X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;h=d5676c5246e20bb01c7e8a7e0fd79af336f64cdf;hb=49f0437d385ee4c6dbe701180a4ba704da76b5f8;hp=19f535cf214ce803f7eb8f6dead60046a222893e;hpb=14c840a69bcdc5d9709fde571d62c1add051e4f6;p=jalview.git diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java index 19f535c..d5676c5 100644 --- a/src/jalview/ext/jmol/JmolCommands.java +++ b/src/jalview/ext/jmol/JmolCommands.java @@ -64,7 +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++) @@ -85,14 +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() : "") + "/" @@ -125,7 +131,7 @@ public class JmolCommands command.append("select " + pos); command.append(newSelcom); } - break; + // break; } } }