package jalview.io;
-import jalview.api.FeaturesDisplayedI;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
+import jalview.api.AlignmentViewPanel;
import jalview.exceptions.NoFileSelectedException;
-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.json.binding.v1.BioJSReleasePojo;
+import jalview.json.binding.v1.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 java.util.Objects;
+import java.util.TreeMap;
-import com.json.JSONException;
public class BioJsHTMLOutput
{
- private AlignmentViewport av;
+ private AlignmentViewPanel ap;
- 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 = jalview.bin.Cache
+ .getDefault("biojs_template_directory", DEFAULT_DIR);
- private String webStartLaunchServletUrl = "http://www.jalview.org/services/launchApp";
+ 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)
+ public BioJsHTMLOutput(AlignmentViewPanel 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();
+ this.ap = ap;
}
}
- private void exportJalviewAlignmentAsBioJsHtmlFile()
+ public void exportJalviewAlignmentAsBioJsHtmlFile()
{
try
{
String outputFile = getOutputFile();
- String jalviewAlignmentJson = getJalviewAlignmentAsJsonString(av
- .getAlignment());
- String bioJSTemplateString = getBioJsTemplateAsString(this);
+ String jalviewAlignmentJson = JSONFile.getJSONData(ap);
+ String bioJSTemplateString = getBioJsTemplateAsString();
String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
.replaceAll(
"#sequenceData#", jalviewAlignmentJson)
{
throw new NoFileSelectedException("No file was selected.");
}
-
return selectedFile;
}
- public String getJalviewAlignmentAsJsonString(AlignmentI alignment)
- throws IOException, JSONException
- {
- BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
-
- 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());
-
- 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)
- {
- ArrayList<BioJsFeaturePojo> bjsSeqFeatures = new ArrayList<BioJsFeaturePojo>();
- 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())));
- 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);
- }
- }
- 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)
+ 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()
+ {
+ public void run()
+ {
+ 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();
+ }
+ }
+ };
+ 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