+/*
+ * 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.FeaturesDisplayedI;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.exceptions.NoFileSelectedException;
-import jalview.gui.AlignViewport;
+import jalview.bin.Cache;
import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
-import jalview.json.binding.v1.BioJsAlignmentPojo;
-import jalview.json.binding.v1.BioJsFeaturePojo;
-import jalview.json.binding.v1.BioJsSeqPojo;
-import jalview.schemes.ColourSchemeProperty;
+import jalview.gui.OOMWarning;
+import jalview.json.binding.biojs.BioJSReleasePojo;
+import jalview.json.binding.biojs.BioJSRepositoryPojo;
import jalview.util.MessageManager;
-import java.awt.Color;
+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.ArrayList;
+import java.util.Objects;
+import java.util.TreeMap;
-import com.json.JSONException;
-
-public class BioJsHTMLOutput
+public class BioJsHTMLOutput extends HTMLOutput
{
- private AlignViewport av;
-
- private jalview.api.FeatureRenderer fr;
+ private static File currentBJSTemplateFile;
- private String globalColorScheme;
+ private static TreeMap<String, File> bioJsMSAVersions;
- private FeaturesDisplayedI displayedFeatures;
+ public static final String DEFAULT_DIR = System.getProperty("user.home")
+ + File.separatorChar + ".biojs_templates" + File.separatorChar;
- private String jalviewVersion;
+ public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = Cache
+ .getDefault("biojs_template_directory", DEFAULT_DIR);
- private String webStartLaunchServletUrl = "http://www.jalview.org/services/launchApp";
+ 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,
- FeatureRenderer fr1)
+ public BioJsHTMLOutput(AlignmentPanel ap)
{
-
- jalviewVersion = jalview.bin.Cache.getProperty("VERSION");
- webStartLaunchServletUrl = jalview.bin.Cache.getDefault(
- "www.jalview.org", "http://www.jalview.org")
- + "/services/launchApp";
- if (ap != null)
- {
- this.av = ap.av;
- this.globalColorScheme = ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme());
- this.fr = ap.cloneFeatureRenderer();
- displayedFeatures = av.getFeaturesDisplayed();
- }
+ super(ap, "BioJS MSA");
}
- private void exportJalviewAlignmentAsBioJsHtmlFile()
+ public static void refreshVersionInfo(String dirName)
+ throws URISyntaxException
{
- try
- {
- String outputFile = getOutputFile();
- String jalviewAlignmentJson = getJalviewAlignmentAsJsonString(av
- .getAlignment());
- String bioJSTemplateString = getBioJsTemplateAsString(this);
- String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
- .replaceAll(
-"#sequenceData#", jalviewAlignmentJson)
- .toString();
+ 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>();
- 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)
+ for (File file : directory.listFiles())
{
- // do noting if no file was selected
- } catch (Exception e)
+ 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)
{
- e.printStackTrace();
+ setCurrentBJSTemplateFile(versionFileMap.lastEntry().getValue());
}
+ setBioJsMSAVersions(versionFileMap);
}
- public String getOutputFile() throws NoFileSelectedException
+ public static void updateBioJS()
{
- 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)
+ Thread updateThread = new Thread()
{
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
- .getSelectedFile().getParent());
- selectedFile = jvFileChooser.getSelectedFile().getPath();
- }
- else
- {
- throw new NoFileSelectedException("No file was selected.");
- }
+ @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();
- return selectedFile;
}
- public String getJalviewAlignmentAsJsonString(AlignmentI alignment)
- throws IOException, JSONException
+ public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
{
- BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
+ 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";
+ }
- bjsAlignment.setGlobalColorScheme(getGlobalColorScheme());
- bjsAlignment.setJalviewVersion(jalviewVersion);
- bjsAlignment.setWebStartUrl(webStartLaunchServletUrl);
+ 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;
+ }
+ }
- int count = 0;
- for (SequenceI seq : alignment.getSequences())
- {
- StringBuilder name = new StringBuilder();
- name.append(seq.getName()).append("/").append(seq.getStart())
- .append("-").append(seq.getEnd());
-
- BioJsSeqPojo seqPojo = new BioJsSeqPojo();
- seqPojo.setId(String.valueOf(++count));
- seqPojo.setEnd(seq.getEnd());
- seqPojo.setStart(seq.getStart());
- seqPojo.setName(name.toString());
- seqPojo.setSeq(seq.getSequenceAsString());
-
- SequenceFeature[] seqFeatures = seq.getSequenceFeatures();
- if (seqFeatures != null)
+ File file = new File(BJS_TEMPLATES_LOCAL_DIRECTORY + releaseFile);
+ if (!file.exists())
{
- ArrayList<BioJsFeaturePojo> bjsSeqFeatures = new ArrayList<BioJsFeaturePojo>();
- for (SequenceFeature sf : seqFeatures)
+
+ 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 (displayedFeatures != null
- && displayedFeatures.isVisible(sf.getType()))
+ if (out != null)
{
-
- // TODO: translate graduated/complex colourschemes to biojs model
- String featureColour = jalview.util.Format.getHexString(fr
- .findFeatureColour(Color.white, seq,
- seq.findIndex(sf.getBegin())));
- BioJsFeaturePojo bjsFeature = new BioJsFeaturePojo();
- bjsFeature.setFillColor(featureColour);
- bjsFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
- bjsFeature.setXend(seq.findIndex(sf.getEnd()));
- bjsFeature.setText(sf.getType());
- bjsSeqFeatures.add(bjsFeature);
+ out.flush();
+ out.close();
}
}
- seqPojo.setFeatures(bjsSeqFeatures);
}
- bjsAlignment.getSeqs().add(seqPojo);
}
- return new com.json.JSONObject(bjsAlignment).toString()
- .replaceAll("xstart", "xStart").replaceAll("xend", "xEnd");
}
- public static String getBioJsTemplateAsString(Object currentObj)
- throws IOException
+ public static String getURLContentAsString(String url)
+ throws OutOfMemoryError
{
- InputStreamReader isReader = null;
- BufferedReader buffReader = null;
- StringBuilder sb = new StringBuilder();
- URL url = currentObj.getClass().getResource(
- "/templates/BioJSTemplate.txt");
- if (url != null)
+ StringBuilder responseStrBuilder = null;
+ InputStream is = null;
+ try
{
- 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);
- }
+ URL resourceUrl = new URL(url);
+ is = new BufferedInputStream(resourceUrl.openStream());
+ BufferedReader br = new BufferedReader(new InputStreamReader(is));
+ responseStrBuilder = new StringBuilder();
+ String lineContent;
- } catch (Exception ex)
+ while ((lineContent = br.readLine()) != null)
{
- ex.printStackTrace();
- } finally
+ responseStrBuilder.append(lineContent).append("\n");
+ }
+ } catch (OutOfMemoryError er)
+ {
+ er.printStackTrace();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } finally
+ {
+ if (is != null)
{
- if (isReader != null)
+ try
{
- isReader.close();
- }
-
- if (buffReader != null)
+ is.close();
+ } catch (IOException e)
{
- buffReader.close();
+ e.printStackTrace();
}
}
}
- return sb.toString();
+ 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 String getGlobalColorScheme()
+ public static void setBioJsMSAVersions(
+ TreeMap<String, File> bioJsMSAVersions)
{
- return globalColorScheme;
+ BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
}
- public void setGlobalColorScheme(String globalColorScheme)
+ @Override
+ public boolean isEmbedData()
{
- this.globalColorScheme = globalColorScheme;
+ 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();
+ }
+
}
}
git://source.jalview.org / jalview.git / blobdiff