X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHTMLOutput.java;fp=src%2Fjalview%2Fio%2FHTMLOutput.java;h=54e7e4b6c3012d5fbe286554b5a8048bad468b95;hb=ec8f3cedf60fb1feed6d34de6b49f6bfa78b9dd8;hp=bebfd280c90be0cb5a8ae3efca3303222f80beb8;hpb=056dad85a910551cc95e44d451a61f6b8c4dd35d;p=jalview.git

diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index bebfd28..54e7e4b 100644
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -20,9 +20,10 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingI;
+import jalview.api.AlignExportSettingsI;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignExportSettingsAdapter;
 import jalview.datamodel.AlignmentExportData;
-import jalview.exceptions.NoFileSelectedException;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.IProgressIndicator;
 import jalview.util.MessageManager;
@@ -38,82 +39,61 @@ public abstract class HTMLOutput implements Runnable
 {
   protected AlignmentPanel ap;
 
+  /*
+   * key for progress or status messages
+   */
   protected long pSessionId;
 
+  /*
+   * (optional) place to write progress messages to
+   */
   protected IProgressIndicator pIndicator;
 
   protected File generatedFile;
 
-  public HTMLOutput(AlignmentPanel ap)
-  {
-    if (ap != null)
-    {
-      this.ap = ap;
-      this.pIndicator = ap.alignFrame;
-    }
-  }
+  String _bioJson = null;
 
-  public String getBioJSONData()
+  private String description;
+
+  /**
+   * Constructor given an alignment panel (which should not be null)
+   * 
+   * @param ap
+   * @param desc 
+   */
+  public HTMLOutput(AlignmentPanel ap, String desc)
   {
-    return getBioJSONData(null);
+    this.ap = ap;
+    this.pIndicator = ap.alignFrame;
+    this.description = desc;
+    this.pSessionId = System.currentTimeMillis();
   }
 
-  public String getBioJSONData(AlignExportSettingI exportSettings)
+  /**
+   * Gets the BioJSON data as a string, with lazy evaluation (first time called
+   * only). If the output format is configured not to embed BioJSON, returns
+   * null.
+   * 
+   * @return
+   */
+  public String getBioJSONData()
   {
     if (!isEmbedData())
     {
       return null;
     }
-    if (exportSettings == null)
+    if (_bioJson == null)
     {
-      exportSettings = new AlignExportSettingI()
-      {
-        @Override
-        public boolean isExportHiddenSequences()
-        {
-          return true;
-        }
-
-        @Override
-        public boolean isExportHiddenColumns()
-        {
-          return true;
-        }
-
-        @Override
-        public boolean isExportAnnotations()
-        {
-          return true;
-        }
-
-        @Override
-        public boolean isExportFeatures()
-        {
-          return true;
-        }
-
-        @Override
-        public boolean isExportGroups()
-        {
-          return true;
-        }
-
-        @Override
-        public boolean isCancelled()
-        {
-          return false;
-        }
-      };
+      AlignExportSettingsI options = new AlignExportSettingsAdapter(true);
+      AlignmentExportData exportData = ap.getAlignViewport()
+              .getAlignExportData(options);
+      _bioJson = new FormatAdapter(ap, options).formatSequences(
+              FileFormat.Json, exportData.getAlignment(),
+              exportData.getOmitHidden(), exportData.getStartEndPostions(),
+              ap.getAlignViewport().getAlignment().getHiddenColumns());
     }
-    AlignmentExportData exportData = jalview.gui.AlignFrame
-            .getAlignmentForExport(FileFormat.Json, ap.getAlignViewport(),
-                    exportSettings);
-    String bioJSON = new FormatAdapter(ap, exportData.getSettings())
-            .formatSequences(FileFormat.Json, exportData.getAlignment(),
-                    exportData.getOmitHidden(),
-                    exportData.getStartEndPostions(), ap.getAlignViewport()
-                            .getAlignment().getHiddenColumns());
-    return bioJSON;
+
+    return _bioJson;
   }
 
   /**
@@ -218,16 +198,18 @@ public abstract class HTMLOutput implements Runnable
 
   }
 
-  public String getOutputFile() throws NoFileSelectedException
+  /**
+   * Prompts the user to choose an output file and returns the file path, or
+   * null on Cancel
+   * 
+   * @return
+   */
+  public String getOutputFile()
   {
     String selectedFile = null;
-    if (pIndicator != null && !isHeadless())
-    {
-      pIndicator.setProgressBar(MessageManager.formatMessage(
-              "status.waiting_for_user_to_select_output_file", "HTML"),
-              pSessionId);
-    }
 
+    // TODO: JAL-3048 generate html rendered view (requires SvgGraphics and/or
+    // Jalview HTML rendering system- probably not required for Jalview-JS)
     JalviewFileChooser jvFileChooser = new JalviewFileChooser("html",
             "HTML files");
     jvFileChooser.setFileView(new JalviewFileView());
@@ -239,14 +221,11 @@ public abstract class HTMLOutput implements Runnable
     int fileChooserOpt = jvFileChooser.showSaveDialog(null);
     if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
     {
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+      Cache.setProperty("LAST_DIRECTORY",
               jvFileChooser.getSelectedFile().getParent());
       selectedFile = jvFileChooser.getSelectedFile().getPath();
     }
-    else
-    {
-      throw new NoFileSelectedException("No file was selected.");
-    }
+
     return selectedFile;
   }
 
@@ -275,16 +254,6 @@ public abstract class HTMLOutput implements Runnable
 
   /**
    * This method provides implementation of consistent behaviour which should
-   * occur before a HTML file export. It MUST be called at the start of the
-   * exportHTML() method implementation.
-   */
-  protected void exportStarted()
-  {
-    pSessionId = System.currentTimeMillis();
-  }
-
-  /**
-   * This method provides implementation of consistent behaviour which should
    * occur after a HTML file export. It MUST be called at the end of the
    * exportHTML() method implementation.
    */
@@ -324,13 +293,51 @@ public abstract class HTMLOutput implements Runnable
    * 
    * @return
    */
-  public abstract File getExportedFile();
+  public File getExportedFile()
+  {
+    return generatedFile;
+  }
+
+  public void exportHTML(String outputFile)
+  {
+    setProgressMessage(MessageManager.formatMessage(
+        "status.exporting_alignment_as_x_file", getDescription()));
+    try
+    {
+      if (outputFile == null)
+      {
+        /*
+         * prompt for output file
+         */
+        outputFile = getOutputFile();
+        if (outputFile == null)
+        {
+          setProgressMessage(MessageManager.formatMessage(
+                  "status.cancelled_image_export_operation",
+                  getDescription()));
+          return;
+        }
+      }
+      generatedFile = new File(outputFile);
+    } catch (Exception e)
+    {
+      setProgressMessage(MessageManager
+              .formatMessage("info.error_creating_file", getDescription()));
+      e.printStackTrace();
+      return;
+    }
+    new Thread(this).start();
+  
+  }
 
   /**
-   * This is the main method to handle the HTML generation.
+   * Answers a short description of the image format suitable for display in
+   * messages
    * 
-   * @param outputFile
-   *          the file path of the generated HTML
+   * @return
    */
-  public abstract void exportHTML(String outputFile);
+  protected final String getDescription()
+  {
+	return description;
+  }
 }
\ No newline at end of file