+public class BioJsHTMLOutput extends HTMLOutput
+{
+ private static File currentBJSTemplateFile;
+
+ 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 = Cache
+ .getDefault("biojs_template_directory", DEFAULT_DIR);
+
+ 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 BioJsHTMLOutput(AlignmentPanel ap)
+ {
+ super(ap, "BioJS MSA");
+ }
+
+ public static void refreshVersionInfo(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()
+ {
+ @Override
+ 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);
+ refreshVersionInfo(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())
+ {
+ jalview.bin.Console.outPrintln("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;
+ }
+
+ @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)
+ {
+ jalview.bin.Console.outPrintln("########################\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();
+ }
+
+ }