X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=ac29d8e8b340926eb847644d0eadc12631c7bf5d;hb=92cccf420dbe7501fae76b9941fd701151bdf5ab;hp=3a3b6653b4cf24a1f844472e39c5d15b91d8310f;hpb=91818aa43666f34bbbd41df9b91659d736b73403;p=jalview.git
diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 3a3b665..ac29d8e 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,11 +1,31 @@
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentExportData;
import jalview.exceptions.NoFileSelectedException;
-import jalview.gui.AlignViewport;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
-import jalview.json.binding.v1.BioJSReleasePojo;
-import jalview.json.binding.v1.BioJSRepositoryPojo;
+import jalview.json.binding.biojs.BioJSReleasePojo;
+import jalview.json.binding.biojs.BioJSRepositoryPojo;
import jalview.util.MessageManager;
import java.io.BufferedInputStream;
@@ -20,30 +40,30 @@ import java.net.URL;
import java.util.Objects;
import java.util.TreeMap;
-
public class BioJsHTMLOutput
{
- private AlignViewport av;
+ private AlignmentViewPanel ap;
private static File currentBJSTemplateFile;
private static TreeMap 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", "/biojs_templates/");
+ .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/tcofoegbu/bjs-template/master/package.json");;
+ "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
- public BioJsHTMLOutput(AlignmentPanel ap,
- FeatureRenderer fr1)
+ public BioJsHTMLOutput(AlignmentViewPanel ap)
{
if (ap != null)
{
- this.av = ap.av;
- av.setFeatureRenderer(new FeatureRenderer(ap));
+ this.ap = ap;
}
}
@@ -52,12 +72,58 @@ public class BioJsHTMLOutput
try
{
String outputFile = getOutputFile();
- String jalviewAlignmentJson = JSONFile.getJSONData(av);
+ // 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#", jalviewAlignmentJson)
- .toString();
+ .replaceAll("#sequenceData#", bioJSON).toString();
PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
outputFile));
@@ -78,15 +144,13 @@ public class BioJsHTMLOutput
{
String selectedFile = null;
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);
@@ -103,9 +167,7 @@ public class BioJsHTMLOutput
return selectedFile;
}
-
- public static String getBioJsTemplateAsString()
- throws IOException
+ public static String getBioJsTemplateAsString() throws IOException
{
InputStreamReader isReader = null;
BufferedReader buffReader = null;
@@ -146,11 +208,10 @@ public class BioJsHTMLOutput
return sb.toString();
}
- public void refreshBioJSVersionsInfo(String dirName)
+ public static void refreshBioJSVersionsInfo(String dirName)
throws URISyntaxException
{
- URL url = getClass().getResource(dirName);
- File directory = new File(url.toURI());
+ 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 versionFileMap = new TreeMap();
@@ -180,23 +241,33 @@ public class BioJsHTMLOutput
setBioJsMSAVersions(versionFileMap);
}
- public void updateBioJS()
+ public static void updateBioJS()
{
- try
- {
- String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO);
- BioJSRepositoryPojo release = new BioJSRepositoryPojo(gitRepoPkgJson);
- syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
- refreshBioJSVersionsInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
- } catch (URISyntaxException e)
+ Thread updateThread = new Thread()
{
- e.printStackTrace();
- }
- }
+ 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 void syncUpdates(String localDir, BioJSRepositoryPojo repo)
- throws URISyntaxException
+ public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
{
for (BioJSReleasePojo bjsRelease : repo.getReleases())
{
@@ -207,23 +278,22 @@ public class BioJsHTMLOutput
{
releaseFile = "Latest_BioJsMSA_" + releaseVersion + ".txt";
}
- File file = null;
- URL url = getClass().getResource(
- BJS_TEMPLATES_LOCAL_DIRECTORY + releaseFile);
- if (url == null)
- {
- String path = getClass().getResource(BJS_TEMPLATES_LOCAL_DIRECTORY)
- .getPath();
- System.out.println("------> " + path);
- file = new File(path + releaseFile);
- }
- else
+
+ File biojsDirectory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
+ if (!biojsDirectory.exists())
{
- file = new File(url.toURI());
+ 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
{