Merge branch 'Jalview-JS/develop' into merge_js_develop

[jalview.git] / src / jalview / io / FileLoader.java

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 0317c7d..df64702 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -50,8 +50,13 @@ import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.utils.UrlDownloadClient;
 
+import java.util.ArrayList;
+import java.util.List;
+
 public class FileLoader implements Runnable
 {
+  private static final String TAB = "\t";
+
   String file;
 
   DataSourceType protocol;
@@ -214,56 +219,79 @@ public class FileLoader implements Runnable
     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
@@ -424,6 +452,22 @@ public class FileLoader implements Runnable
             }
             // 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
           {
@@ -531,7 +575,12 @@ 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)
     {