JAL-2446 merged to spike branch

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

diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index d58bd67..77006db 100755 (executable)
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -1,23 +1,3 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- * 
- * This file is part of Jalview.
- * 
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *  
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License
- * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
 package jalview.io;
 
 import jalview.api.AlignExportSettingI;
@@ -34,7 +14,6 @@ import java.io.InputStreamReader;
 import java.net.URL;
 import java.util.Objects;
 
-
 public abstract class HTMLOutput implements Runnable
 {
   protected AlignmentPanel ap;
@@ -107,13 +86,13 @@ public abstract class HTMLOutput implements Runnable
       };
     }
     AlignmentExportData exportData = jalview.gui.AlignFrame
-            .getAlignmentForExport(JSONFile.FILE_DESC,
+            .getAlignmentForExport(FileFormat.Json,
                     ap.getAlignViewport(), exportSettings);
     String bioJSON = new FormatAdapter(ap, exportData.getSettings())
-            .formatSequences(JSONFile.FILE_DESC, exportData.getAlignment(),
+            .formatSequences(FileFormat.Json, exportData.getAlignment(),
                     exportData.getOmitHidden(), exportData
-                            .getStartEndPostions(), ap.getAlignViewport()
-                            .getColumnSelection());
+.getStartEndPostions(), ap.getAlignViewport()
+                            .getAlignment().getHiddenColumns());
     return bioJSON;
   }
 
@@ -263,9 +242,7 @@ public abstract class HTMLOutput implements Runnable
               pSessionId);
     }
 
-    JalviewFileChooser jvFileChooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            new String[] { "html" }, new String[] { "HTML files" },
+    JalviewFileChooser jvFileChooser = new JalviewFileChooser("html",
             "HTML files");
     jvFileChooser.setFileView(new JalviewFileView());
 
@@ -370,4 +347,4 @@ public abstract class HTMLOutput implements Runnable
    *          the file path of the generated HTML
    */
   public abstract void exportHTML(String outputFile);
-}
+}
\ No newline at end of file