X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureCommandsI.java;h=fc8b8283c4ff42f2b78dd0c38919e8334a65e5c3;hb=refs%2Fheads%2Fbug%2FJAL-4290_headless_alignment_figure_with_sse;hp=09344881ce8e78a3c66daa85507ae5d2fb939e89;hpb=42f4227ed213d422a87d3b22fc9e85d14ffaf53f;p=jalview.git
diff --git a/src/jalview/structure/StructureCommandsI.java b/src/jalview/structure/StructureCommandsI.java
index 0934488..fc8b828 100644
--- a/src/jalview/structure/StructureCommandsI.java
+++ b/src/jalview/structure/StructureCommandsI.java
@@ -1,9 +1,27 @@
+/*
+ * 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 .
+ * 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.Collections;
import java.util.List;
import java.util.Map;
@@ -82,31 +100,19 @@ public interface StructureCommandsI
List showChains(List 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 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 {@ 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
+ * @param backbone
+ * - superpose based on which kind of atomType
* @return
*/
List superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec);
+ AtomSpecModel atomSpec, AtomSpecType backbone);
/**
* Returns a command to open a file of commands at the given path
@@ -125,16 +131,21 @@ 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 +173,91 @@ 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 setAttributes(
+ Map> featureValues);
+
+ /**
+ * Returns command to open a saved structure viewer session file, or null if
+ * not supported
+ *
+ * @param filepath
+ * @return
+ */
+ StructureCommandI openSession(String filepath);
+
+ /**
+ * Returns command to restore a previously saved version of an existing
+ * structure viewer session file. Default implementation calls 'openSession'
+ *
+ * @param filePath
+ * @return
+ */
+ StructureCommandI restoreSession(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 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 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);
+
+ List centerViewOn(List residues);
+
+ default List showHetatms(List toShow)
+ {
+ return Collections.EMPTY_LIST;
+ }
}