+/*
+ * 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.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentExportData;
import jalview.exceptions.NoFileSelectedException;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
-import jalview.json.binding.v1.AlignmentPojo;
-import jalview.json.binding.v1.SequenceFeaturesPojo;
-import jalview.json.binding.v1.SequencePojo;
-import jalview.schemes.ColourSchemeProperty;
+import jalview.gui.IProgressIndicator;
+import jalview.gui.OOMWarning;
+import jalview.json.binding.biojs.BioJSReleasePojo;
+import jalview.json.binding.biojs.BioJSRepositoryPojo;
import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-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 com.json.JSONException;
+import java.util.Objects;
+import java.util.TreeMap;
public class BioJsHTMLOutput
{
- private AlignmentViewport av;
+ private AlignmentViewPanel ap;
- private jalview.api.FeatureRenderer fr;
+ private long pSessionId;
- private String globalColorScheme;
+ private IProgressIndicator pIndicator;
- private FeaturesDisplayedI displayedFeatures;
+ private boolean headless;
- private String jalviewVersion;
+ private static File currentBJSTemplateFile;
- private String webStartLaunchServletUrl = "http://www.jalview.org/services/launchApp";
+ private static TreeMap<String, File> bioJsMSAVersions;
- public BioJsHTMLOutput(AlignmentPanel ap,
- FeatureRenderer fr1)
- {
+ 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");
- jalviewVersion = jalview.bin.Cache.getProperty("VERSION");
- webStartLaunchServletUrl = jalview.bin.Cache.getDefault(
- "www.jalview.org", "http://www.jalview.org")
- + "/services/launchApp";
+ public BioJsHTMLOutput(AlignmentViewPanel ap,
+ IProgressIndicator pIndicator)
+ {
if (ap != null)
{
- this.av = ap.av;
- this.globalColorScheme = ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme());
- this.fr = ap.cloneFeatureRenderer();
- displayedFeatures = av.getFeaturesDisplayed();
+ this.ap = ap;
+ this.pSessionId = System.currentTimeMillis();
+ this.pIndicator = pIndicator;
+ this.headless = (System.getProperty("java.awt.headless") != null && System
+ .getProperty("java.awt.headless").equals("true"));
}
}
- private void exportJalviewAlignmentAsBioJsHtmlFile()
+ public void exportJalviewAlignmentAsBioJsHtmlFile()
{
+ String outputFile = null;
try
{
- String outputFile = getOutputFile();
- String jalviewAlignmentJson = getJalviewAlignmentAsJsonString(av
- .getAlignment());
- String bioJSTemplateString = getBioJsTemplateAsString(this);
+ outputFile = getOutputFile();
+ 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);
+ String bioJSON = 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();
+ .replaceAll("#sequenceData#", bioJSON).toString();
PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
outputFile));
out.flush();
out.close();
jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
+ if (pIndicator != null && !headless)
+ {
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "status.export_complete", "BioJS"), pSessionId);
+ }
} catch (NoFileSelectedException ex)
{
// do noting if no file was selected
+ } catch (OutOfMemoryError err)
+ {
+ System.out.println("########################\n" + "OUT OF MEMORY "
+ + outputFile + "\n" + "########################");
+ new OOMWarning("Creating Image for " + outputFile, err);
} catch (Exception e)
{
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "info.error_creating_file", "HTML"), pSessionId);
e.printStackTrace();
}
}
public String getOutputFile() throws NoFileSelectedException
{
String selectedFile = null;
+ if (pIndicator != null && !headless)
+ {
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "status.waiting_for_user_to_select_output_file", "HTML"),
+ pSessionId);
+ }
+
JalviewFileChooser jvFileChooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "html" }, new String[]
- { "HTML files" }, "HTML files");
+ 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);
}
else
{
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation", "BioJS"),
+ pSessionId);
throw new NoFileSelectedException("No file was selected.");
}
-
return selectedFile;
}
- public String getJalviewAlignmentAsJsonString(AlignmentI alignment)
- throws IOException, JSONException
- {
- AlignmentPojo bjsAlignment = new AlignmentPojo();
-
- // bjsAlignment.setGlobalColorScheme(getGlobalColorScheme());
- // bjsAlignment.setJalviewVersion(jalviewVersion);
- // bjsAlignment.setWebStartUrl(webStartLaunchServletUrl);
-
- int count = 0;
- for (SequenceI seq : alignment.getSequences())
- {
- StringBuilder name = new StringBuilder();
- name.append(seq.getName()).append("/").append(seq.getStart())
- .append("-").append(seq.getEnd());
-
- SequencePojo seqPojo = new SequencePojo();
- 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)
- {
- ArrayList<SequenceFeaturesPojo> bjsSeqFeatures = new ArrayList<SequenceFeaturesPojo>();
- for (SequenceFeature sf : seqFeatures)
- {
- if (displayedFeatures != null
- && displayedFeatures.isVisible(sf.getType()))
- {
-
- // TODO: translate graduated/complex colourschemes to biojs model
- String featureColour = jalview.util.Format.getHexString(fr
- .findFeatureColour(Color.white, seq,
- seq.findIndex(sf.getBegin())));
- // SequenceFeaturesPojo bjsFeature = new SequenceFeaturesPojo();
- // bjsFeature.setFillColor(featureColour);
- // bjsFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
- // bjsFeature.setXend(seq.findIndex(sf.getEnd()));
- // bjsFeature.setType(sf.getType());
- // bjsSeqFeatures.add(bjsFeature);
- }
- }
- // 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 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
return sb.toString();
}
- public String getGlobalColorScheme()
+ 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()
+ {
+ @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);
+ 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 globalColorScheme;
+ return bioJsMSAVersions;
}
- public void setGlobalColorScheme(String globalColorScheme)
+ public static void setBioJsMSAVersions(
+ TreeMap<String, File> bioJsMSAVersions)
{
- this.globalColorScheme = globalColorScheme;
+ BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
}
}
git://source.jalview.org / jalview.git / blobdiff