X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=f8fa1f5d90d33ad7b6181b8f36ed58268f6f38f6;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=494530622c90e72e8c8e20dfaacc9cfba2c2f3bf;hpb=a40bbc57a85658544e2e5d7cc2a7596b762566dc;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 4945306..f8fa1f5 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,73 +1,142 @@
+/*
+ * 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));
@@ -75,11 +144,23 @@ public class BioJsHTMLOutput
       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();
     }
   }
@@ -87,16 +168,21 @@ public class BioJsHTMLOutput
   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);
@@ -108,74 +194,23 @@ public class BioJsHTMLOutput
     }
     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
@@ -208,14 +243,173 @@ public class BioJsHTMLOutput
     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;
   }
 
 }