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=359eac6f86c898a2fb0338066455246c07b7c89e;hpb=9c1a9d682a2664d525bfd0f38bae861292dc3921;p=jalview.git
diff --git a/src/jalview/structure/StructureCommandsI.java b/src/jalview/structure/StructureCommandsI.java
index 359eac6..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;
@@ -17,47 +35,11 @@ import java.util.Map;
public interface StructureCommandsI
{
/**
- * Data bean class to simplify parameterisation in superposeStructures
- */
- public class SuperposeData
- {
- public String filename;
-
- public String pdbId;
-
- public String chain = "";
-
- public boolean isRna;
-
- /*
- * The pdb residue number (if any) mapped to columns of the alignment
- */
- public int[] pdbResNo; // or use SparseIntArray?
-
- public int modelNo;
-
- /**
- * Constructor
- *
- * @param width
- * width of alignment (number of columns that may potentially
- * participate in superposition)
- * @param model
- * structure viewer model number
- */
- public SuperposeData(int width, int model)
- {
- pdbResNo = new int[width];
- modelNo = model;
- }
- }
-
- /**
* Returns the command to colour by chain
*
* @return
*/
- String colourByChain();
+ StructureCommandI colourByChain();
/**
* Returns the command to colour residues using a charge-based scheme:
@@ -70,7 +52,7 @@ public interface StructureCommandsI
*
* @return
*/
- String colourByCharge();
+ List colourByCharge();
/**
* Returns the command to colour residues with the colours provided in the
@@ -79,7 +61,7 @@ public interface StructureCommandsI
* @param colours
* @return
*/
- String colourByResidues(Map colours);
+ List colourByResidues(Map colours);
/**
* Returns the command to set the background colour of the structure viewer
@@ -87,7 +69,7 @@ public interface StructureCommandsI
* @param col
* @return
*/
- String setBackgroundColour(Color col);
+ StructureCommandI setBackgroundColour(Color col);
/**
* Returns commands to colour mapped residues of structures according to
@@ -98,49 +80,39 @@ public interface StructureCommandsI
* @return
*/
- String[] colourBySequence(Map