X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=e41403c42c2dbc2cb3c46e66cf52c598e04ab33f;hb=e4496f5b27c5a01a1cc494653bd3f9f49080d544;hp=11c40c3b7764e81b8f0a1baffc6f36425cd03146;hpb=0fd1986d18c3093cc5386697ed49301599b74379;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 11c40c3..e41403c 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -21,7 +21,10 @@
 package jalview.io;
 
 import jalview.api.ComplexAlignFile;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
+import jalview.api.FeaturesSourceI;
+import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
@@ -31,6 +34,8 @@ import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
+import jalview.gui.JvSwingUtils;
 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
@@ -39,18 +44,18 @@ import jalview.util.MessageManager;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
-import javax.swing.JOptionPane;
 import javax.swing.SwingUtilities;
 
 public class FileLoader implements Runnable
 {
   String file;
 
-  String protocol;
+  DataSourceType protocol;
 
-  String format;
+  FileFormatI format;
 
-  FileParse source = null; // alternative specification of where data comes
+  AlignmentFileReaderI source = null; // alternative specification of where data
+                                      // comes
 
   // from
 
@@ -84,22 +89,18 @@ public class FileLoader implements Runnable
   }
 
   public void LoadFile(AlignViewport viewport, String file,
-          String protocol, String format)
+          DataSourceType protocol, FileFormatI format)
   {
     this.viewport = viewport;
-    LoadFile(file, protocol, format);
-  }
-
-  public void LoadFile(String file, String protocol, String format)
-  {
     this.file = file;
     this.protocol = protocol;
     this.format = format;
-
+    
     final Thread loader = new Thread(this);
-
+    
     SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         loader.start();
@@ -108,58 +109,31 @@ public class FileLoader implements Runnable
   }
 
   /**
-   * Load a (file, protocol) source of unknown type
-   * 
-   * @param file
-   * @param protocol
-   */
-  public void LoadFile(String file, String protocol)
-  {
-    LoadFile(file, protocol, null);
-  }
-
-  /**
    * Load alignment from (file, protocol) and wait till loaded
    * 
    * @param file
-   * @param protocol
+   * @param sourceType
    * @return alignFrame constructed from file contents
    */
-  public AlignFrame LoadFileWaitTillLoaded(String file, String protocol)
+  public AlignFrame LoadFileWaitTillLoaded(String file,
+          DataSourceType sourceType)
   {
-    return LoadFileWaitTillLoaded(file, protocol, null);
+    return LoadFileWaitTillLoaded(file, sourceType, null);
   }
 
   /**
    * Load alignment from (file, protocol) of type format and wait till loaded
    * 
    * @param file
-   * @param protocol
+   * @param sourceType
    * @param format
    * @return alignFrame constructed from file contents
    */
-  public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
-          String format)
+  public AlignFrame LoadFileWaitTillLoaded(String file,
+          DataSourceType sourceType, FileFormatI format)
   {
     this.file = file;
-    this.protocol = protocol;
-    this.format = format;
-    return _LoadFileWaitTillLoaded();
-  }
-
-  /**
-   * Load alignment from FileParse source of type format and wait till loaded
-   * 
-   * @param source
-   * @param format
-   * @return alignFrame constructed from file contents
-   */
-  public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
-  {
-    this.source = source;
-
-    file = source.getInFile();
-    protocol = source.type;
+    this.protocol = sourceType;
     this.format = format;
     return _LoadFileWaitTillLoaded();
   }
@@ -191,13 +165,13 @@ public class FileLoader implements Runnable
   public void updateRecentlyOpened()
   {
     Vector recent = new Vector();
-    if (protocol.equals(FormatAdapter.PASTE))
+    if (protocol == DataSourceType.PASTE)
     {
       // do nothing if the file was pasted in as text... there is no filename to
       // refer to it as.
       return;
     }
-    String type = protocol.equals(FormatAdapter.FILE) ? "RECENT_FILE"
+    String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
             : "RECENT_URL";
 
