+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 static java.nio.file.Files.readAllBytes;
-import static java.nio.file.Paths.get;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignViewport;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
-import jalview.gui.SequenceRenderer;
-import jalview.json.binding.v1.BioJsAlignmentPojo;
-import jalview.json.binding.v1.BioJsSeqPojo;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentExportData;
+import jalview.exceptions.NoFileSelectedException;
+import jalview.json.binding.biojs.BioJSReleasePojo;
+import jalview.json.binding.biojs.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;
-import org.json.simple.parser.ParseException;
-
-import com.json.JSONException;
-
-public class BioJsHTMLOutput {
- private AlignViewport av;
- private FeatureRenderer fr;
-
- public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr, FeatureRenderer fr1) {
- this.av = ap.av;
- this.fr = new FeatureRenderer(ap);
- fr.transferSettings(fr1);
- exportAsBioJsHtml();
- }
-
- private void exportAsBioJsHtml() {
- 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) {
- ex.printStackTrace();
- }
- }
-
- private JalviewFileChooser getJalviewFileChooserOption() {
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { "html" }, new String[] { "HTML files" }, "HTML files");
- 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"));
-
- return chooser;
- }
-
- private String generateBioJsAlignmentData(AlignmentI alignment) throws IOException, JSONException {
- BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
- int count = 0;
- for (SequenceI seq : alignment.getSequences()) {
- StringBuilder name = new StringBuilder();
- name.append(seq.getName()).append("/").append(seq.getStart()).append("-").append(seq.getEnd());
- bjsAlignment.getSeqs().add(new BioJsSeqPojo(String.valueOf(++count), name.toString(), seq.getSequenceAsString()));
- }
-
- // Taylor
- // av.getGlobalColourScheme().;
- String seqs = new com.json.JSONObject(bjsAlignment).getString("seqs");
- String bioJSTemplate = new String(readAllBytes(get("resources/templates/BioJSTemplate.txt")));
-
- // av.get
- // fr.
- return bioJSTemplate.replaceAll("#sequenceData#", seqs).replaceAll("#scheme#", "zappo");
- }
-
- public static void main(String[] args) throws IOException, ParseException {
-
- }
+public class BioJsHTMLOutput
+{
+ private AlignmentViewPanel ap;
+
+ 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 = 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/jalview/exporter-templates/master/biojs/package.json");
+
+ public BioJsHTMLOutput(AlignmentViewPanel ap)
+ {
+ if (ap != null)
+ {
+ this.ap = ap;
+ }
+ }
+
+ public void exportJalviewAlignmentAsBioJsHtmlFile()
+ {
+ try
+ {
+ String outputFile = getOutputFile();
+ // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
+ AlignExportSettingI exportSettings = new AlignExportSettingI()
+ {
+ @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);
+ 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 String getOutputFile() throws NoFileSelectedException
+ {
+ 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());
+
+ jvFileChooser.setDialogTitle(MessageManager
+ .getString("label.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;
+ }
+
+ 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)
+ 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff