JAL-3664 hmm related TODOs
[jalview.git] / src / jalview / io / FileLoader.java
index 4f83ab1..1126de6 100755 (executable)
@@ -27,26 +27,32 @@ import jalview.api.FeaturesSourceI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 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.ws.utils.UrlDownloadClient;
 
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.StringTokenizer;
-import java.util.Vector;
 
 import javax.swing.SwingUtilities;
 
 public class FileLoader implements Runnable
 {
+  private static final String TAB = "\t";
+
   String file;
 
   DataSourceType protocol;
@@ -190,62 +196,111 @@ public class FileLoader implements Runnable
         Thread.sleep(500);
       } catch (Exception ex)
       {
+        System.out.println(
+                "Exception caught while waiting for FileLoader thread");
+        ex.printStackTrace();
       }
     }
 
     return alignFrame;
   }
 
-  public void updateRecentlyOpened()
+  public void LoadFileOntoAlignmentWaitTillLoaded(AlignViewport viewport,
+          String file, DataSourceType sourceType, FileFormatI format)
+  {
+    this.viewport = viewport;
+    this.file = file;
+    this.protocol = sourceType;
+    this.format = format;
+    _LoadAlignmentFileWaitTillLoaded();
+  }
+
+  protected void _LoadAlignmentFileWaitTillLoaded()
   {
-    Vector recent = new Vector();
-    if (protocol == DataSourceType.PASTE)
+    Thread loader = new Thread(this);
+    loader.start();
+
+    while (loader.isAlive())
     {
-      // do nothing if the file was pasted in as text... there is no filename to
-      // refer to it as.
-      return;
+      try
+      {
+        Thread.sleep(500);
+      } catch (Exception ex)
+      {
+      }
     }
-    String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
-            : "RECENT_URL";
+  }
 
-    String historyItems = jalview.bin.Cache.getProperty(type);
+  /**
+   * 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)
+    {
+      return null;
+    }
 
-    StringTokenizer st;
+    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 null;
+    }
+
+    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.nextElement().toString().trim());
+        String trimmed = st.nextToken().trim();
+        if (!recent.contains(trimmed))
+        {
+          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
   public void run()
   {
-    String title = protocol == DataSourceType.PASTE ? "Copied From Clipboard"
+    String title = protocol == DataSourceType.PASTE
+            ? "Copied From Clipboard"
             : file;
     Runtime rt = Runtime.getRuntime();
     try
@@ -276,8 +331,7 @@ public class FileLoader implements Runnable
                 + "\" has null or unidentifiable data content!");
         if (!Jalview.isHeadlessMode())
         {
-          JvOptionPane.showInternalMessageDialog(
-                  Desktop.desktop,
+          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                   MessageManager.getString("label.couldnt_read_data")
                           + " in " + file + "\n"
                           + AppletFormatAdapter.getSupportedFormats(),
@@ -304,8 +358,8 @@ public class FileLoader implements Runnable
         if (source != null)
         {
           // Tell the user (developer?) that this is going to cause a problem
-          System.err
-                  .println("IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
+          System.err.println(
+                  "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);
@@ -325,9 +379,28 @@ public class FileLoader implements Runnable
 
             // 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.
+            boolean downloadStructureFile = format.isStructureFile()
+                    && protocol.equals(DataSourceType.URL);
+            if (downloadStructureFile)
+            {
+              String structExt = format.getExtensions().split(",")[0];
+              String urlLeafName = file.substring(
+                      file.lastIndexOf(
+                              System.getProperty("file.separator")),
+                      file.lastIndexOf("."));
+              String tempStructureFileStr = createNamedJvTempFile(
+                      urlLeafName, structExt);
+              UrlDownloadClient.download(file, tempStructureFileStr);
+              al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
+                      format);
+              source = fa.getAlignFile();
+            }
+            else
+            {
+              al = fa.readFile(file, protocol, format);
+              source = fa.getAlignFile(); // keep reference for later if
+                                          // necessary.
+            }
           }
         } catch (java.io.IOException ex)
         {
@@ -349,8 +422,9 @@ public class FileLoader implements Runnable
               {
                 // register PDB entries with desktop's structure selection
                 // manager
-                StructureSelectionManager.getStructureSelectionManager(
-                        Desktop.instance).registerPDBEntry(pdbe);
+                StructureSelectionManager
+                        .getStructureSelectionManager(Desktop.instance)
+                        .registerPDBEntry(pdbe);
               }
             }
           }
@@ -365,6 +439,28 @@ public class FileLoader implements Runnable
             }
             // append to existing alignment
             viewport.addAlignment(al, title);
+            if (source instanceof HMMFile)
+            {
+              // TODO: absorb into viewport.addAlignment above ?
+              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();
+              // update HMM colour optionsĀ 
+              if (alignFrame != null)
+              {
+                alignFrame.buildColourMenu();
+              }
+            }
           }
           else
           {
@@ -372,8 +468,8 @@ public class FileLoader implements Runnable
 
