X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureCommandsI.java;h=c8c8070f756614dca7c1e315d768093b10d32f45;hb=d654b1f014790b7ae25e6eec631847170a930987;hp=eda5aa938c3d288dd0374882a3b780dd993871bc;hpb=6cb920bb7a7f285a165cd34b3429dabba71f7518;p=jalview.git

diff --git a/src/jalview/structure/StructureCommandsI.java b/src/jalview/structure/StructureCommandsI.java
index eda5aa9..c8c8070 100644
--- a/src/jalview/structure/StructureCommandsI.java
+++ b/src/jalview/structure/StructureCommandsI.java
@@ -1,9 +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.api.SequenceRenderer;
-import jalview.datamodel.SequenceI;
-
 import java.awt.Color;
 import java.util.List;
 import java.util.Map;
@@ -17,13 +33,12 @@ import java.util.Map;
  */
 public interface StructureCommandsI
 {
-
   /**
    * Returns the command to colour by chain
    * 
    * @return
    */
-  String colourByChain();
+  StructureCommandI colourByChain();
 
   /**
    * Returns the command to colour residues using a charge-based scheme:
@@ -36,7 +51,7 @@ public interface StructureCommandsI
    * 
    * @return
    */
-  String colourByCharge();
+  List<StructureCommandI> colourByCharge();
 
   /**
    * Returns the command to colour residues with the colours provided in the
@@ -45,7 +60,7 @@ 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
@@ -53,51 +68,179 @@ public interface StructureCommandsI
    * @param col
    * @return
    */
-  String setBackgroundColour(Color col);
+  StructureCommandI setBackgroundColour(Color col);
 
   /**
    * Returns commands to colour mapped residues of structures according to
-   * Jalview's colouring (including feature colouring if applied)
+   * Jalview's colouring (including feature colouring if applied). Parameter is
+   * a map from Color to a model of all residues assigned that colour.
    * 
-   * @param structureSelectionManager
-   * @param files
-   * @param seqs
-   * @param sr
-   * @param alignmentv
+   * @param colourMap
    * @return
    */
-  String[] colourBySequence(
-          StructureSelectionManager structureSelectionManager,
-          String[] files, SequenceI[][] seqs, SequenceRenderer sr,
-          AlignmentViewPanel alignmentv);
+
+  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);
+  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
+   * highlight the residues that were used for the superposition.
+   * 
+   * @param refAtoms
+   * @param atomSpec
+   * @param backbone
+   *          - superpose based on which kind of atomType
+   * @return
+   */
+  List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
+          AtomSpecModel atomSpec, AtomSpecType backbone);
+
+  /**
+   * Returns a command to open a file of commands at the given path
+   * 
+   * @param path
+   * @return
+   */
+  StructureCommandI openCommandFile(String path);
 
   /**
-   * Returns zero, one or more commands to set attributes on mapped residues in
-   * the structure viewer for any features present and displayed in Jalview
+   * Returns a command to save the current viewer session state to the given
+   * file
    * 
-   * @param ssm
-   * @param files
-   * @param sequence
-   * @param avp
+   * @param filepath
    * @return
    */
-  String[] setAttributesForFeatures(StructureSelectionManager ssm,
-          String[] files, SequenceI[][] sequence, AlignmentViewPanel avp);
+  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 specType
+   * @return
+   */
+  String getAtomSpec(AtomSpecModel model, AtomSpecType specType);
+
+  /**
+   * 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)
+   * 
+   * @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
+   */
+  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);
 }