X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fstructure%2FStructureCommandsBase.java;h=ec6032de9c38c6e8a1b0e71ff8b789c0065ca2ea;hb=fccc58b804b576fcd39f3e7f2c9699c0ba75d5f9;hp=774327c153e56e8545902703f887336058c662fa;hpb=4994aa94fd62af0058f2db96f0ea6c4ca1abe80b;p=jalview.git
diff --git a/src/jalview/structure/StructureCommandsBase.java b/src/jalview/structure/StructureCommandsBase.java
index 774327c..ec6032d 100644
--- a/src/jalview/structure/StructureCommandsBase.java
+++ b/src/jalview/structure/StructureCommandsBase.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;
@@ -6,6 +26,8 @@ import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
+import jalview.bin.Console;
+
/**
* A base class holding methods useful to all classes that implement commands
* for structure viewers
@@ -15,15 +37,16 @@ import java.util.Map.Entry;
*/
public abstract class StructureCommandsBase implements StructureCommandsI
{
- private static final String CMD_SEPARATOR = ";";
public static final String NAMESPACE_PREFIX = "jv_";
+ private static final String CMD_SEPARATOR = ";";
+
/**
* Returns something that separates concatenated commands
*
* @return
*/
- protected static String getCommandSeparator()
+ protected String getCommandSeparator()
{
return CMD_SEPARATOR;
}
@@ -40,8 +63,9 @@ public abstract class StructureCommandsBase implements StructureCommandsI
}
/**
- * Helper method to add one contiguous range to the AtomSpec model for the given
- * value (creating the model if necessary). As used by Jalview, {@code value} is
+ * Helper method to add one contiguous range to the AtomSpec model for the
+ * given value (creating the model if necessary). As used by Jalview,
+ * {@code value} is
*
* - a colour, when building a 'colour structure by sequence' command
* - a feature value, when building a 'set Chimera attributes from features'
@@ -68,7 +92,7 @@ public abstract class StructureCommandsBase implements StructureCommandsI
atomSpec = new AtomSpecModel();
map.put(value, atomSpec);
}
-
+
atomSpec.addRange(model, startPos, endPos, chain);
}
@@ -140,7 +164,7 @@ public abstract class StructureCommandsBase implements StructureCommandsI
protected StructureCommandI getColourCommand(AtomSpecModel atomSpecModel,
Color colour)
{
- String atomSpec = getAtomSpec(atomSpecModel, false);
+ String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
return colourResidues(atomSpec, colour);
}
@@ -241,4 +265,22 @@ public abstract class StructureCommandsBase implements StructureCommandsI
{
return null;
}
+
+ @Override
+ public StructureCommandI listResidueAttributes()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI getResidueAttributes(String attName)
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI restoreSession(String filePath)
+ {
+ return loadFile(filePath);
+ }
}