X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=834e0040edfc27c617480aa9ae2416f9c862af5f;hb=c49683bef626d9c1de9d06e5f11039e6d4df55c3;hp=4b2f797ae18183858a5270eab540c91e9a837d1d;hpb=75b38b407cf19737bcc9013a483e1beee32f5523;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 4b2f797..834e004 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -20,6 +20,14 @@
  */
 package jalview.io;
 
+import java.awt.Dimension;
+import java.io.File;
+import java.io.IOException;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.SwingUtilities;
+
 import jalview.api.ComplexAlignFile;
 import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
@@ -33,29 +41,20 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
-import jalview.gui.Jalview2XML;
 import jalview.gui.JvOptionPane;
 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
+import jalview.project.Jalview2XML;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.ws.utils.UrlDownloadClient;
 
-import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.SwingUtilities;
-
+import java.util.ArrayList;
+import java.util.List;
 public class FileLoader implements Runnable
 {
+  private static final String TAB = "\t";
   String file;
 
   DataSourceType protocol;
@@ -102,7 +101,8 @@ public class FileLoader implements Runnable
           DataSourceType protocol, FileFormatI format)
   {
     this.viewport = viewport;
-    if (file instanceof File) {
+    if (file instanceof File)
+    {
       this.selectedFile = (File) file;
       file = selectedFile.getPath();
     }
@@ -214,59 +214,82 @@ public class FileLoader implements Runnable
   protected AlignFrame _LoadFileWaitTillLoaded()
   {
     this.run();
+
     return alignFrame;
   }
 
-  public void updateRecentlyOpened()
+  public void LoadFileOntoAlignmentWaitTillLoaded(AlignViewport viewport,
+          String file, DataSourceType sourceType, FileFormatI format)
   {
     Vector<String> recent = new Vector<>();
     if (protocol == DataSourceType.PASTE)
+    this.viewport = viewport;
+    this.file = file;
+    this.protocol = sourceType;
+    this.format = format;
+    _LoadFileWaitTillLoaded();
+  }
+
+
+  /**
+   * Updates (or creates) the tab-separated list of recently opened files held
+   * under the given property name by inserting the filePath at the front of the
+   * list. Duplicates are removed, and the list is limited to 11 entries. The
+   * method returns the updated value of the property.
+   * 
+   * @param filePath
+   * @param sourceType
+   */
+  public static String updateRecentlyOpened(String filePath,
+          DataSourceType sourceType)
+  {
+    if (sourceType != DataSourceType.FILE
+            && sourceType != DataSourceType.URL)
     {
-      // do nothing if the file was pasted in as text... there is no filename to
-      // refer to it as.
-      return;
+      return null;
     }
-    if (file != null
-            && file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
+    String propertyName = sourceType == DataSourceType.FILE ? "RECENT_FILE"
+            : "RECENT_URL";
+    String historyItems = Cache.getProperty(propertyName);
+    if (filePath != null
+            && filePath.indexOf(System.getProperty("java.io.tmpdir")) > -1)
     {
       // ignore files loaded from the system's temporary directory
-      return;
+      return null;
     }
-    String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
-            : "RECENT_URL";
-
-    String historyItems = Cache.getProperty(type);
 
-    StringTokenizer st;
+    List<String> recent = new ArrayList<>();
 
     if (historyItems != null)
     {
-      st = new StringTokenizer(historyItems, "\t");
+      StringTokenizer st = new StringTokenizer(historyItems, TAB);
 
       while (st.hasMoreTokens())
       {
-        recent.addElement(st.nextToken().trim());
+        String trimmed = st.nextToken().trim();
+	recent.add(trimmed);
       }
     }
 
-    if (recent.contains(file))
+    /*
+     * if file was already in the list, it moves to the top
+     */
+    if (recent.contains(filePath))
     {
-      recent.remove(file);
+      recent.remove(filePath);
     }
 
-    StringBuffer newHistory = new StringBuffer(file);
+    StringBuilder newHistory = new StringBuilder(filePath);
     for (int i = 0; i < recent.size() && i < 10; i++)
     {
-      newHistory.append("\t");
-      newHistory.append(recent.elementAt(i));
+      newHistory.append(TAB);
+      newHistory.append(recent.get(i));
     }
 
-    Cache.setProperty(type, newHistory.toString());
+    String newProperty = newHistory.toString();
+    Cache.setProperty(propertyName, newProperty);
 
-    if (protocol == DataSourceType.FILE)
-    {
-      Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
-    }
+    return newProperty;
   }
 
   @Override
@@ -278,9 +301,9 @@ public class FileLoader implements Runnable
     Runtime rt = Runtime.getRuntime();
     try
     {
-      if (Desktop.instance != null)
+      if (Desktop.getInstance() != null)
       {
-        Desktop.instance.startLoading(file);
+        Desktop.getInstance().startLoading(file);
       }
       if (format == null)
       {
@@ -290,7 +313,8 @@ public class FileLoader implements Runnable
           format = new IdentifyFile().identify(source, false);
           // identify stream and rewind rather than close
         }
-        else if (selectedFile != null) {
+        else if (selectedFile != null)
+        {
           format = new IdentifyFile().identify(selectedFile, protocol);
         }
         else
@@ -302,12 +326,12 @@ public class FileLoader implements Runnable
 
       if (format == null)
       {
-        Desktop.instance.stopLoading();
+        Desktop.getInstance().stopLoading();
         System.err.println("The input file \"" + file
                 + "\" has null or unidentifiable data content!");
         if (!Jalview.isHeadlessMode())
         {
-          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+          JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                   MessageManager.getString("label.couldnt_read_data")
                           + " in " + file + "\n"
                           + AppletFormatAdapter.getSupportedFormats(),
@@ -318,7 +342,7 @@ public class FileLoader implements Runnable
       }
       // TODO: cache any stream datasources as a temporary file (eg. PDBs
       // retrieved via URL)
-      if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+      if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
       {
         System.gc();
         memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
@@ -338,7 +362,9 @@ public class FileLoader implements Runnable
                   "IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
           // We read the data anyway - it might make sense.
         }
-        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file);
+        // BH 2018 switch to File object here instead of filename
+        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(
+                selectedFile == null ? file : selectedFile);
       }
       else
       {
@@ -366,27 +392,29 @@ public class FileLoader implements Runnable
                       file.lastIndexOf("."));
               String tempStructureFileStr = createNamedJvTempFile(
                       urlLeafName, structExt);
-              
+
               // BH - switching to File object here so as to hold
               // ._bytes array directly
               File tempFile = new File(tempStructureFileStr);
               UrlDownloadClient.download(file, tempFile);
-              
-              al = fa.readFile(tempFile, DataSourceType.FILE,
-                      format);
+
+              al = fa.readFile(tempFile, DataSourceType.FILE, format);
               source = fa.getAlignFile();
             }
             else
             {
-              if (selectedFile == null) {
+              if (selectedFile == null)
+              {
                 al = fa.readFile(file, protocol, format);
-                
-              } else {
+
+              }
+              else
+              {
                 al = fa.readFile(selectedFile, protocol, format);
-                             }
+              }
               source = fa.getAlignFile(); // keep reference for later if
-              
-                                          // necessary.
+
+              // necessary.
             }
           }
         } catch (java.io.IOException ex)
@@ -410,7 +438,7 @@ public class FileLoader implements Runnable
                 // register PDB entries with desktop's structure selection
                 // manager
                 StructureSelectionManager
-                        .getStructureSelectionManager(Desktop.instance)
+                        .getStructureSelectionManager(Desktop.getInstance())
                         .registerPDBEntry(pdbe);
               }
             }
@@ -420,12 +448,29 @@ public class FileLoader implements Runnable
                   .getFeatureColourScheme();
           if (viewport != null)
           {
+            // TODO: test if this needs to be done after addAlignment ? (like in 2.11.2)  
             if (proxyColourScheme != null)
             {
               viewport.applyFeaturesStyle(proxyColourScheme);
             }
             // append to existing alignment
             viewport.addAlignment(al, title);
+            if (source instanceof HMMFile)
+            {
+              AlignmentI alignment = viewport.getAlignment();
+              SequenceI seq = alignment
+                      .getSequenceAt(alignment.getHeight() - 1);
+              if (seq.hasHMMProfile())
+              {
+                /* 
+                 * fudge: move HMM consensus sequence from last to first
+                 */
+                alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+                alignment.insertSequenceAt(0, seq);
+              }
+              viewport.getAlignPanel().adjustAnnotationHeight();
+              viewport.updateSequenceIdColours();
+            }
           }
           else
           {
@@ -465,15 +510,14 @@ public class FileLoader implements Runnable
             // add metadata and update ui
             if (!(protocol == DataSourceType.PASTE))
             {
-              alignFrame.setFileName(file, format);
-              alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
+              alignFrame.setFile(file, selectedFile, protocol, format);
             }
             if (proxyColourScheme != null)
             {
               alignFrame.getViewport()
                       .applyFeaturesStyle(proxyColourScheme);
             }
-            alignFrame.statusBar.setText(MessageManager.formatMessage(
+            alignFrame.setStatus(MessageManager.formatMessage(
                     "label.successfully_loaded_file", new String[]
                     { title }));
 
