JAL-1541 Modified BioJs exporter to take advantage of the abstracted JSONFile export...

[jalview.git] / src / jalview / io / BioJsHTMLOutput.java

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 068b4b2..86b4c28 100644 (file)
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,16 +1,9 @@
 package jalview.io;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
+import jalview.exceptions.NoFileSelectedException;
 import jalview.gui.AlignViewport;
 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 java.io.BufferedReader;
@@ -18,134 +11,82 @@ import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.PrintWriter;
 import java.net.URL;
-import java.util.ArrayList;
-
-import com.json.JSONException;
 
 public class BioJsHTMLOutput
 {
   private AlignViewport av;
 
-  private FeatureRenderer fr;
 
-  public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
+  public BioJsHTMLOutput(AlignmentPanel ap,
           FeatureRenderer fr1)
   {
-    this.av = ap.av;
-    this.fr = new FeatureRenderer(ap);
-    fr.transferSettings(fr1);
 
-    exportAsBioJsHtml();
+    if (ap != null)
+    {
+
+      this.av = ap.av;
+      av.setFeatureRenderer(new FeatureRenderer(ap));
+    }
+    exportJalviewAlignmentAsBioJsHtmlFile();
   }
 
-  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 = JSONFile.getJSONData(av);
+      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)
+    {
+      // do noting if no file was selected
+    } catch (Exception e)
     {
-      ex.printStackTrace();
+      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");
-    chooser.setFileView(new JalviewFileView());
+    jvFileChooser.setFileView(new JalviewFileView());
 
     // TODO uncomment when supported by MassageManager
-    chooser.setDialogTitle(MessageManager
+    jvFileChooser.setDialogTitle(MessageManager
             .getString("label.save_as_biojs_html"));
-    chooser.setDialogTitle("save as BioJs HTML");
-    chooser.setToolTipText(MessageManager.getString("action.save"));
+    jvFileChooser.setDialogTitle("save as BioJs HTML");
+    jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
 
-    return chooser;
-  }
-
-  private String generateBioJsAlignmentData(AlignmentI alignment)
-          throws IOException, JSONException
-  {
-    BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
-    bjsAlignment.setGlobalColorScheme(ColourSchemeProperty.getColourName(av
-            .getGlobalColourScheme()));
-
-    // av.setGlobalColourScheme(cs);
-    int count = 0;
-    for (SequenceI seq : alignment.getSequences())
+    int fileChooserOpt = jvFileChooser.showSaveDialog(null);
+    if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
     {
-      StringBuilder name = new StringBuilder();
-      name.append(seq.getName()).append("/").append(seq.getStart())
-              .append("-").append(seq.getEnd());
-      // BioJsSeqPojo seqPojo = new BioJsSeqPojo(seq.getStart(), seq.getEnd(),
-      // String.valueOf(++count),
-      // name.toString(), seq.getSequenceAsString());
-      //
-      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)
-        {
-
-          String featureColour = jalview.util.Format.getHexString(fr
-                  .getColour(sf));
-          BioJsFeaturePojo bjsFeature = new BioJsFeaturePojo();
-          bjsFeature.setFillColor(featureColour);
-          bjsFeature.setXstart(sf.getBegin());
-          bjsFeature.setXend(sf.getEnd());
-          bjsFeature.setText(sf.getType());
-
-          bjsSeqFeatures.add(bjsFeature);
-
-        }
-
-        seqPojo.setFeatures(bjsSeqFeatures);
-      }
-      bjsAlignment.getSeqs().add(seqPojo);
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
+              .getSelectedFile().getParent());
+      selectedFile = jvFileChooser.getSelectedFile().getPath();
     }
-
-    String jalviewData = new com.json.JSONObject(bjsAlignment).toString()
-            .replaceAll("xstart", "xStart").replaceAll("xend", "xEnd");
-    // String bioJSTemplate = new String(
-    // java.nio.file.Files.readAllBytes(java.nio.file.Paths
-    // .get("resources/templates/BioJSTemplate.txt")));
-    String bioJSTemplate = getBioJsTemplateAsString(this);
-
-    return bioJSTemplate.replaceAll("#sequenceData#", jalviewData)
-            .replaceAll(
-                    "#jalview_logo#",
-                    alignment.getClass()
-                            .getResource("/images/Jalview_Logo.png")
-                            .toString());
+    else
+    {
+      throw new NoFileSelectedException("No file was selected.");
+    }
+    return selectedFile;
   }
 
+
   public static String getBioJsTemplateAsString(Object currentObj)
           throws IOException
   {
@@ -183,8 +124,6 @@ public class BioJsHTMLOutput
         }
       }
     }
-
     return sb.toString();
   }
-
 }