JAL-3551 copy Jalview features to Pymol 'p' (with pull refactoring)

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

diff --git a/src/jalview/structure/StructureCommandsI.java b/src/jalview/structure/StructureCommandsI.java
index 359eac6..871d84b 100644 (file)
--- a/src/jalview/structure/StructureCommandsI.java
+++ b/src/jalview/structure/StructureCommandsI.java
@@ -1,12 +1,12 @@
 package jalview.structure;
 
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.SequenceI;
-
 import java.awt.Color;
 import java.util.List;
 import java.util.Map;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.SequenceI;
+
 /**
  * Methods that generate commands that can be sent to a molecular structure
  * viewer program (e.g. Jmol, Chimera, ChimeraX)
@@ -17,47 +17,11 @@ import java.util.Map;
 public interface StructureCommandsI
 {
   /**
-   * Data bean class to simplify parameterisation in superposeStructures
-   */
-  public class SuperposeData
-  {
-    public String filename;
-
-    public String pdbId;
-
-    public String chain = "";
-
-    public boolean isRna;
-
-    /*
-     * The pdb residue number (if any) mapped to columns of the alignment
-     */
-    public int[] pdbResNo; // or use SparseIntArray?
-
-    public int modelNo;
-
-    /**
-     * Constructor
-     * 
-     * @param width
-     *          width of alignment (number of columns that may potentially
-     *          participate in superposition)
-     * @param model
-     *          structure viewer model number
-     */
-    public SuperposeData(int width, int model)
-    {
-      pdbResNo = new int[width];
-      modelNo = model;
-    }
-  }
-
-  /**
    * Returns the command to colour by chain
    * 
    * @return
    */
-  String colourByChain();
+  StructureCommandI colourByChain();
 
   /**
    * Returns the command to colour residues using a charge-based scheme:
@@ -70,7 +34,7 @@ public interface StructureCommandsI
    * 
    * @return
    */
-  String colourByCharge();
+  List<StructureCommandI> colourByCharge();
 
   /**
    * Returns the command to colour residues with the colours provided in the
@@ -79,7 +43,7 @@ public interface StructureCommandsI
    * @param colours
    * @return
    */
-  String colourByResidues(Map<String, Color> colours);
+  List<StructureCommandI> colourByResidues(Map<String, Color> colours);
 
   /**
    * Returns the command to set the background colour of the structure viewer
@@ -87,7 +51,7 @@ public interface StructureCommandsI
    * @param col
    * @return
    */
-  String setBackgroundColour(Color col);
+  StructureCommandI setBackgroundColour(Color col);
 
   /**
    * Returns commands to colour mapped residues of structures according to
@@ -98,48 +62,36 @@ public interface StructureCommandsI
    * @return
    */
 
-  String[] colourBySequence(Map<Object, AtomSpecModel> colourMap);
+  List<StructureCommandI> colourBySequence(
+          Map<Object, AtomSpecModel> colourMap);
 
   /**
    * Returns a command to centre the display in the structure viewer
    * 
    * @return
    */
-  String focusView();
+  StructureCommandI focusView();
 
   /**
    * Returns a command to show only the selected chains. The items in the input
-   * list should be formatted as "modelno:chainid".
+   * list should be formatted as "modelid:chainid".
    * 
    * @param toShow
    * @return
    */
-  String showChains(List<String> toShow);
-
-  /**
-   * Returns zero, one or more commands to set attributes on mapped residues in
-   * the structure viewer for any features present and displayed in Jalview
-   * 
-   * @param ssm
-   * @param files
-   * @param sequence
-   * @param avp
-   * @return
-   */
-  String[] setAttributesForFeatures(StructureSelectionManager ssm,
-          String[] files, SequenceI[][] sequence, AlignmentViewPanel avp);
+  List<StructureCommandI> showChains(List<String> toShow);
 
   /**
    * Returns a command to superpose structures by closest positioning of
-   * residues in {@code atomSpec} to the corresponding residues in {@ refAtoms}.
-   * If wanted, this may include commands to visually highlight the residues
-   * that were used for the superposition.
+   * residues in {@code atomSpec} to the corresponding residues in
+   * {@code refAtoms}. If wanted, this may include commands to visually
+   * highlight the residues that were used for the superposition.
    * 
    * @param refAtoms
    * @param atomSpec
    * @return
    */
-  String superposeStructures(AtomSpecModel refAtoms,
+  List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
           AtomSpecModel atomSpec);
 
   /**
@@ -148,7 +100,7 @@ public interface StructureCommandsI
    * @param path
    * @return
    */
-  String openCommandFile(String path);
+  StructureCommandI openCommandFile(String path);
 
   /**
    * Returns a command to save the current viewer session state to the given
@@ -157,7 +109,7 @@ public interface StructureCommandsI
    * @param filepath
    * @return
    */
-  String saveSession(String filepath);
+  StructureCommandI saveSession(String filepath);
 
   /**
    * Returns a representation of the atom set represented by the model, in
@@ -181,9 +133,31 @@ public interface StructureCommandsI
   int getModelStartNo();
 
   /**
-   * Show only the backbone of the peptide (cartoons in Jmol, chain in Chimera)
+   * Returns command(s) to show only the backbone of the peptide (cartoons in
+   * Jmol, chain in Chimera)
+   * 
+   * @return
+   */
+  List<StructureCommandI> showBackbone();
+
+  /**
+   * Returns a command to open a file at the given path
+   * 
+   * @param file
+   * @return
+   */
+  // refactor if needed to distinguish loading data or session files
+  StructureCommandI loadFile(String file);
+
+  /**
+   * Returns commands to set atom attributes or properties, given a map of
+   * Jalview features as {featureType, {featureValue, AtomSpecModel}}. The
+   * assumption is that one command can be constructed for each feature type and
+   * value combination, to apply it to one or more residues.
    * 
+   * @param featureValues
    * @return
    */
-  String showBackbone();
+  List<StructureCommandI> setAttributes(
+          Map<String, Map<Object, AtomSpecModel>> featureValues);
 }