JAL-1342 new command-line parameter -jabaws <URL>

[jalview.git] / src / jalview / gui / Desktop.java

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 63f0caa..7a1202c 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -26,6 +26,7 @@ import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
+import jalview.structure.StructureSelectionManager;
 import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.ws.params.ParamManager;
@@ -286,7 +287,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     instance = this;
     doVamsasClientCheck();
     doGroovyCheck();
-
+    doConfigureStructurePrefs();
     setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
     boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
@@ -416,6 +417,27 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             });
   }
 
+  public void doConfigureStructurePrefs()
+  {
+    // configure services
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(this);
+    if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
+    {
+      ssm.setAddTempFacAnnot(jalview.bin.Cache.getDefault(
+              Preferences.ADD_TEMPFACT_ANN, true));
+    ssm.setProcessSecondaryStructure(jalview.bin.Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
+    ssm.setSecStructServices(jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW,
+            true));
+    }
+    else
+    {
+      ssm.setAddTempFacAnnot(false);
+      ssm.setProcessSecondaryStructure(false);
+      ssm.setSecStructServices(false);
+    }
+  }
+
   public void checkForNews()
   {
     final Desktop me = this;
@@ -2152,7 +2174,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       if (showMemoryUsage && g != null && df != null)
       {
         if (percentUsage < 20)
+        {
           g.setColor(Color.red);
+        }
         FontMetrics fm = g.getFontMetrics();
         if (fm != null)
         {
@@ -2578,7 +2602,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                                                 + ermsg
                                                 + "</td></tr></table>"
                                                 + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
-                                                + " or mis-configured HTTP proxy settings.</p>"
+                                                + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
                                                 + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
                                                 + " Tools->Preferences dialog box to change them.</p></html>"),
                                 "Web Service Configuration Problem",
@@ -2762,7 +2786,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     invalidate();
     File of;
-    ImageMaker im = new jalview.util.ImageMaker(this, ImageMaker.EPS, "View of Desktop", getWidth(), getHeight(), of=new File("Jalview_snapshot"+System.currentTimeMillis()+".eps"), "View of desktop");
+    ImageMaker im = new jalview.util.ImageMaker(this, ImageMaker.TYPE.EPS,
+            "View of Desktop", getWidth(), getHeight(), of = new File(
+                    "Jalview_snapshot" + System.currentTimeMillis()
+                            + ".eps"), "View of desktop");
     try {
       paintAll(im.getGraphics());
       im.writeImage();