+/*
+ * 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;
*/
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:
*
* @return
*/
- String colourByCharge();
+ List<StructureCommandI> colourByCharge();
/**
* Returns the command to colour residues with the colours provided in the
* @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
* @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);
}
git://source.jalview.org / jalview.git / blobdiff