X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=1be97f507c6004abdcb36cb395c880baff5c9e53;hb=e60cacff9260c47c12cf34a7e191678cfc97d265;hp=9b6a15a24fc5f0b0eb2d7c5b4a4250ff89169026;hpb=a8362b85de4f21440433bc9385bd9b3a24354532;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 9b6a15a..1be97f5 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -20,11 +20,8 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingI;
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignmentExportData;
 import jalview.exceptions.NoFileSelectedException;
-import jalview.gui.IProgressIndicator;
+import jalview.gui.AlignmentPanel;
 import jalview.gui.OOMWarning;
 import jalview.json.binding.biojs.BioJSReleasePojo;
 import jalview.json.binding.biojs.BioJSRepositoryPojo;
@@ -42,15 +39,8 @@ import java.net.URL;
 import java.util.Objects;
 import java.util.TreeMap;
 
-public class BioJsHTMLOutput
+public class BioJsHTMLOutput extends HTMLOutput
 {
-  private AlignmentViewPanel ap;
-
-  private long pSessionId;
-
-  private IProgressIndicator pIndicator;
-
-  private boolean headless;
 
   private static File currentBJSTemplateFile;
 
@@ -67,91 +57,38 @@ public class BioJsHTMLOutput
                   "biojs_template_git_repo",
                   "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
 
-  public BioJsHTMLOutput(AlignmentViewPanel ap,
-          IProgressIndicator pIndicator)
+  public BioJsHTMLOutput(AlignmentPanel ap)
   {
-    if (ap != null)
-    {
-      this.ap = ap;
-      this.pSessionId = System.currentTimeMillis();
-      this.pIndicator = pIndicator;
-      this.headless = (System.getProperty("java.awt.headless") != null && System
-              .getProperty("java.awt.headless").equals("true"));
-    }
+    super(ap);
   }
 
-  public void exportJalviewAlignmentAsBioJsHtmlFile(String outputFile)
+  @Override
+  public void exportHTML(String outputFile)
   {
-    // String outputFile = null;
+    exportStarted();
     try
     {
+
       if (outputFile == null)
       {
         outputFile = getOutputFile();
       }
-      AlignExportSettingI exportSettings = new AlignExportSettingI()
-      {
-        @Override
-        public boolean isExportHiddenSequences()
-        {
-          return true;
-        }
-
-        @Override
-        public boolean isExportHiddenColumns()
-        {
-          return true;
-        }
+      generatedFile = new File(outputFile);
 
-        @Override
-        public boolean isExportAnnotations()
-        {
-          return true;
-        }
-
-        @Override
-        public boolean isExportFeatures()
-        {
-          return true;
-        }
-
-        @Override
-        public boolean isExportGroups()
-        {
-          return true;
-        }
-
-        @Override
-        public boolean isCancelled()
-        {
-          return false;
-        }
-
-      };
-      AlignmentExportData exportData = jalview.gui.AlignFrame
-              .getAlignmentForExport(JSONFile.FILE_DESC,
-                      ap.getAlignViewport(), exportSettings);
-      String bioJSON = new FormatAdapter(ap, exportData.getSettings())
-              .formatSequences(JSONFile.FILE_DESC, exportData
-                      .getAlignment(), exportData.getOmitHidden(),
-                      exportData.getStartEndPostions(), ap
-                              .getAlignViewport().getColumnSelection());
-
-      String bioJSTemplateString = HtmlFile.readFileAsString(getCurrentBJSTemplateFile());
+      String bioJSON = getBioJSONData();
+      String bioJSTemplateString = HTMLOutput.readFileAsString(getCurrentBJSTemplateFile());
       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
               .replaceAll("#sequenceData#", bioJSON).toString();
 
       PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
-              outputFile));
+              generatedFile));
       out.print(generatedBioJsWithJalviewAlignmentAsJson);
       out.flush();
       out.close();
-      jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
-      if (pIndicator != null && !headless)
-      {
-        pIndicator.setProgressBar(MessageManager.formatMessage(
-                "status.export_complete", "BioJS"), pSessionId);
-      }
+      exportCompleted();
+      setProgressMessage(MessageManager.formatMessage(
+              "status.export_complete", "BioJS"));
+
     } catch (NoFileSelectedException ex)
     {
       // do noting if no file was selected
@@ -162,54 +99,15 @@ public class BioJsHTMLOutput
       new OOMWarning("Creating Image for " + outputFile, err);
     } catch (Exception e)
     {
-      if (pIndicator != null && !headless)
-      {
-      pIndicator.setProgressBar(MessageManager.formatMessage(
-              "info.error_creating_file", "HTML"), pSessionId);
-      }
+      setProgressMessage(MessageManager.formatMessage(
+              "info.error_creating_file", "HTML"));
       e.printStackTrace();
     }
   }
 
-  public String getOutputFile() throws NoFileSelectedException
-  {
-    String selectedFile = null;
-    if (pIndicator != null && !headless)
-    {
-      pIndicator.setProgressBar(MessageManager.formatMessage(
-              "status.waiting_for_user_to_select_output_file", "HTML"),
-              pSessionId);
-    }
-
-    JalviewFileChooser jvFileChooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            new String[] { "html" }, new String[] { "HTML files" },
-            "HTML files");
-    jvFileChooser.setFileView(new JalviewFileView());
-
-    jvFileChooser.setDialogTitle(MessageManager
-            .getString("label.save_as_biojs_html"));
-    jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
-
-    int fileChooserOpt = jvFileChooser.showSaveDialog(null);
-    if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
-    {
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
-              .getSelectedFile().getParent());
-      selectedFile = jvFileChooser.getSelectedFile().getPath();
-    }
-    else
-    {
-      pIndicator.setProgressBar(MessageManager.formatMessage(
-              "status.cancelled_image_export_operation", "BioJS"),
-              pSessionId);
-      throw new NoFileSelectedException("No file was selected.");
-    }
-    return selectedFile;
-  }
 
 
-  public static void refreshBioJSVersionsInfo(String dirName)
+  public static void refreshVersionInfo(String dirName)
           throws URISyntaxException
   {
     File directory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
@@ -257,7 +155,7 @@ public class BioJsHTMLOutput
             BioJSRepositoryPojo release = new BioJSRepositoryPojo(
                     gitRepoPkgJson);
             syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
-            refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
+            refreshVersionInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
           }
         } catch (URISyntaxException e)
         {
@@ -378,4 +276,22 @@ public class BioJsHTMLOutput
     BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
   }
 
+  @Override
+  public boolean isEmbedData()
+  {
+    return true;
+  }
+
+  @Override
+  public boolean isLaunchInBrowserAfterExport()
+  {
+    return true;
+  }
+
+  @Override
+  public File getExportedFile()
+  {
+    return generatedFile;
+  }
+
 }