X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureCommandsI.java;h=c8c8070f756614dca7c1e315d768093b10d32f45;hb=af1f57f65bad11f8e0329be6f539ae001630948d;hp=871d84b36b85349c4760212512228a71f9c0c873;hpb=2107a91322a1988a8a6b724c74f9d244795341e3;p=jalview.git
diff --git a/src/jalview/structure/StructureCommandsI.java b/src/jalview/structure/StructureCommandsI.java
index 871d84b..c8c8070 100644
--- a/src/jalview/structure/StructureCommandsI.java
+++ b/src/jalview/structure/StructureCommandsI.java
@@ -1,12 +1,29 @@
+/*
+ * 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 java.awt.Color;
import java.util.List;
import java.util.Map;
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.SequenceI;
-
/**
* Methods that generate commands that can be sent to a molecular structure
* viewer program (e.g. Jmol, Chimera, ChimeraX)
@@ -89,10 +106,12 @@ public interface StructureCommandsI
*
* @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
@@ -111,16 +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
@@ -160,4 +184,63 @@ public interface StructureCommandsI
*/
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 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);
}