JAL-2536 Overview window sizing not subject to min size restrictions

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

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index ac957d8..b669ebf 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -20,7 +20,6 @@
  */
 package jalview.gui;
 
-import static jalview.util.UrlConstants.EMBLEBI_STRING;
 import static jalview.util.UrlConstants.SEQUENCE_ID;
 
 import jalview.api.AlignViewportI;
@@ -31,6 +30,7 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FileLoader;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
@@ -38,11 +38,14 @@ import jalview.io.JalviewFileView;
 import jalview.jbgui.GSplitFrame;
 import jalview.jbgui.GStructureViewer;
 import jalview.structure.StructureSelectionManager;
+import jalview.urls.IdOrgSettings;
 import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.util.UrlConstants;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.params.ParamManager;
+import jalview.ws.utils.UrlDownloadClient;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -77,6 +80,7 @@ import java.beans.PropertyChangeListener;
 import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.FileOutputStream;
+import java.io.IOException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -125,6 +129,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         DropTargetListener, ClipboardOwner, IProgressIndicator,
         jalview.api.StructureSelectionManagerProvider
 {
+  private static int DEFAULT_MIN_WIDTH = 300;
+
+  private static int DEFAULT_MIN_HEIGHT = 250;
 
   private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
 
@@ -391,6 +398,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     showNews.setVisible(false);
 
+    getIdentifiersOrgData();
+
     checkURLLinks();
 
     this.addWindowListener(new WindowAdapter()
@@ -524,6 +533,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     });
   }
 
+  public void getIdentifiersOrgData()
+  {
+    // Thread off the identifiers fetcher
+    addDialogThread(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        Cache.log.debug("Downloading data from identifiers.org");
+        UrlDownloadClient client = new UrlDownloadClient();
+        try
+        {
+          client.download(IdOrgSettings.getUrl(),
+                  IdOrgSettings.getDownloadLocation());
+        } catch (IOException e)
+        {
+          Cache.log.debug("Exception downloading identifiers.org data"
+                  + e.getMessage());
+        }
+      }
+    });
+  }
+
   @Override
   protected void showNews_actionPerformed(ActionEvent e)
   {
@@ -713,7 +745,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public static synchronized void addInternalFrame(
           final JInternalFrame frame, String title, int w, int h)
   {
-    addInternalFrame(frame, title, true, w, h, true);
+    addInternalFrame(frame, title, true, w, h, true, false);
   }
 
   /**
@@ -735,7 +767,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           final JInternalFrame frame, String title, boolean makeVisible,
           int w, int h)
   {
-    addInternalFrame(frame, title, makeVisible, w, h, true);
+    addInternalFrame(frame, title, makeVisible, w, h, true, false);
   }
 
   /**
@@ -756,7 +788,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           final JInternalFrame frame, String title, int w, int h,
           boolean resizable)
   {
-    addInternalFrame(frame, title, true, w, h, resizable);
+    addInternalFrame(frame, title, true, w, h, resizable, false);
   }
 
   /**
@@ -775,10 +807,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    *          height
    * @param resizable
    *          Allow resize
+   * @param ignoreMinSize
+   *          No minimum size is set for the dialog
    */
   public static synchronized void addInternalFrame(
           final JInternalFrame frame, String title, boolean makeVisible,
-          int w, int h, boolean resizable)
+          int w, int h, boolean resizable, boolean ignoreMinSize)
   {
 
     // TODO: allow callers to determine X and Y position of frame (eg. via
@@ -804,6 +838,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     openFrameCount++;
 
+    if (!ignoreMinSize)
+    {
+      frame.setMinimumSize(new Dimension(DEFAULT_MIN_WIDTH,
+              DEFAULT_MIN_HEIGHT));
+    }
     frame.setVisible(makeVisible);
     frame.setClosable(true);
     frame.setResizable(resizable);
@@ -1025,20 +1064,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
 
-      FileFormatI format = null;
-      FileFormatI selectedFormat = chooser.getSelectedFormat();
-      if (FileFormat.Jalview.equals(selectedFormat))
-      {
-        format = FileFormat.Jalview;
-      }
-      else
+      FileFormatI format = chooser.getSelectedFormat();
+
+      /*
+       * Call IdentifyFile to verify the file contains what its extension implies.
+       * Skip this step for dynamically added file formats, because
+       * IdentifyFile does not know how to recognise them.
+       */
+      if (FileFormats.getInstance().isIdentifiable(format))
       {
         try
         {
           format = new IdentifyFile().identify(choice, DataSourceType.FILE);
         } catch (FileFormatException e)
         {
-          // format is null
+          // format = null; //??
         }
       }
 
@@ -1529,8 +1569,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   @Override
   public void saveState_actionPerformed(ActionEvent e)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-            Cache.getProperty("LAST_DIRECTORY"), "jvp", "Jalview Project");
+    JalviewFileChooser chooser = new JalviewFileChooser("jvp",
+            "Jalview Project");
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.save_state"));
@@ -2183,8 +2223,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (v_client != null)
     {
-      JalviewFileChooser chooser = new JalviewFileChooser(
-              Cache.getProperty("LAST_DIRECTORY"), "vdj",// TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+   // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+      JalviewFileChooser chooser = new JalviewFileChooser("vdj",
               "Vamsas Document");
 
       chooser.setFileView(new JalviewFileView());
@@ -2288,7 +2328,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         {
           // check what the actual links are - if it's just the default don't
           // bother with the warning
-          Vector<String> links = Preferences.sequenceURLLinks;
+          List<String> links = Preferences.sequenceUrlLinks
+                  .getLinksForMenu();
 
           // only need to check links if there is one with a
           // SEQUENCE_ID which is not the default EMBL_EBI link
@@ -2298,7 +2339,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           while (li.hasNext())
           {
             String link = li.next();
-            if (link.contains(SEQUENCE_ID) && !link.equals(EMBLEBI_STRING))
+            if (link.contains(SEQUENCE_ID)
+                    && !link.equals(UrlConstants.DEFAULT_STRING))
             {
               check = true;
               int barPos = link.indexOf("|");
@@ -2822,13 +2864,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
     {
-      if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning())
-      {
-        jalview.ws.jws2.Jws2Discoverer.getDiscoverer().setAborted(true);
-      }
       t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(
               changeSupport);
-
     }
     Thread t3 = null;
     {