Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

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

diff --git a/src/jalview/structure/StructureCommandsI.java b/src/jalview/structure/StructureCommandsI.java
index 91e0494..f647e71 100644 (file)
--- a/src/jalview/structure/StructureCommandsI.java
+++ b/src/jalview/structure/StructureCommandsI.java
@@ -70,15 +70,6 @@ public interface StructureCommandsI
   StructureCommandI focusView();
 
   /**
-   * Returns a command to show only the selected chains. The items in the input
-   * list should be formatted as "modelid:chainid".
-   * 
-   * @param toShow
-   * @return
-   */
-  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
    * {@code refAtoms}. If wanted, this may include commands to visually
@@ -120,16 +111,6 @@ public interface StructureCommandsI
   String getAtomSpec(AtomSpecModel model, boolean alphaOnly);
 
   /**
-   * Returns the lowest model number used by the structure viewer (likely 0 or
-   * 1)
-   * 
-   * @return
-   */
-  // TODO remove by refactoring so command generation is purely driven by
-  // AtomSpecModel objects derived in the binding classes?
-  int getModelStartNo();
-
-  /**
    * Returns command(s) to show only the backbone of the peptide (cartoons in
    * Jmol, chain in Chimera)
    * 
@@ -168,6 +149,32 @@ public interface StructureCommandsI
   StructureCommandI openSession(String filepath);
 
   /**
+   * Returns a command to show structures in the viewer. If {@code restrictTo}
+   * is null, all structures are included, otherwise the display is restricted
+   * to positions represented in the model
+   * 
+   * @param restrictTo
+   * @return
+   */
+  StructureCommandI showStructures(AtomSpecModel restrictTo);
+
+  /**
+   * Returns a command to hide the specified model chain in the structure viewer
+   * 
+   * @param modelId
+   * @param chainId
+   * @return
+   */
+  StructureCommandI hideChain(String modelId, String chainId);
+
+  /**
+   * Returns a command to hide everything in the structure viewer
+   * 
+   * @return
+   */
+  StructureCommandI hideAll();
+
+  /**
    * Returns a command to ask the viewer to close down
    * 
    * @return