X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=73be79f132ff6282e7e7469784e02f3841dbfe20;hb=fddf3084802b37e5cee17829e32692a4aac3e60d;hp=86b4c2855283ca0a9292b9817fe807ba14c2f942;hpb=5d59bb58f5bcecc6b240d125e13bbe1f1868f681;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 86b4c28..73be79f 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,42 +1,72 @@
 package jalview.io;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentExportData;
 import jalview.exceptions.NoFileSelectedException;
-import jalview.gui.AlignViewport;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
+import jalview.json.binding.v1.BioJSReleasePojo;
+import jalview.json.binding.v1.BioJSRepositoryPojo;
 import jalview.util.MessageManager;
 
+import java.io.BufferedInputStream;
 import java.io.BufferedReader;
+import java.io.File;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.PrintWriter;
+import java.net.URISyntaxException;
 import java.net.URL;
+import java.util.Objects;
+import java.util.TreeMap;
+
 
 public class BioJsHTMLOutput
 {
-  private AlignViewport av;
+  private AlignmentViewPanel ap;
 
+  private static File currentBJSTemplateFile;
 
-  public BioJsHTMLOutput(AlignmentPanel ap,
-          FeatureRenderer fr1)
-  {
+  private static TreeMap<String, File> bioJsMSAVersions;
+
+  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
+          .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.av = ap.av;
-      av.setFeatureRenderer(new FeatureRenderer(ap));
+      this.ap = ap;
     }
-    exportJalviewAlignmentAsBioJsHtmlFile();
   }
 
-  private void exportJalviewAlignmentAsBioJsHtmlFile()
+  public void exportJalviewAlignmentAsBioJsHtmlFile()
   {
     try
     {
       String outputFile = getOutputFile();
-      String jalviewAlignmentJson = JSONFile.getJSONData(av);
-      String bioJSTemplateString = getBioJsTemplateAsString(this);
+      // 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)
@@ -66,7 +96,6 @@ public class BioJsHTMLOutput
             { "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");
@@ -87,14 +116,16 @@ public class BioJsHTMLOutput
   }
 
 
-  public static String getBioJsTemplateAsString(Object currentObj)
+  public static String getBioJsTemplateAsString()
           throws IOException
   {
     InputStreamReader isReader = null;
     BufferedReader buffReader = null;
     StringBuilder sb = new StringBuilder();
-    URL url = currentObj.getClass().getResource(
-            "/templates/BioJSTemplate.txt");
+    Objects.requireNonNull(getCurrentBJSTemplateFile(),
+            "BioJsTemplate File not initialized!");
+    @SuppressWarnings("deprecation")
+    URL url = getCurrentBJSTemplateFile().toURL();
     if (url != null)
     {
       try
@@ -126,4 +157,174 @@ public class BioJsHTMLOutput
     }
     return sb.toString();
   }
+
+  public static void refreshBioJSVersionsInfo(String dirName)
+          throws URISyntaxException
+  {
+    File directory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
+    Objects.requireNonNull(dirName, "dirName MUST not be null!");
+    Objects.requireNonNull(directory, "directory MUST not be null!");
+    TreeMap<String, File> versionFileMap = new TreeMap<String, File>();
+
+    for (File file : directory.listFiles())
+    {
+      if (file.isFile())
+      {
+        String fileName = file.getName().substring(0,
+                file.getName().lastIndexOf("."));
+        String fileMeta[] = fileName.split("_");
+        if (fileMeta.length > 2)
+        {
+          setCurrentBJSTemplateFile(file);
+          versionFileMap.put(fileMeta[2], file);
+        }
+        else if (fileMeta.length > 1)
+        {
+          versionFileMap.put(fileMeta[1], file);
+        }
+      }
+    }
+    if (getCurrentBJSTemplateFile() == null && versionFileMap.size() > 0)
+    {
+      setCurrentBJSTemplateFile(versionFileMap.lastEntry().getValue());
+    }
+    setBioJsMSAVersions(versionFileMap);
+  }
+
+  public static void updateBioJS()
+  {
+    Thread updateThread = new Thread()
+    {
+      public void run()
+      {
+        try
+        {
+          String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO);
+          if (gitRepoPkgJson != null)
+          {
+            BioJSRepositoryPojo release = new BioJSRepositoryPojo(
+                    gitRepoPkgJson);
+            syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
+            refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
+          }
+        } catch (URISyntaxException e)
+        {
+          e.printStackTrace();
+        }
+      }
+    };
+    updateThread.start();
+
+  }
+
+
+  public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
+  {
+    for (BioJSReleasePojo bjsRelease : repo.getReleases())
+    {
+      String releaseUrl = bjsRelease.getUrl();
+      String releaseVersion = bjsRelease.getVersion();
+      String releaseFile = "BioJsMSA_" + releaseVersion + ".txt";
+      if (releaseVersion.equals(repo.getLatestReleaseVersion()))
+      {
+        releaseFile = "Latest_BioJsMSA_" + releaseVersion + ".txt";
+      }
+
+      File biojsDirectory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
+      if (!biojsDirectory.exists())
+      {
+        if (!biojsDirectory.mkdirs())
+        {
+          System.out.println("Couldn't create local directory : "
+                  + BJS_TEMPLATES_LOCAL_DIRECTORY);
+          return;
+        }
+      }
+
+      File file = new File(BJS_TEMPLATES_LOCAL_DIRECTORY + releaseFile);
+      if (!file.exists())
+      {
+
+        PrintWriter out = null;
+        try
+        {
+          out = new java.io.PrintWriter(new java.io.FileWriter(file));
+          out.print(getURLContentAsString(releaseUrl));
+        } catch (IOException e)
+        {
+          e.printStackTrace();
+        } finally
+        {
+          if (out != null)
+          {
+            out.flush();
+            out.close();
+          }
+        }
+      }
+    }
+
+  }
+
+  public static String getURLContentAsString(String url)
+          throws OutOfMemoryError
+  {
+    StringBuilder responseStrBuilder = null;
+    InputStream is = null;
+    try
+    {
+      URL resourceUrl = new URL(url);
+      is = new BufferedInputStream(resourceUrl.openStream());
+      BufferedReader br = new BufferedReader(new InputStreamReader(is));
+      responseStrBuilder = new StringBuilder();
+      String lineContent;
+
+      while ((lineContent = br.readLine()) != null)
+      {
+        responseStrBuilder.append(lineContent).append("\n");
+      }
+    } catch (OutOfMemoryError er)
+    {
+      er.printStackTrace();
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    } finally
+    {
+      if (is != null)
+      {
+        try
+        {
+          is.close();
+        } catch (IOException e)
+        {
+          e.printStackTrace();
+        }
+      }
+    }
+    return responseStrBuilder == null ? null : responseStrBuilder
+            .toString();
+  }
+
+  public static File getCurrentBJSTemplateFile()
+  {
+    return currentBJSTemplateFile;
+  }
+
+  public static void setCurrentBJSTemplateFile(File currentBJSTemplateFile)
+  {
+    BioJsHTMLOutput.currentBJSTemplateFile = currentBJSTemplateFile;
+  }
+
+  public static TreeMap<String, File> getBioJsMSAVersions()
+  {
+    return bioJsMSAVersions;
+  }
+
+  public static void setBioJsMSAVersions(
+          TreeMap<String, File> bioJsMSAVersions)
+  {
+    BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
+  }
+
 }