X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=7423e20c1b34d580bb05947ea9e8e182ef6903f7;hb=d884105fcd0ac029684c62573e706e5d88b4301c;hp=6e2ec8c05f9d9f2e4a022a282ac85156fc7e4983;hpb=f511799b8f00b4a224f0f902ad6f25df862c60ed;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 6e2ec8c..7423e20 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,7 +1,5 @@
 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;
@@ -12,75 +10,122 @@ import jalview.json.binding.v1.BioJsAlignmentPojo;
 import jalview.json.binding.v1.BioJsSeqPojo;
 import jalview.util.MessageManager;
 
+import java.io.BufferedReader;
 import java.io.IOException;
+import java.io.InputStreamReader;
 import java.io.PrintWriter;
-
-import org.json.simple.parser.ParseException;
+import java.net.URL;
 
 import com.json.JSONException;
 
-public class BioJsHTMLOutput {
-	private AlignViewport av;
-	private FeatureRenderer fr;
-
-	public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr, FeatureRenderer fr1) {
-		this.av = ap.av;
-		this.fr = new FeatureRenderer(ap);
-		fr.transferSettings(fr1);
-		exportAsBioJsHtml();
-	}
-
-	private void exportAsBioJsHtml() {
-		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) {
-			ex.printStackTrace();
-		}
-	}
-
-	private JalviewFileChooser getJalviewFileChooserOption() {
-		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;
-	}
-
-	private String generateBioJsAlignmentData(AlignmentI alignment) throws IOException, JSONException {
-		BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
-		int count = 0;
-		for (SequenceI seq : alignment.getSequences()) {
-			StringBuilder name = new StringBuilder();
-			name.append(seq.getName()).append("/").append(seq.getStart()).append("-").append(seq.getEnd());
-			bjsAlignment.getSeqs().add(new BioJsSeqPojo(String.valueOf(++count), name.toString(), seq.getSequenceAsString()));
-		}
-
-		// Taylor
-		// av.getGlobalColourScheme().;
-		String seqs = new com.json.JSONObject(bjsAlignment).getString("seqs");
-		String bioJSTemplate = new String(readAllBytes(get("resources/templates/BioJSTemplate.txt")));
-
-		// av.get
-		// fr.
-		return bioJSTemplate.replaceAll("#sequenceData#", seqs).replaceAll("#scheme#", "zappo");
-	}
-
-	public static void main(String[] args) throws IOException, ParseException {
-
-	}
+public class BioJsHTMLOutput
+{
+  private AlignViewport av;
+
+  private FeatureRenderer fr;
+
+  public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
+          FeatureRenderer fr1)
+  {
+    this.av = ap.av;
+    this.fr = new FeatureRenderer(ap);
+    fr.transferSettings(fr1);
+    exportAsBioJsHtml();
+  }
+
+  private void exportAsBioJsHtml()
+  {
+    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)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  private JalviewFileChooser getJalviewFileChooserOption()
+  {
+    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;
+  }
+
+  private String generateBioJsAlignmentData(AlignmentI alignment)
+          throws IOException, JSONException
+  {
+    BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
+    int count = 0;
+    for (SequenceI seq : alignment.getSequences())
+    {
+      StringBuilder name = new StringBuilder();
+      name.append(seq.getName()).append("/").append(seq.getStart())
+              .append("-").append(seq.getEnd());
+      bjsAlignment.getSeqs().add(
+              new BioJsSeqPojo(String.valueOf(++count), name.toString(),
+                      seq.getSequenceAsString()));
+    }
+
+    String seqs = new com.json.JSONObject(bjsAlignment).getString("seqs");
+    // String bioJSTemplate = new String(
+    // java.nio.file.Files.readAllBytes(java.nio.file.Paths
+    // .get("resources/templates/BioJSTemplate.txt")));
+    String bioJSTemplate = getBioJsTemplateAsString(alignment);
+
+    return bioJSTemplate.replaceAll("#sequenceData#", seqs).replaceAll(
+            "#scheme#", "zappo");
+  }
+
+
+  public static String getBioJsTemplateAsString(AlignmentI bio)
+          throws IOException
+  {
+     StringBuilder sb = new StringBuilder();
+    URL url = bio.getClass().getResource(
+            "/templates/BioJSTemplate.txt");
+    if (url != null)
+    {
+      try
+      {
+        BufferedReader reader = new BufferedReader(new InputStreamReader(
+                url.openStream()));
+        String line;
+        String lineSeparator = System.getProperty("line.separator");
+        while ((line = reader.readLine()) != null)
+        {
+          sb.append(line).append(lineSeparator);
+        }
+      } catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+
+    return sb.toString();
+  }
 
 }