@@ -484,14 +528,18 @@ public class FileLoader implements Runnable
               // 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,
+              
+              Dimension dim = Platform.getDimIfEmbedded(alignFrame,
                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+              alignFrame.setSize(dim);
+              Desktop.addInternalFrame(alignFrame, title, dim.width,
+                      dim.height);
             }
 
             try
             {
-              alignFrame.setMaximum(jalview.bin.Cache
-                      .getDefault("SHOW_FULLSCREEN", false));
+              alignFrame.setMaximum(
+                      Cache.getDefault("SHOW_FULLSCREEN", false));
             } catch (java.beans.PropertyVetoException ex)
             {
             }
@@ -499,23 +547,23 @@ public class FileLoader implements Runnable
         }
         else
         {
-          if (Desktop.instance != null)
+          if (Desktop.getInstance() != null)
           {
-            Desktop.instance.stopLoading();
+            Desktop.getInstance().stopLoading();
           }
 
           final String errorMessage = MessageManager.getString(
                   "label.couldnt_load_file") + " " + title + "\n" + error;
           // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
           // bits ?
-          if (raiseGUI && Desktop.desktop != null)
+          if (raiseGUI && Desktop.getDesktopPane() != null)
           {
             javax.swing.SwingUtilities.invokeLater(new Runnable()
             {
               @Override
               public void run()
               {
-                JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                         errorMessage,
                         MessageManager
                                 .getString("label.error_loading_file"),
@@ -530,7 +578,12 @@ public class FileLoader implements Runnable
         }
       }
 
-      updateRecentlyOpened();
+      updateRecentlyOpened(file, protocol);
+
+      if (protocol == DataSourceType.FILE && format != null)
+      {
+        Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
+      }
 
     } catch (Exception er)
     {
@@ -543,7 +596,7 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                     MessageManager.formatMessage(
                             "label.problems_opening_file", new String[]
                             { file }),
@@ -565,7 +618,7 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                     MessageManager.formatMessage(
                             "warn.out_of_memory_loading_file", new String[]
                             { file }),
@@ -587,7 +640,7 @@ public class FileLoader implements Runnable
     // memory
     // after
     // load
-    if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+    if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
     {
       if (alignFrame != null)
       {
@@ -609,9 +662,9 @@ public class FileLoader implements Runnable
       }
     }
     // remove the visual delay indicator
-    if (Desktop.instance != null)
+    if (Desktop.getInstance() != null)
     {
-      Desktop.instance.stopLoading();
+      Desktop.getInstance().stopLoading();
     }
 
   }
@@ -639,21 +692,4 @@ public class FileLoader implements Runnable
     return tempStructFile.toString();
   }
 
-  /**
-   * 
-   * @param file a File, or a String which is a name of a file
-   * @return
-   * @throws FileNotFoundException 
-   */
-  @SuppressWarnings("unused")
-  public static BufferedReader getBuffereReader(Object file) throws FileNotFoundException {
-    if (file instanceof String)
-      return new BufferedReader(new FileReader((String) file));
-    
-    byte[] bytes = /** @j2sNative file._bytes || */ null;
-    if (bytes != null)
-      return new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes)));
-    return  new BufferedReader(new FileReader((File) file));
-  }
-
 }