X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;h=b38979b06227c8d7d34a902b3b3e2a69c89b5a8e;hb=9f7269a91e9d2fd7992c11939aa797446783ce61;hp=0e6cac3fb5d7a02a32e29c05339fc1c2723a59b9;hpb=3d56aaf4e194de0e0e814ac027de3233ed5457e7;p=jalview.git
diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 0e6cac3..b38979b 100644
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -1,3 +1,20 @@
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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 .
+ *******************************************************************************/
/**
*
*/
@@ -8,14 +25,16 @@ import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.util.Comparison;
import java.awt.Color;
import java.util.ArrayList;
-
/**
* Routines for generating Jmol commands for Jalview/Jmol binding
+ * another cruisecontrol test.
+ *
* @author JimP
*
*/
@@ -24,20 +43,24 @@ public class JmolCommands
/**
* Jmol utility which constructs the commands to colour chains by the given alignment
+ * @returns Object[] { Object[] { ,
*
*/
- public static String[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)
+ public static StructureMappingcommandSet[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)
{
- ArrayList str = new ArrayList();
- StringBuffer command = new StringBuffer();
-
+
+ ArrayList cset = new ArrayList();
+
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+ StringBuffer command = new StringBuffer();
+ StructureMappingcommandSet smc;
+ ArrayList str = new ArrayList();
if (mapping == null || mapping.length < 1)
continue;
-
+
int lastPos = -1;
for (int s = 0; s < sequence[pdbfnum].length; s++)
{
@@ -98,13 +121,16 @@ public class JmolCommands
}
}
}
+ {
+ // add final chunk
+ str.add(command.toString());
+ command.setLength(0);
+ }
+ // Finally, add the command set ready to be returned.
+ cset.add(new StructureMappingcommandSet(JmolCommands.class,files[pdbfnum], str.toArray(new String[str.size()])));
+
}
- {
- // add final chunk
- str.add(command.toString());
- command.setLength(0);
- }
- return str.toArray(new String[str.size()]);
+ return cset.toArray(new StructureMappingcommandSet[cset.size()]);
}
public static StringBuffer condenseCommand(StringBuffer command, int pos)