X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPymolBindingModel.java;h=62dce240cd759bb47463cadc47022a8814c6477b;hb=HEAD;hp=6aba7b6a6b4e31bca8cd4ed4639fe475378c8610;hpb=35d4103a7cac775db1e4c6598d957ed28c4d3ff5;p=jalview.git
diff --git a/src/jalview/gui/PymolBindingModel.java b/src/jalview/gui/PymolBindingModel.java
index 6aba7b6..62dce24 100644
--- a/src/jalview/gui/PymolBindingModel.java
+++ b/src/jalview/gui/PymolBindingModel.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.gui;
import java.util.ArrayList;
@@ -77,8 +97,7 @@ public class PymolBindingModel extends AAStructureBindingModel
{
// todo promote to StructureCommandsI.showLabel()
String modelId = getModelIdForFile(atom.getPdbFile());
- sb.append(String.format(" %s//%s/%d/*", modelId,
- atom.getChain(),
+ sb.append(String.format(" %s//%s/%d/*", modelId, atom.getChain(),
atom.getPdbResNum()));
}
String labelSpec = sb.toString();
@@ -102,7 +121,7 @@ public class PymolBindingModel extends AAStructureBindingModel
protected List executeCommand(StructureCommandI command,
boolean getReply)
{
- // System.out.println(command.toString()); // debug
+ // jalview.bin.Console.outPrintln(command.toString()); // debug
return pymolManager.sendCommand(command, getReply);
}
@@ -121,7 +140,7 @@ public class PymolBindingModel extends AAStructureBindingModel
@Override
public boolean isViewerRunning()
{
- return pymolManager.isPymolLaunched();
+ return pymolManager != null && pymolManager.isPymolLaunched();
}
@Override
@@ -161,20 +180,21 @@ public class PymolBindingModel extends AAStructureBindingModel
* a second parameter sets the pdbid as the loaded PyMOL object name
*/
String pdbId = pe.getId();
- try {
- String safePDBId = java.net.URLEncoder.encode(pdbId,"UTF-8");
+ try
+ {
+ String safePDBId = java.net.URLEncoder.encode(pdbId, "UTF-8");
pdbId = safePDBId.replace('%', '_');
pdbId = pdbId.replace("-", "__");
char fc = pdbId.charAt(0);
// put an 's' before any numerics
- if (fc>='0' && fc<='9')
+ if (fc >= '0' && fc <= '9')
{
- pdbId = 's'+pdbId;
+ pdbId = 's' + pdbId;
}
-// pdbId.replace('-', 0)
+ // pdbId.replace('-', 0)
} catch (Exception x)
{
- Console.error("Unxpected encoding exception for '"+pdbId+"'",x);
+ Console.error("Unxpected encoding exception for '" + pdbId + "'", x);
}
cmd.addParameter(pdbId);