     String historyItems = jalview.bin.Cache.getProperty(type);
@@ -226,17 +200,18 @@ public class FileLoader implements Runnable
       newHistory.append(recent.elementAt(i));
     }
 
-    jalview.bin.Cache.setProperty(type, newHistory.toString());
+    Cache.setProperty(type, newHistory.toString());
 
-    if (protocol.equals(FormatAdapter.FILE))
+    if (protocol == DataSourceType.FILE)
     {
-      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+      Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
     }
   }
 
+  @Override
   public void run()
   {
-    String title = protocol.equals(AppletFormatAdapter.PASTE) ? "Copied From Clipboard"
+    final String title = protocol == DataSourceType.PASTE ? "Copied From Clipboard"
             : file;
     Runtime rt = Runtime.getRuntime();
     try
@@ -250,32 +225,30 @@ public class FileLoader implements Runnable
         // just in case the caller didn't identify the file for us
         if (source != null)
         {
-          format = new IdentifyFile().Identify(source, false); // identify
-          // stream and
-          // rewind rather
-          // than close
+          format = new IdentifyFile().identify(source, false);
+          // identify stream and rewind rather than close
         }
         else
         {
-          format = new IdentifyFile().Identify(file, protocol);
+          format = new IdentifyFile().identify(file, protocol);
         }
 
       }
 
-      if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE"))
+      if (format == null)
       {
         Desktop.instance.stopLoading();
         System.err.println("The input file \"" + file
                 + "\" has null or unidentifiable data content!");
         if (!Jalview.isHeadlessMode())
         {
-          javax.swing.JOptionPane.showInternalMessageDialog(
+          JvOptionPane.showInternalMessageDialog(
                   Desktop.desktop,
                   MessageManager.getString("label.couldnt_read_data")
                           + " in " + file + "\n"
-                          + AppletFormatAdapter.SUPPORTED_FORMATS,
+                          + AppletFormatAdapter.getSupportedFormats(),
                   MessageManager.getString("label.couldnt_read_data"),
-                  JOptionPane.WARNING_MESSAGE);
+                  JvOptionPane.WARNING_MESSAGE);
         }
         return;
       }
@@ -284,15 +257,13 @@ public class FileLoader implements Runnable
       if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
       {
         System.gc();
-        memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
-        // memory
-        // before
-        // load
+        // free memory before loading file
+        memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory());
       }
       loadtime = -System.currentTimeMillis();
       AlignmentI al = null;
 
-      if (format.equalsIgnoreCase("Jalview"))
+      if (FileFormat.Jalview.equals(format))
       {
         if (source != null)
         {
@@ -305,40 +276,44 @@ public class FileLoader implements Runnable
       }
       else
       {
-        String error = AppletFormatAdapter.SUPPORTED_FORMATS;
-        if (FormatAdapter.isValidFormat(format))
+        String error = AppletFormatAdapter.getSupportedFormats();
+        try
         {
-          try
+          if (source != null)
           {
-            if (source != null)
-            {
-              // read from the provided source
-              al = new FormatAdapter().readFromFile(source, format);
-            }
-            else
-            {
-
-              // open a new source and read from it
-              FormatAdapter fa = new FormatAdapter();
-              al = fa.readFile(file, protocol, format);
-              source = fa.getAlignFile(); // keep reference for later if
-                                          // necessary.
-            }
-          } catch (java.io.IOException ex)
+            // read from the provided source
+            al = new FormatAdapter().readFromFile(source, format);
+          }
+          else
           {
-            error = ex.getMessage();
+
+            // open a new source and read from it
+            FormatAdapter fa = new FormatAdapter();
+            al = fa.readFile(file, protocol, format);
+            source = fa.getAlignFile(); // keep reference for later if
+                                        // necessary.
           }
+        } catch (java.io.IOException ex)
+        {
+          error = ex.getMessage();
         }
-        else
+
+        if (!format.hasSequenceData())
         {
-          if (format != null && format.length() > 7)
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
           {
-            // ad hoc message in format.
-            error = format + "\n" + error;
-          }
+            @Override
+            public void run()
+            {
+              String msg = MessageManager.formatMessage("label.successfully_loaded_file_type", format.getName(), title);
+              msg = JvSwingUtils.wrapTooltip(true, msg);
+              JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
+                      "", JvOptionPane.INFORMATION_MESSAGE);
+            }
+          });
         }
-
-        if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
+        else if ((al != null) && (al.getHeight() > 0)
+                && al.hasValidSequence())
         {
           // construct and register dataset sequences
           for (SequenceI sq : al.getSequences())
@@ -351,81 +326,26 @@ public class FileLoader implements Runnable
             {
               for (PDBEntry pdbe : sq.getAllPDBEntries())
               {
-                // register PDB entries with desktop's structure selection
-                // manager
                 StructureSelectionManager.getStructureSelectionManager(
                         Desktop.instance).registerPDBEntry(pdbe);
               }
             }
           }
 
