package jalview.io;
-import static java.nio.file.Files.readAllBytes;
-import static java.nio.file.Paths.get;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
+import jalview.exceptions.NoFileSelectedException;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.FeatureRenderer;
-import jalview.gui.SequenceRenderer;
+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 FeatureRenderer fr;
- public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
+ private static File currentBJSTemplateFile;
+
+ private static TreeMap<String, File> bioJsMSAVersions;
+
+ public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
+ .getDefault("biojs_template_directory", "/biojs_templates/");
+
+ 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(AlignmentPanel ap,
FeatureRenderer fr1)
{
- System.out.println("BioJs working as expected so far");
- this.av = ap.av;
-
- this.fr = new FeatureRenderer(ap);
- fr.transferSettings(fr1);
- exportAsBioJsHtml();
+ if (ap != null)
+ {
+ this.av = ap.av;
+ av.setFeatureRenderer(new FeatureRenderer(ap));
+ }
}
- private void exportAsBioJsHtml()
+ public void exportJalviewAlignmentAsBioJsHtmlFile()
{
try
{
- JalviewFileChooser jvFileChooser = getJalviewFileChooserOption();
- int fileChooserOpt = jvFileChooser.showSaveDialog(null);
- if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
- {
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
- .getSelectedFile().getParent());
- String selectedFile = jvFileChooser.getSelectedFile().getPath();
- String generartedBioJs = generateBioJsAlignmentData(av
- .getAlignment());
- PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
- selectedFile));
- out.print(generartedBioJs);
- out.close();
- jalview.util.BrowserLauncher.openURL("file:///" + selectedFile);
- }
- } catch (Exception ex)
+ String outputFile = getOutputFile();
+ String jalviewAlignmentJson = JSONFile.getJSONData(av);
+ 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)
{
- ex.printStackTrace();
+ // do noting if no file was selected
+ } catch (Exception e)
+ {
+ e.printStackTrace();
}
}
- private JalviewFileChooser getJalviewFileChooserOption()
+ public String getOutputFile() throws NoFileSelectedException
{
- JalviewFileChooser chooser = new JalviewFileChooser(
+ 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());
- chooser.setFileView(new JalviewFileView());
// TODO uncomment when supported by MassageManager
- // chooser.setDialogTitle(MessageManager.getString("label.save_as_biojs_html"));
- chooser.setDialogTitle("save as BioJs HTML");
- chooser.setToolTipText(MessageManager.getString("action.save"));
+ jvFileChooser.setDialogTitle(MessageManager
+ .getString("label.save_as_biojs_html"));
+ jvFileChooser.setDialogTitle("save as BioJs HTML");
+ jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
- return chooser;
+ 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;
}
- private String generateBioJsAlignmentData(AlignmentI alignment)
+
+ public static String getBioJsTemplateAsString()
throws IOException
{
- StringBuilder bioJsData = new StringBuilder();
- int count = 0;
- for (SequenceI seq : alignment.getSequences())
+ 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)
{
- bioJsData.append("seqOnFly.push({seq:'" + seq.getSequenceAsString()
- + "', name:'" + seq.getName() + "', id:" + ++count + "});");
+ 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();
+ }
+ }
}
- String bioJSTemplate = new String(
- readAllBytes(get("resources/templates/BioJSTemplate.txt")));
+ return sb.toString();
+ }
+
+ public void refreshBioJSVersionsInfo(String dirName)
+ throws URISyntaxException
+ {
+ URL url = getClass().getResource(dirName);
+ File directory = new File(url.toURI());
+ Objects.requireNonNull(dirName, "dirName MUST not be null!");
+ Objects.requireNonNull(directory, "directory MUST not be null!");
+ TreeMap<String, File> versionFileMap = new TreeMap<String, File>();
- return bioJSTemplate.replaceAll("#sequenceData#", bioJsData.toString());
+ 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 void updateBioJS()
+ {
+ try
+ {
+ String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO);
+ BioJSRepositoryPojo release = new BioJSRepositoryPojo(gitRepoPkgJson);
+ syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
+ refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ }
-}
+ public void syncUpdates(String localDir, BioJSRepositoryPojo repo)
+ throws URISyntaxException
+ {
+ 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 file = null;
+ URL url = getClass().getResource(
+ BJS_TEMPLATES_LOCAL_DIRECTORY + releaseFile);
+ if (url == null)
+ {
+ String path = getClass().getResource(BJS_TEMPLATES_LOCAL_DIRECTORY)
+ .getPath();
+ System.out.println("------> " + path);
+ file = new File(path + releaseFile);
+ }
+ else
+ {
+ file = new File(url.toURI());
+ }
+
+ 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;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff