X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=48988cf527b2516f748bc19b217d27e210de3ee1;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=089f50b0ed03b389508055fd7d74f8d7c2f073af;hpb=a8aec438cd92c74061c89487b2431a52bb0c2799;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 089f50b..48988cf 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,10 +1,30 @@
+/*
+ * 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.AlignmentViewPanel;
-import jalview.datamodel.AlignmentExportData;
-import jalview.exceptions.NoFileSelectedException;
-import jalview.json.binding.v1.BioJSReleasePojo;
-import jalview.json.binding.v1.BioJSRepositoryPojo;
+import jalview.bin.Cache;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.OOMWarning;
+import jalview.json.binding.biojs.BioJSReleasePojo;
+import jalview.json.binding.biojs.BioJSRepositoryPojo;
 import jalview.util.MessageManager;
 
 import java.io.BufferedInputStream;
@@ -19,11 +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 static File currentBJSTemplateFile;
 
   private static TreeMap<String, File> bioJsMSAVersions;
@@ -31,135 +48,19 @@ public class BioJsHTMLOutput
   public static final String DEFAULT_DIR = System.getProperty("user.home")
           + File.separatorChar + ".biojs_templates" + File.separatorChar;
 
-  public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
+  public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = Cache
           .getDefault("biojs_template_directory", DEFAULT_DIR);
 
-  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");
-
-  public BioJsHTMLOutput(AlignmentViewPanel ap)
-  {
-    if (ap != null)
-    {
-      this.ap = ap;
-    }
-  }
-
-  public void exportJalviewAlignmentAsBioJsHtmlFile()
-  {
-    try
-    {
-      String outputFile = getOutputFile();
-      // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
-      AlignmentExportData exportData = jalview.gui.AlignFrame
-              .getAlignmentForExport(
-              JSONFile.FILE_DESC, ap.getAlignViewport());
-      if (exportData.getSettings().isCancelled())
-      {
-        return;
-      }
-      String jalviewAlignmentJson = 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();
-
-      PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
-              outputFile));
-      out.print(generatedBioJsWithJalviewAlignmentAsJson);
-      out.flush();
-      out.close();
-      jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
-    } catch (NoFileSelectedException ex)
-    {
-      // do noting if no file was selected
-    } catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
+  public static final String BJS_TEMPLATE_GIT_REPO = Cache
+          .getDefault("biojs_template_git_repo",
+                  "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
 
-  public String getOutputFile() throws NoFileSelectedException
+  public BioJsHTMLOutput(AlignmentPanel ap)
   {
-    String selectedFile = null;
-    JalviewFileChooser jvFileChooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "html" }, new String[]
-            { "HTML files" }, "HTML files");
-    jvFileChooser.setFileView(new JalviewFileView());
-
-    // TODO uncomment when supported by MassageManager
-    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);
-    if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
-    {
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
-              .getSelectedFile().getParent());
-      selectedFile = jvFileChooser.getSelectedFile().getPath();
-    }
-    else
-    {
-      throw new NoFileSelectedException("No file was selected.");
-    }
-    return selectedFile;
+    super(ap, "BioJS MSA");
   }
 
-
-  public static String getBioJsTemplateAsString()
-          throws IOException
-  {
-    InputStreamReader isReader = null;
-    BufferedReader buffReader = null;
-    StringBuilder sb = new StringBuilder();
-    Objects.requireNonNull(getCurrentBJSTemplateFile(),
-            "BioJsTemplate File not initialized!");
-    @SuppressWarnings("deprecation")
-    URL url = getCurrentBJSTemplateFile().toURL();
-    if (url != null)
-    {
-      try
-      {
-        isReader = new InputStreamReader(url.openStream());
-        buffReader = new BufferedReader(isReader);
-        String line;
-        String lineSeparator = System.getProperty("line.separator");
-        while ((line = buffReader.readLine()) != null)
-        {
-          sb.append(line).append(lineSeparator);
-        }
-
-      } catch (Exception ex)
-      {
-        ex.printStackTrace();
-      } finally
-      {
-        if (isReader != null)
-        {
-          isReader.close();
-        }
-
-        if (buffReader != null)
-        {
-          buffReader.close();
-        }
-      }
-    }
-    return sb.toString();
-  }
-
-  public static void refreshBioJSVersionsInfo(String dirName)
+  public static void refreshVersionInfo(String dirName)
           throws URISyntaxException
   {
     File directory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
@@ -196,15 +97,20 @@ public class BioJsHTMLOutput
   {
     Thread updateThread = new Thread()
     {
+      @Override
       public void run()
       {
         try
         {
-          String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO);
-          BioJSRepositoryPojo release = new BioJSRepositoryPojo(
-                  gitRepoPkgJson);
-          syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
-          refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
+          String gitRepoPkgJson = getURLContentAsString(
+                  BJS_TEMPLATE_GIT_REPO);
+          if (gitRepoPkgJson != null)
+          {
+            BioJSRepositoryPojo release = new BioJSRepositoryPojo(
+                    gitRepoPkgJson);
+            syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
+            refreshVersionInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
+          }
         } catch (URISyntaxException e)
         {
           e.printStackTrace();
@@ -215,7 +121,6 @@ public class BioJsHTMLOutput
 
   }
 
-
   public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
   {
     for (BioJSReleasePojo bjsRelease : repo.getReleases())
@@ -300,8 +205,8 @@ public class BioJsHTMLOutput
         }
       }
     }
-    return responseStrBuilder == null ? null : responseStrBuilder
-            .toString();
+    return responseStrBuilder == null ? null
+            : responseStrBuilder.toString();
   }
 
   public static File getCurrentBJSTemplateFile()
@@ -325,4 +230,50 @@ public class BioJsHTMLOutput
     BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
   }
 
+  @Override
+  public boolean isEmbedData()
+  {
+    return true;
+  }
+
+  @Override
+  public boolean isLaunchInBrowserAfterExport()
+  {
+    return true;
+  }
+
+  @Override
+  public void run()
+  {
+    try
+    {
+      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(generatedFile));
+      out.print(generatedBioJsWithJalviewAlignmentAsJson);
+      out.flush();
+      out.close();
+      setProgressMessage(MessageManager
+              .formatMessage("status.export_complete", getDescription()));
+      exportCompleted();
+
+    } catch (OutOfMemoryError err)
+    {
+      System.out.println("########################\n" + "OUT OF MEMORY "
+              + generatedFile + "\n" + "########################");
+      new OOMWarning("Creating Image for " + generatedFile, err);
+    } catch (Exception e)
+    {
+      setProgressMessage(MessageManager
+              .formatMessage("info.error_creating_file", getDescription()));
+      e.printStackTrace();
+    }
+
+  }
+
 }