+          FeatureSettingsModelI proxyColourScheme = source
+                  .getFeatureColourScheme();
           if (viewport != null)
           {
+            if (proxyColourScheme != null)
+            {
+              viewport.applyFeaturesStyle(proxyColourScheme);
+            }
             // append to existing alignment
             viewport.addAlignment(al, title);
           }
           else
           {
-            // otherwise construct the alignFrame
-
-            if (source instanceof ComplexAlignFile)
-            {
-              ColumnSelection colSel = ((ComplexAlignFile) source)
-                      .getColumnSelection();
-              SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
-                      .getHiddenSequences();
-              boolean showSeqFeatures = ((ComplexAlignFile) source)
-                      .isShowSeqFeatures();
-              String colourSchemeName = ((ComplexAlignFile) source)
-                      .getGlobalColourScheme();
-              FeaturesDisplayedI fd = ((ComplexAlignFile) source)
-                      .getDisplayedFeatures();
-              alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
-                      AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
-
-              alignFrame.getViewport().setShowSequenceFeatures(
-                      showSeqFeatures);
-              alignFrame.getViewport().setFeaturesDisplayed(fd);
-              ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
-                      colourSchemeName, al);
-              if (cs != null)
-              {
-                alignFrame.changeColour(cs);
-              }
-            }
-            else
-            {
-              alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
-                      AlignFrame.DEFAULT_HEIGHT);
-            }
-            // add metadata and update ui
-            if (!protocol.equals(AppletFormatAdapter.PASTE))
-            {
-              alignFrame.setFileName(file, format);
-            }
-
-            alignFrame.statusBar.setText(MessageManager.formatMessage(
-                    "label.successfully_loaded_file",
-                    new String[] { title }));
-
-            if (raiseGUI)
-            {
-              // add the window to the GUI
-              // note - this actually should happen regardless of raiseGUI
-              // status in Jalview 3
-              // TODO: define 'virtual desktop' for benefit of headless scripts
-              // that perform queries to find the 'current working alignment'
-              Desktop.addInternalFrame(alignFrame, title,
-                      AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
-            }
-
-            try
-            {
-              alignFrame.setMaximum(jalview.bin.Cache.getDefault(
-                      "SHOW_FULLSCREEN", false));
-            } catch (java.beans.PropertyVetoException ex)
-            {
-            }
+            addAlignFrame(al, title);
           }
         }
         else
@@ -442,16 +362,18 @@ public class FileLoader implements Runnable
                   + "\n" + error;
           // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
           // bits ?
-          if (raiseGUI && Desktop.desktop != null)
+          if (format.hasSequenceData() && raiseGUI
+                  && Desktop.desktop != null)
           {
             javax.swing.SwingUtilities.invokeLater(new Runnable()
             {
+              @Override
               public void run()
               {
-                JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                         errorMessage, MessageManager
                                 .getString("label.error_loading_file"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
               }
             });
           }
@@ -472,14 +394,15 @@ public class FileLoader implements Runnable
       {
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
+          @Override
           public void run()
           {
-            javax.swing.JOptionPane.showInternalMessageDialog(
+            JvOptionPane.showInternalMessageDialog(
                     Desktop.desktop, MessageManager.formatMessage(
                             "label.problems_opening_file",
                             new String[] { file }), MessageManager
                             .getString("label.file_open_error"),
-                    javax.swing.JOptionPane.WARNING_MESSAGE);
+                    JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -493,14 +416,15 @@ public class FileLoader implements Runnable
       {
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
+          @Override
           public void run()
           {
-            javax.swing.JOptionPane.showInternalMessageDialog(
+            JvOptionPane.showInternalMessageDialog(
                     Desktop.desktop, MessageManager.formatMessage(
                             "warn.out_of_memory_loading_file", new String[]
                             { file }), MessageManager
                             .getString("label.out_of_memory"),
-                    javax.swing.JOptionPane.WARNING_MESSAGE);
+                    JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -546,17 +470,81 @@ public class FileLoader implements Runnable
 
