X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fstructure%2FStructureCommandsBase.java;h=0b5874ac58b03797eab3a294926c7ec5165bf705;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=921c9cde88b8dafe1982b45b07a4e416509cce81;hpb=9c1a9d682a2664d525bfd0f38bae861292dc3921;p=jalview.git
diff --git a/src/jalview/structure/StructureCommandsBase.java b/src/jalview/structure/StructureCommandsBase.java
index 921c9cd..0b5874a 100644
--- a/src/jalview/structure/StructureCommandsBase.java
+++ b/src/jalview/structure/StructureCommandsBase.java
@@ -1,18 +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.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-import jalview.util.Comparison;
-
import java.awt.Color;
import java.util.ArrayList;
-import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
@@ -26,6 +35,8 @@ import java.util.Map.Entry;
*/
public abstract class StructureCommandsBase implements StructureCommandsI
{
+ public static final String NAMESPACE_PREFIX = "jv_";
+
private static final String CMD_SEPARATOR = ";";
/**
@@ -33,19 +44,11 @@ public abstract class StructureCommandsBase implements StructureCommandsI
*
* @return
*/
- protected static String getCommandSeparator()
+ protected String getCommandSeparator()
{
return CMD_SEPARATOR;
}
- @Override
- public String[] setAttributesForFeatures(StructureSelectionManager ssm,
- String[] files, SequenceI[][] sequence, AlignmentViewPanel avp)
- {
- // default does nothing, override where this is implemented
- return null;
- }
-
/**
* Returns the lowest model number used by the structure viewer
*
@@ -58,120 +61,9 @@ public abstract class StructureCommandsBase implements StructureCommandsI
}
/**
- *
- * Build a data structure which records contiguous subsequences for each colour.
- * From this we can easily generate the viewer command for colour by sequence.
- * Color
- * Model number
- * Chain
- * list of start/end ranges
- * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
- *