modelId = Integer.valueOf(
+              subModelPos > 0 ? modelSubmodel.substring(0, subModelPos)
+                      : modelSubmodel);
+    } catch (NumberFormatException e)
+    {
+      // ignore, default to model 0
+    }
+
+    /*
+     * now process what follows the model, either
+     * Chimera:  atoms.chain
+     * ChimeraX: chain:atoms
+     */
+    String atomsAndChain = spec.substring(modelSeparatorPos + 1);
+    String[] tokens = atomsAndChain.split("\\:");
+    String atoms = tokens.length == 1 ? atomsAndChain : (tokens[1]);
+    int resNum = 0;
+    try
+    {
+      resNum = Integer.parseInt(atoms);
+    } catch (NumberFormatException e)
+    {
+      // could be a range e.g. #1:4-7.B
+      throw new IllegalArgumentException(spec);
+    }
+
+    String chainId = tokens.length == 1 ? "" : (tokens[0]);
+
+    return new AtomSpec(modelId, chainId, resNum, 0);
+  }
 }