   }
 
-  /*
-   * (non-Javadoc)
+  /**
+   * Helper method that adds the alignment as a new frame on the Desktop
    * 
-   * @see java.lang.Object#finalize()
+   * @param al
+   * @param title
    */
-  protected void finalize() throws Throwable
+  protected void addAlignFrame(AlignmentI al, String title)
   {
-    source = null;
-    alignFrame = null;
-    viewport = null;
-    super.finalize();
+    // otherwise construct the alignFrame
+
+    if (source instanceof ComplexAlignFile)
+    {
+      ColumnSelection colSel = ((ComplexAlignFile) source)
+              .getColumnSelection();
+      SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+              .getHiddenSequences();
+      String colourSchemeName = ((ComplexAlignFile) source)
+              .getGlobalColourScheme();
+      FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+              .getDisplayedFeatures();
+      alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
+              AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+      alignFrame.getViewport().setFeaturesDisplayed(fd);
+      alignFrame.getViewport().setShowSequenceFeatures(
+              ((ComplexAlignFile) source).isShowSeqFeatures());
+      ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+              colourSchemeName, al);
+      if (cs != null)
+      {
+        alignFrame.changeColour(cs);
+      }
+    }
+    else
+    {
+      alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+              AlignFrame.DEFAULT_HEIGHT);
+      if (source instanceof FeaturesSourceI)
+      {
+        alignFrame.getViewport().setShowSequenceFeatures(true);
+      }
+    }
+    // add metadata and update ui
+    if (!(protocol == DataSourceType.PASTE))
+    {
+      alignFrame.setFileName(file, format);
+    }
+    FeatureSettingsModelI proxyColourScheme = source
+            .getFeatureColourScheme();
+    if (proxyColourScheme != null)
+    {
+      alignFrame.getViewport()
+              .applyFeaturesStyle(proxyColourScheme);
+    }
+    alignFrame.statusBar.setText(MessageManager.formatMessage(
+            "label.successfully_loaded_file",
+            new String[] { title }));
+
+    if (raiseGUI)
+    {
+      // add the window to the GUI
+      // note - this actually should happen regardless of raiseGUI
+      // status in Jalview 3
+      // TODO: define 'virtual desktop' for benefit of headless scripts
+      // that perform queries to find the 'current working alignment'
+      Desktop.addInternalFrame(alignFrame, title,
+              AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+    }
+
+    try
+    {
+      alignFrame.setMaximum(jalview.bin.Cache.getDefault(
+              "SHOW_FULLSCREEN", false));
+    } catch (java.beans.PropertyVetoException ex)
+    {
+    }
   }
 
 }