X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHTMLOutput.java;h=bebfd280c90be0cb5a8ae3efca3303222f80beb8;hb=91d83d4836ba3f8c6c395d46d607faf693946e66;hp=d58bd67a6566b56eb49c685803ee06fea51455f3;hpb=26371ff5c38bbb092e432d5616313bc1088e87a2;p=jalview.git
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
old mode 100755
new mode 100644
index d58bd67..bebfd28
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -34,7 +34,6 @@ import java.io.InputStreamReader;
import java.net.URL;
import java.util.Objects;
-
public abstract class HTMLOutput implements Runnable
{
protected AlignmentPanel ap;
@@ -107,13 +106,13 @@ public abstract class HTMLOutput implements Runnable
};
}
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;
}
@@ -145,7 +144,7 @@ public abstract class HTMLOutput implements Runnable
{
sb.append(line).append(lineSeparator);
}
-
+
} catch (Exception ex)
{
ex.printStackTrace();
@@ -155,7 +154,7 @@ public abstract class HTMLOutput implements Runnable
{
isReader.close();
}
-
+
if (buffReader != null)
{
buffReader.close();
@@ -167,89 +166,55 @@ public abstract class HTMLOutput implements Runnable
public static String getImageMapHTML()
{
- return new String(
- "\n"
- + "\n"
- + "\n"
- + "\n"
- + "\n"
- + "\n"
- + "\n");
+ return new String("\n" + "\n"
+ + "\n" + "\n" + "\n"
+ + "\n"
+ + "\n");
}
@@ -263,21 +228,19 @@ public abstract class HTMLOutput implements Runnable
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_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
@@ -370,4 +333,4 @@ public abstract class HTMLOutput implements Runnable
* the file path of the generated HTML
*/
public abstract void exportHTML(String outputFile);
-}
+}
\ No newline at end of file