X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;h=d5676c5246e20bb01c7e8a7e0fd79af336f64cdf;hb=17fa35af8bae6956fdee231e10ef5928f34ca810;hp=21fbb983978f53d7cec8c831d9a9cb168e441a9e;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 21fbb98..d5676c5 100644
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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 .
+ * 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.ext.jmol;
@@ -62,7 +64,9 @@ public class JmolCommands
ArrayList str = new ArrayList();
if (mapping == null || mapping.length < 1)
+ {
continue;
+ }
int lastPos = -1;
for (int s = 0; s < sequence[pdbfnum].length; s++)
@@ -83,14 +87,18 @@ public class JmolCommands
int pos = mapping[m].getPDBResNum(asp.findPosition(r));
if (pos < 1 || pos == lastPos)
+ {
continue;
+ }
lastPos = pos;
Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
if (fr != null)
+ {
col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
+ }
String newSelcom = (mapping[m].getChain() != " " ? ":"
+ mapping[m].getChain() : "")
+ "/"
@@ -123,7 +131,7 @@ public class JmolCommands
command.append("select " + pos);
command.append(newSelcom);
}
- break;
+ // break;
}
}
}