From 9c66e390c2195d640a50bb645655c12158454f1e Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 11 Oct 2016 09:27:33 +0100 Subject: [PATCH] JAL-2233 reverted changes to Jmol logging levels --- src/jalview/appletgui/AppletJmol.java | 3 --- src/jalview/ext/jmol/JalviewJmolBinding.java | 3 +++ src/jalview/ext/jmol/JmolParser.java | 5 ++--- src/jalview/gui/AppJmol.java | 5 +---- 4 files changed, 6 insertions(+), 10 deletions(-) diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index 264ac14..8374721 100644 --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.java @@ -64,8 +64,6 @@ import java.util.Hashtable; import java.util.List; import java.util.Vector; -import org.jmol.util.Logger; - public class AppletJmol extends EmbmenuFrame implements // StructureListener, KeyListener, ActionListener, ItemListener @@ -271,7 +269,6 @@ public class AppletJmol extends EmbmenuFrame implements jmb.allocateViewer(renderPanel, true, ap.av.applet.getName() + "_jmol_", ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(), "-applet", scriptWindow, null); - Logger.setLogLevel(Logger.LEVEL_WARN); } catch (Exception e) { System.err diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 2f3464b..a577559 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -307,6 +307,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel * 'matched' array will hold 'true' for visible alignment columns where * all sequences have a residue with a mapping to the PDB structure */ + // TODO could use a BitSet for matched boolean matched[] = new boolean[alignment.getWidth()]; for (int m = 0; m < matched.length; m++) { @@ -352,6 +353,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel * generate select statements to select regions to superimpose structures */ { + // TODO extract method to construct selection statements for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { String chainCd = ":" + structures[pdbfnum].chain; @@ -449,6 +451,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } if (selectioncom.length() > 0) { + // TODO is performing selectioncom redundant here? is done later on // System.out.println("Select regions:\n" + selectioncom.toString()); evalStateCommand("select *; cartoons off; backbone; select (" + selectioncom.toString() + "); cartoons; "); diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java index 1800ef0..ca45d7b 100644 --- a/src/jalview/ext/jmol/JmolParser.java +++ b/src/jalview/ext/jmol/JmolParser.java @@ -124,12 +124,11 @@ public class JmolParser extends StructureFile implements JmolStatusListener try { /* - * params -o (output to sysout) -i (no info logging, less verbose) - * -n (nodisplay) -x (exit when finished) + * params -o (output to sysout) -n (nodisplay) -x (exit when finished) * see http://wiki.jmol.org/index.php/Jmol_Application */ viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null, - null, "-x -o -n -i", this); + null, "-x -o -n", this); // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used viewer.setBooleanProperty("defaultStructureDSSP", true); } catch (ClassCastException x) diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 24604ed..021a004 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -381,10 +381,7 @@ public class AppJmol extends StructureViewerBase scriptWindow.setVisible(false); } - /* - * -i for no info logging (less verbose) - */ - jmb.allocateViewer(renderPanel, true, "", null, null, "-i", + jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, null); // jmb.newJmolPopup("Jmol"); if (command == null) -- 1.7.10.2