JAL-674 make temperature factor, local secondary structure and service based secondar...

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

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index a3cec98..23ba893 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;
@@ -89,9 +90,9 @@ import javax.swing.JPopupMenu;
 import javax.swing.JProgressBar;
 import javax.swing.SwingUtilities;
 import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkEvent.EventType;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
-import javax.swing.event.HyperlinkEvent.EventType;
 
 /**
  * Jalview Desktop
@@ -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",
@@ -317,8 +318,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     else
     {
       Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-      setBounds((int) (screenSize.width - 900) / 2,
-              (int) (screenSize.height - 650) / 2, 900, 650);
+      setBounds((screenSize.width - 900) / 2,
+              (screenSize.height - 650) / 2, 900, 650);
     }
     jconsole = new Console(this, showjconsole);
     // add essential build information
@@ -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;
@@ -1039,7 +1061,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(viewport);
-    Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+    Desktop.addInternalFrame(cap, MessageManager.getString("label.cut_paste_alignmen_file"), 600, 500);
   }
 
   /*
@@ -1183,13 +1205,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     try
     {
-      ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
-      java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
-      javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
-
-      javax.help.HelpBroker hb = hs.createHelpBroker();
-      hb.setCurrentID("home");
-      hb.setDisplayed(true);
+      Help.showHelpWindow();
     } catch (Exception ex)
     {
     }
@@ -2158,7 +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)
         {
@@ -2364,7 +2382,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
     }
     progressBarHandlers.put(new Long(id), handler);
-    final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+    final JPanel progressPanel = progressBars.get(new Long(id));
     if (handler.canCancel())
     {
       JButton cancel = new JButton(
@@ -2768,7 +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();