X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fstructure%2FStructureCommandsI.java;h=b1e1486f4e6d3b9af9842454041f68b91f34cc66;hb=d622d93ba5a3e596a4ea29bc1ba75bf2acacfdf0;hp=c224187524ea42544848338fc1596d1aa82c8e1f;hpb=4994aa94fd62af0058f2db96f0ea6c4ca1abe80b;p=jalview.git
diff --git a/src/jalview/structure/StructureCommandsI.java b/src/jalview/structure/StructureCommandsI.java
index c224187..b1e1486 100644
--- a/src/jalview/structure/StructureCommandsI.java
+++ b/src/jalview/structure/StructureCommandsI.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -86,10 +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
@@ -108,16 +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
@@ -166,6 +193,15 @@ public interface StructureCommandsI
* @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
@@ -200,4 +236,22 @@ public interface StructureCommandsI
* @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);
}