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JAL-2446 FeatureStore with NCList - work in progress
[jalview.git]
/
src
/
jalview
/
ext
/
jmol
/
JmolCommands.java
diff --git
a/src/jalview/ext/jmol/JmolCommands.java
b/src/jalview/ext/jmol/JmolCommands.java
index
333a422
..
d5676c5
100644
(file)
--- a/
src/jalview/ext/jmol/JmolCommands.java
+++ b/
src/jalview/ext/jmol/JmolCommands.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 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.
*
*
* This file is part of Jalview.
*
@@
-64,7
+64,9
@@
public class JmolCommands
ArrayList<String> str = new ArrayList<String>();
if (mapping == null || mapping.length < 1)
ArrayList<String> str = new ArrayList<String>();
if (mapping == null || mapping.length < 1)
+ {
continue;
continue;
+ }
int lastPos = -1;
for (int s = 0; s < sequence[pdbfnum].length; s++)
int lastPos = -1;
for (int s = 0; s < sequence[pdbfnum].length; s++)
@@
-85,14
+87,18
@@
public class JmolCommands
int pos = mapping[m].getPDBResNum(asp.findPosition(r));
if (pos < 1 || pos == lastPos)
int pos = mapping[m].getPDBResNum(asp.findPosition(r));
if (pos < 1 || pos == lastPos)
+ {
continue;
continue;
+ }
lastPos = pos;
Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
if (fr != null)
lastPos = pos;
Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
if (fr != null)
+ {
col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
+ }
String newSelcom = (mapping[m].getChain() != " " ? ":"
+ mapping[m].getChain() : "")
+ "/"
String newSelcom = (mapping[m].getChain() != " " ? ":"
+ mapping[m].getChain() : "")
+ "/"
@@
-125,7
+131,7
@@
public class JmolCommands
command.append("select " + pos);
command.append(newSelcom);
}
command.append("select " + pos);
command.append(newSelcom);
}
- break;
+ // break;
}
}
}
}
}
}