X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=1126de6a0a27c8191d3b6260f572b10c0ceebde7;hb=1595128a4bfc730f1e55c347f0a52eb0d491ca92;hp=fd8429bb51782d30bc2c2213d7af7035c9ecf27e;hpb=6076783c7a50cc6d318b2478b10800aedb9288c4;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index fd8429b..1126de6 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -33,9 +33,9 @@ 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;
@@ -43,13 +43,16 @@ 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;
@@ -193,6 +196,9 @@ public class FileLoader implements Runnable
         Thread.sleep(500);
       } catch (Exception ex)
       {
+        System.out.println(
+                "Exception caught while waiting for FileLoader thread");
+        ex.printStackTrace();
       }
     }
 
@@ -225,56 +231,69 @@ public class FileLoader implements Runnable
     }
   }
 
-  public void updateRecentlyOpened()
+  /**
+   * 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)
   {
-    Vector recent = new Vector();
-    if (protocol == DataSourceType.PASTE)
+    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 = jalview.bin.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.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
@@ -422,14 +441,25 @@ public class FileLoader implements Runnable
             viewport.addAlignment(al, title);
             if (source instanceof HMMFile)
             {
+              // TODO: absorb into viewport.addAlignment above ?
               AlignmentI alignment = viewport.getAlignment();
               SequenceI seq = alignment
-                      .getSequenceAt(alignment.getAbsoluteHeight() - 1);
-              seq.setIsHMMConsensusSequence(true);
-              alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+                      .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 options 
+              if (alignFrame != null)
+              {
+                alignFrame.buildColourMenu();
+              }
             }
           }
           else
@@ -477,7 +507,7 @@ public class FileLoader implements Runnable
               alignFrame.getViewport()
                       .applyFeaturesStyle(proxyColourScheme);
             }
-            alignFrame.statusBar.setText(MessageManager.formatMessage(
+            alignFrame.setStatus(MessageManager.formatMessage(
                     "label.successfully_loaded_file", new String[]
                     { title }));
 
@@ -534,7 +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)
     {
@@ -643,18 +678,4 @@ public class FileLoader implements Runnable
     return tempStructFile.toString();
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see java.lang.Object#finalize()
-   */
-  @Override
-  protected void finalize() throws Throwable
-  {
-    source = null;
-    alignFrame = null;
-    viewport = null;
-    super.finalize();
-  }
-
 }