JAL-3746 apply copyright to source

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

diff --git a/src/jalview/structure/StructureCommandsI.java b/src/jalview/structure/StructureCommandsI.java
index 8725b3d..c8c8070 100644 (file)
--- a/src/jalview/structure/StructureCommandsI.java
+++ b/src/jalview/structure/StructureCommandsI.java
@@ -1,8 +1,25 @@
+/*
+ * 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;
 
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.SequenceI;
-
 import java.awt.Color;
 import java.util.List;
 import java.util.Map;
@@ -82,20 +99,6 @@ public interface StructureCommandsI
   List<StructureCommandI> 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
-   */
-  List<StructureCommandI> setAttributesForFeatures(
-          StructureSelectionManager ssm,
-          String[] files, SequenceI[][] sequence, AlignmentViewPanel avp);
-
-  /**
    * 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
@@ -103,10 +106,12 @@ public interface StructureCommandsI
    * 
    * @param refAtoms
    * @param atomSpec
+   * @param backbone
+   *          - superpose based on which kind of atomType
    * @return
    */
   List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
-          AtomSpecModel atomSpec);
+          AtomSpecModel atomSpec, AtomSpecType backbone);
 
   /**
    * Returns a command to open a file of commands at the given path
@@ -125,16 +130,21 @@ public interface StructureCommandsI
    */
   StructureCommandI saveSession(String filepath);
 
+  enum AtomSpecType
+  {
+    RESIDUE_ONLY, ALPHA, PHOSPHATE
+  };
+
   /**
    * Returns a representation of the atom set represented by the model, in
    * viewer syntax format. If {@code alphaOnly} is true, this is restricted to
    * Alpha Carbon (peptide) or Phosphorous (rna) only
    * 
    * @param model
-   * @param alphaOnly
+   * @param specType
    * @return
    */
-  String getAtomSpec(AtomSpecModel model, boolean alphaOnly);
+  String getAtomSpec(AtomSpecModel model, AtomSpecType specType);
 
   /**
    * Returns the lowest model number used by the structure viewer (likely 0 or
@@ -162,4 +172,75 @@ public interface StructureCommandsI
    */
   // 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
+   */
+  List<StructureCommandI> setAttributes(
+          Map<String, Map<Object, AtomSpecModel>> featureValues);
+
+  /**
+   * Returns command to open a saved structure viewer session file, or null if
+   * not supported
+   * 
+   * @param filepath
+   * @return
+   */
+  StructureCommandI openSession(String filepath);
+
+  /**
+   * Returns a command to ask the viewer to close down
+   * 
+   * @return
+   */
+  StructureCommandI closeViewer();
+
+  /**
+   * Returns one or more commands to ask the viewer to notify model or selection
+   * changes to the given uri. Returns null if this is not supported by the
+   * structure viewer.
+   * 
+   * @param uri
+   * @return
+   */
+  List<StructureCommandI> startNotifications(String uri);
+
+  /**
+   * Returns one or more commands to ask the viewer to stop notifying model or
+   * selection changes. Returns null if this is not supported by the structure
+   * viewer.
+   * 
+   * @return
+   */
+  List<StructureCommandI> stopNotifications();
+
+  /**
+   * Returns a command to ask the viewer for its current residue selection, or
+   * null if no such command is supported
+   * 
+   * @return
+   */
+  StructureCommandI getSelectedResidues();
+
+  /**
+   * Returns a command to list the unique names of residue attributes, or null
+   * if no such command is supported
+   * 
+   * @return
+   */
+  StructureCommandI listResidueAttributes();
+
+  /**
+   * Returns a command to list residues with an attribute of the given name,
+   * with attribute value, or null if no such command is supported
+   * 
+   * @return
+   */
+  StructureCommandI getResidueAttributes(String attName);
 }