X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=ad3b79f5bde5c7557834cfb4848f8778e413673b;hb=330289271fe2239a59fa318d6b2b19fdd319f8a4;hp=6869292e97a02345e7d07b42a99ceb8f8d187200;hpb=9e5effcac65476958e619298a1a939254f77bc4b;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 6869292..ad3b79f 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,111 +1,222 @@
 package jalview.io;
 
-import static java.nio.file.Files.readAllBytes;
-import static java.nio.file.Paths.get;
+import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.gui.AlignViewport;
+import jalview.exceptions.NoFileSelectedException;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.FeatureRenderer;
-import jalview.gui.SequenceRenderer;
 import jalview.json.binding.v1.BioJsAlignmentPojo;
+import jalview.json.binding.v1.BioJsFeaturePojo;
 import jalview.json.binding.v1.BioJsSeqPojo;
+import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.Color;
+import java.io.BufferedReader;
 import java.io.IOException;
+import java.io.InputStreamReader;
 import java.io.PrintWriter;
-
-import org.jsoup.Jsoup;
-import org.jsoup.nodes.Document;
-import org.jsoup.nodes.Element;
+import java.net.URL;
+import java.util.ArrayList;
 
 import com.json.JSONException;
-import com.json.JSONObject;
 
 public class BioJsHTMLOutput
 {
-  private AlignViewport av;
-  private FeatureRenderer fr;
+  private AlignmentViewport av;
+
+  private jalview.api.FeatureRenderer fr;
+
+  private String globalColorScheme;
+
+  private FeaturesDisplayedI displayedFeatures;
 
-  public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
+  private String jalviewVersion;
+
+  private String webStartLaunchServletUrl = "http://www.jalview.org/services/launchApp";
+
+  public BioJsHTMLOutput(AlignmentPanel ap,
           FeatureRenderer fr1)
   {
-    this.av = ap.av;
 
-    this.fr = new FeatureRenderer(ap);
-    fr.transferSettings(fr1);
-    exportAsBioJsHtml();
+    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();
+    }
   }
 
-  private void exportAsBioJsHtml()
+  private void exportJalviewAlignmentAsBioJsHtmlFile()
   {
     try
     {
-      JalviewFileChooser jvFileChooser = getJalviewFileChooserOption();
-      int fileChooserOpt = jvFileChooser.showSaveDialog(null);
-      if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
-      {
-        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);
-      }
-    } catch (Exception ex)
+      String outputFile = getOutputFile();
+      String jalviewAlignmentJson = getJalviewAlignmentAsJsonString(av
+              .getAlignment());
+      String bioJSTemplateString = getBioJsTemplateAsString(this);
+      String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
+              .replaceAll(
+"#sequenceData#", jalviewAlignmentJson)
+              .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)
     {
-      ex.printStackTrace();
+      // do noting if no file was selected
+    } catch (Exception e)
+    {
+      e.printStackTrace();
     }
   }
 
-  private JalviewFileChooser getJalviewFileChooserOption()
+  public String getOutputFile() throws NoFileSelectedException
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
+    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());
 
-    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"));
+    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)
+    {
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
+              .getSelectedFile().getParent());
+      selectedFile = jvFileChooser.getSelectedFile().getPath();
+    }
+    else
+    {
+      throw new NoFileSelectedException("No file was selected.");
+    }
 
-    return chooser;
+    return selectedFile;
   }
 
-  private String generateBioJsAlignmentData(AlignmentI alignment)
+  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())
     {
-      bjsAlignment.getSeqs().add(
-              new BioJsSeqPojo(String.valueOf(++count), seq.getName(), seq
-                      .getSequenceAsString()));
+      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.getDatasetSequence()
+              .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);
     }
 
-    String seqs = new JSONObject(bjsAlignment).getString("seqs");
-    String bioJSTemplate = new String(
-            readAllBytes(get("resources/templates/BioJSTemplate.txt")));
+    return new com.json.JSONObject(bjsAlignment).toString()
+            .replaceAll("xstart", "xStart").replaceAll("xend", "xEnd");
+  }
 
-    return bioJSTemplate.replaceAll("#sequenceData#", seqs);
+  public static String getBioJsTemplateAsString(Object currentObj)
+          throws IOException
+  {
+    InputStreamReader isReader = null;
+    BufferedReader buffReader = null;
+    StringBuilder sb = new StringBuilder();
+    URL url = currentObj.getClass().getResource(
+            "/templates/BioJSTemplate.txt");
+    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);
+        }
+
+      } catch (Exception ex)
+      {
+        ex.printStackTrace();
+      } finally
+      {
+        if (isReader != null)
+        {
+          isReader.close();
+        }
+
+        if (buffReader != null)
+        {
+          buffReader.close();
+        }
+      }
+    }
+    return sb.toString();
   }
 
-  public static void main(String[] args) throws IOException
+  public String getGlobalColorScheme()
   {
-    Document doc = Jsoup.parse(new String(
-            readAllBytes(get("resources/templates/BioJSTemplate.txt"))));
+    return globalColorScheme;
+  }
 
-    Element content = doc.getElementById("seqData");
-    System.out.println(content.val());
+  public void setGlobalColorScheme(String globalColorScheme)
+  {
+    this.globalColorScheme = globalColorScheme;
   }
 
 }
-