X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=9454cae12b65f3adba5f5fead6759bd7e2430758;hb=c70d42a1afc972ddb3757b9ec4cece3458d396a1;hp=73be79f132ff6282e7e7469784e02f3841dbfe20;hpb=330763451812f4422e4027a8ee7dc81ab52b269d;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 73be79f..9454cae 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,10 +1,32 @@
+/*
+ * 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;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentExportData;
 import jalview.exceptions.NoFileSelectedException;
-import jalview.json.binding.v1.BioJSReleasePojo;
-import jalview.json.binding.v1.BioJSRepositoryPojo;
+import jalview.gui.IProgressIndicator;
+import jalview.json.binding.biojs.BioJSReleasePojo;
+import jalview.json.binding.biojs.BioJSRepositoryPojo;
 import jalview.util.MessageManager;
 
 import java.io.BufferedInputStream;
@@ -19,11 +41,16 @@ import java.net.URL;
 import java.util.Objects;
 import java.util.TreeMap;
 
-
 public class BioJsHTMLOutput
 {
   private AlignmentViewPanel ap;
 
+  private long pSessionId;
+
+  private IProgressIndicator pIndicator;
+
+  private boolean headless;
+
   private static File currentBJSTemplateFile;
 
   private static TreeMap<String, File> bioJsMSAVersions;
@@ -37,13 +64,18 @@ public class BioJsHTMLOutput
   public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache
           .getDefault(
                   "biojs_template_git_repo",
-                  "https://raw.githubusercontent.com/tcofoegbu/bjs-template/master/package.json");
+                  "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
 
-  public BioJsHTMLOutput(AlignmentViewPanel ap)
+  public BioJsHTMLOutput(AlignmentViewPanel ap,
+          IProgressIndicator pIndicator)
   {
     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"));
     }
   }
 
@@ -53,24 +85,57 @@ public class BioJsHTMLOutput
     {
       String outputFile = getOutputFile();
       // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
-      AlignmentExportData exportData = jalview.gui.AlignFrame
-              .getAlignmentForExport(
-              JSONFile.FILE_DESC, ap.getAlignViewport());
-      if (exportData.getSettings().isCancelled())
+      AlignExportSettingI exportSettings = new AlignExportSettingI()
       {
-        return;
-      }
-      String jalviewAlignmentJson = new FormatAdapter(ap,
-              exportData.getSettings()).formatSequences(JSONFile.FILE_DESC,
-              exportData.getAlignment(), exportData.getOmitHidden(),
-              exportData.getStartEndPostions(), ap.getAlignViewport()
-                      .getColumnSelection());
+        @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;
+        }
+
+      };
+      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 = getBioJsTemplateAsString();
       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
-              .replaceAll(
-"#sequenceData#", jalviewAlignmentJson)
-              .toString();
+              .replaceAll("#sequenceData#", bioJSON).toString();
 
       PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
               outputFile));
@@ -78,11 +143,18 @@ public class BioJsHTMLOutput
       out.flush();
       out.close();
       jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
+      if (pIndicator != null && !headless)
+      {
+        pIndicator.setProgressBar(MessageManager.formatMessage(
+                "status.export_complete", "BioJS"), pSessionId);
+      }
     } catch (NoFileSelectedException ex)
     {
       // do noting if no file was selected
     } catch (Exception e)
     {
+      pIndicator.setProgressBar(MessageManager.formatMessage(
+              "info.error_creating_file", "HTML"), pSessionId);
       e.printStackTrace();
     }
   }
@@ -90,15 +162,21 @@ public class BioJsHTMLOutput
   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");
+            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.setDialogTitle("save as BioJs HTML");
     jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
 
     int fileChooserOpt = jvFileChooser.showSaveDialog(null);
@@ -110,14 +188,15 @@ public class BioJsHTMLOutput
     }
     else
     {
+      pIndicator.setProgressBar(MessageManager.formatMessage(
+              "status.cancelled_image_export_operation", "BioJS"),
+              pSessionId);
       throw new NoFileSelectedException("No file was selected.");
     }
     return selectedFile;
   }
 
-
-  public static String getBioJsTemplateAsString()
-          throws IOException
+  public static String getBioJsTemplateAsString() throws IOException
   {
     InputStreamReader isReader = null;
     BufferedReader buffReader = null;
@@ -195,6 +274,7 @@ public class BioJsHTMLOutput
   {
     Thread updateThread = new Thread()
     {
+      @Override
       public void run()
       {
         try
@@ -217,7 +297,6 @@ public class BioJsHTMLOutput
 
   }
 
-
   public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
   {
     for (BioJSReleasePojo bjsRelease : repo.getReleases())