             if (source instanceof ComplexAlignFile)
             {
-              ColumnSelection colSel = ((ComplexAlignFile) source)
-                      .getColumnSelection();
+              HiddenColumns colSel = ((ComplexAlignFile) source)
+                      .getHiddenColumns();
               SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
                       .getHiddenSequences();
               String colourSchemeName = ((ComplexAlignFile) source)
@@ -385,8 +481,8 @@ public class FileLoader implements Runnable
               alignFrame.getViewport().setFeaturesDisplayed(fd);
               alignFrame.getViewport().setShowSequenceFeatures(
                       ((ComplexAlignFile) source).isShowSeqFeatures());
-              ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
-                      colourSchemeName, al);
+              ColourSchemeI cs = ColourSchemeMapper
+                      .getJalviewColourScheme(colourSchemeName, al);
               if (cs != null)
               {
                 alignFrame.changeColour(cs);
@@ -411,9 +507,9 @@ public class FileLoader implements Runnable
               alignFrame.getViewport()
                       .applyFeaturesStyle(proxyColourScheme);
             }
-            alignFrame.statusBar.setText(MessageManager.formatMessage(
-                    "label.successfully_loaded_file",
-                    new String[] { title }));
+            alignFrame.setStatus(MessageManager.formatMessage(
+                    "label.successfully_loaded_file", new String[]
+                    { title }));
 
             if (raiseGUI)
             {
@@ -428,8 +524,8 @@ public class FileLoader implements Runnable
 
             try
             {
-              alignFrame.setMaximum(jalview.bin.Cache.getDefault(
-                      "SHOW_FULLSCREEN", false));
+              alignFrame.setMaximum(jalview.bin.Cache
+                      .getDefault("SHOW_FULLSCREEN", false));
             } catch (java.beans.PropertyVetoException ex)
             {
             }
@@ -442,11 +538,8 @@ public class FileLoader implements Runnable
             Desktop.instance.stopLoading();
           }
 
-          final String errorMessage = MessageManager
-                  .getString("label.couldnt_load_file")
-                  + " "
-                  + title
-                  + "\n" + error;
+          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)
@@ -457,7 +550,8 @@ public class FileLoader implements Runnable
               public void run()
               {
                 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                        errorMessage, MessageManager
+                        errorMessage,
+                        MessageManager
                                 .getString("label.error_loading_file"),
                         JvOptionPane.WARNING_MESSAGE);
               }
@@ -470,7 +564,12 @@ 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)
     {
@@ -483,11 +582,11 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(
-                    Desktop.desktop, MessageManager.formatMessage(
-                            "label.problems_opening_file",
-                            new String[] { file }), MessageManager
-                            .getString("label.file_open_error"),
+            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                    MessageManager.formatMessage(
+                            "label.problems_opening_file", new String[]
+                            { file }),
+                    MessageManager.getString("label.file_open_error"),
                     JvOptionPane.WARNING_MESSAGE);
           }
         });
@@ -505,11 +604,11 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(
-                    Desktop.desktop, MessageManager.formatMessage(
+            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                    MessageManager.formatMessage(
                             "warn.out_of_memory_loading_file", new String[]
-                            { file }), MessageManager
-                            .getString("label.out_of_memory"),
+                            { file }),
+                    MessageManager.getString("label.out_of_memory"),
                     JvOptionPane.WARNING_MESSAGE);
           }
         });
@@ -556,18 +655,27 @@ public class FileLoader implements Runnable
 
   }
 
-  /*
-   * (non-Javadoc)
+  /**
+   * This method creates the file -
+   * {tmpdir}/jalview/{current_timestamp}/fileName.exetnsion using the supplied
+   * file name and extension
    * 
-   * @see java.lang.Object#finalize()
+   * @param fileName
+   *          the name of the temp file to be created
+   * @param extension
+   *          the extension of the temp file to be created
+   * @return
    */
-  @Override
-  protected void finalize() throws Throwable
+  private static String createNamedJvTempFile(String fileName,
+          String extension) throws IOException
   {
-    source = null;
-    alignFrame = null;
-    viewport = null;
-    super.finalize();
+    String seprator = System.getProperty("file.separator");
+    String jvTempDir = System.getProperty("java.io.tmpdir") + "jalview"
+            + seprator + System.currentTimeMillis();
+    File tempStructFile = new File(
+            jvTempDir + seprator + fileName + "." + extension);
+    tempStructFile.mkdirs();
+    return tempStructFile.toString();
   }
 
 }