X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=a1679c3958d50426d10a43ed132540eaa2b170e0;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=5a236dc80e2d27cceb4c464e5f86ea37c1c1f065;hpb=961eec1363ddc5f0f5a08b9063a7a2a9b1c9d2bd;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 5a236dc..a1679c3 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,91 +1,379 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * 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.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;
 
 public class BioJsHTMLOutput
 {
-  private AlignViewport av;
-  private FeatureRenderer fr;
+  private AlignmentViewPanel ap;
 
-  public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
-          FeatureRenderer fr1)
+  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);
+      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#", bioJSON).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
   {
-    System.out.println("BioJs working as expected so far");
-    this.av = ap.av;
+    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);
+        }
 
-    this.fr = new FeatureRenderer(ap);
-    fr.transferSettings(fr1);
-    exportAsBioJsHtml();
+      } catch (Exception ex)
+      {
+        ex.printStackTrace();
+      } finally
+      {
+        if (isReader != null)
+        {
+          isReader.close();
+        }
+
+        if (buffReader != null)
+        {
+          buffReader.close();
+        }
+      }
+    }
+    return sb.toString();
   }
 
-  private void exportAsBioJsHtml()
+  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
     {
-      JalviewFileChooser jvFileChooser = getJalviewFileChooserOption();
-      int fileChooserOpt = jvFileChooser.showSaveDialog(null);
-      if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
+      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)
       {
-        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);
+        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();
   }
 
-  private JalviewFileChooser getJalviewFileChooserOption()
+  public static File getCurrentBJSTemplateFile()
   {
-    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;
+    return currentBJSTemplateFile;
   }
 
-  private String generateBioJsAlignmentData(AlignmentI alignment)
-          throws IOException
+  public static void setCurrentBJSTemplateFile(File currentBJSTemplateFile)
   {
-    StringBuilder bioJsData = new StringBuilder();
-    int count = 0;
-    for (SequenceI seq : alignment.getSequences())
-    {
-      bioJsData.append("seqOnFly.push({seq:'" + seq.getSequenceAsString()
-              + "', name:'" + seq.getName() + "', id:" + ++count + "});");
-    }
-    String bioJSTemplate = new String(
-            readAllBytes(get("resources/templates/BioJSTemplate.txt")));
+    BioJsHTMLOutput.currentBJSTemplateFile = currentBJSTemplateFile;
+  }
 
-    return bioJSTemplate.replaceAll("#sequenceData#", bioJsData.toString());
+  public static TreeMap<String, File> getBioJsMSAVersions()
+  {
+    return bioJsMSAVersions;
   }
 
+  public static void setBioJsMSAVersions(
+          TreeMap<String, File> bioJsMSAVersions)
+  {
+    BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
+  }
 
 }
-