X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fstructure%2FStructureCommandsI.java;h=b1e1486f4e6d3b9af9842454041f68b91f34cc66;hb=d622d93ba5a3e596a4ea29bc1ba75bf2acacfdf0;hp=eda5aa938c3d288dd0374882a3b780dd993871bc;hpb=6cb920bb7a7f285a165cd34b3429dabba71f7518;p=jalview.git
diff --git a/src/jalview/structure/StructureCommandsI.java b/src/jalview/structure/StructureCommandsI.java
index eda5aa9..b1e1486 100644
--- a/src/jalview/structure/StructureCommandsI.java
+++ b/src/jalview/structure/StructureCommandsI.java
@@ -1,9 +1,25 @@
+/*
+ * 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.api.SequenceRenderer;
-import jalview.datamodel.SequenceI;
-
import java.awt.Color;
import java.util.List;
import java.util.Map;
@@ -17,13 +33,12 @@ 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:
@@ -36,7 +51,7 @@ public interface StructureCommandsI
*
* @return
*/
- String colourByCharge();
+ List colourByCharge();
/**
* Returns the command to colour residues with the colours provided in the
@@ -45,7 +60,7 @@ 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
@@ -53,51 +68,190 @@ public interface StructureCommandsI
* @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 colourBySequence(
+ Map