X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHTMLOutput.java;h=bebfd280c90be0cb5a8ae3efca3303222f80beb8;hb=fa0d259c1527df04693dd3a44f2aa9ad09e6da8d;hp=ccf1ea4bd1b8c410dea1a570e9bd913a3b467dde;hpb=e60cacff9260c47c12cf34a7e191678cfc97d265;p=jalview.git
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
old mode 100755
new mode 100644
index ccf1ea4..bebfd28
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -34,8 +34,7 @@ import java.io.InputStreamReader;
import java.net.URL;
import java.util.Objects;
-
-public abstract class HTMLOutput
+public abstract class HTMLOutput implements Runnable
{
protected AlignmentPanel ap;
@@ -43,8 +42,6 @@ public abstract class HTMLOutput
protected IProgressIndicator pIndicator;
- private boolean headless;
-
protected File generatedFile;
public HTMLOutput(AlignmentPanel ap)
@@ -56,60 +53,66 @@ public abstract class HTMLOutput
}
}
-
public String getBioJSONData()
{
+ return getBioJSONData(null);
+ }
+
+ public String getBioJSONData(AlignExportSettingI exportSettings)
+ {
if (!isEmbedData())
{
return null;
}
- AlignExportSettingI exportSettings = new AlignExportSettingI()
+ if (exportSettings == null)
{
- @Override
- public boolean isExportHiddenSequences()
- {
- return true;
- }
-
- @Override
- public boolean isExportHiddenColumns()
+ exportSettings = new AlignExportSettingI()
{
- return true;
- }
+ @Override
+ public boolean isExportHiddenSequences()
+ {
+ return true;
+ }
- @Override
- public boolean isExportAnnotations()
- {
- return true;
- }
+ @Override
+ public boolean isExportHiddenColumns()
+ {
+ return true;
+ }
- @Override
- public boolean isExportFeatures()
- {
- return true;
- }
+ @Override
+ public boolean isExportAnnotations()
+ {
+ return true;
+ }
- @Override
- public boolean isExportGroups()
- {
- return true;
- }
+ @Override
+ public boolean isExportFeatures()
+ {
+ return true;
+ }
- @Override
- public boolean isCancelled()
- {
- return false;
- }
+ @Override
+ public boolean isExportGroups()
+ {
+ return true;
+ }
- };
+ @Override
+ public boolean isCancelled()
+ {
+ return false;
+ }
+ };
+ }
AlignmentExportData exportData = jalview.gui.AlignFrame
- .getAlignmentForExport(JSONFile.FILE_DESC,
- ap.getAlignViewport(), exportSettings);
+ .getAlignmentForExport(FileFormat.Json, ap.getAlignViewport(),
+ exportSettings);
String bioJSON = new FormatAdapter(ap, exportData.getSettings())
- .formatSequences(JSONFile.FILE_DESC, exportData.getAlignment(),
- exportData.getOmitHidden(), exportData
- .getStartEndPostions(), ap.getAlignViewport()
- .getColumnSelection());
+ .formatSequences(FileFormat.Json, exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(), ap.getAlignViewport()
+ .getAlignment().getHiddenColumns());
return bioJSON;
}
@@ -141,7 +144,7 @@ public abstract class HTMLOutput
{
sb.append(line).append(lineSeparator);
}
-
+
} catch (Exception ex)
{
ex.printStackTrace();
@@ -151,7 +154,7 @@ public abstract class HTMLOutput
{
isReader.close();
}
-
+
if (buffReader != null)
{
buffReader.close();
@@ -163,124 +166,85 @@ public abstract class HTMLOutput
public static String getImageMapHTML()
{
- return new String(
- "\n"
- + "\n"
- + "\n"
- + "\n"
- + "\n"
- + "\n"
- + "\n");
+ return new String("\n" + "\n"
+ + "\n" + "\n" + "\n"
+ + "\n"
+ + "\n");
}
public String getOutputFile() throws NoFileSelectedException
{
String selectedFile = null;
- if (pIndicator != null && !headless)
+ if (pIndicator != null && !isHeadless())
{
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" },
+ JalviewFileChooser jvFileChooser = new JalviewFileChooser("html",
"HTML files");
jvFileChooser.setFileView(new JalviewFileView());
- jvFileChooser.setDialogTitle(MessageManager
- .getString("label.save_as_biojs_html"));
+ jvFileChooser
+ .setDialogTitle(MessageManager.getString("label.save_as_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());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ jvFileChooser.getSelectedFile().getParent());
selectedFile = jvFileChooser.getSelectedFile().getPath();
}
else
{
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "status.cancelled_image_export_operation", "BioJS"),
- pSessionId);
throw new NoFileSelectedException("No file was selected.");
}
return selectedFile;
@@ -288,7 +252,7 @@ public abstract class HTMLOutput
protected void setProgressMessage(String message)
{
- if (pIndicator != null && !headless)
+ if (pIndicator != null && !isHeadless())
{
pIndicator.setProgressBar(message, pSessionId);
}
@@ -369,4 +333,4 @@ public abstract class HTMLOutput
* the file path of the generated HTML
*/
public abstract void exportHTML(String outputFile);
-}
+}
\ No newline at end of file