X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHTMLOutput.java;h=e7054c7704ce11ea82953770d13af9632f557921;hb=c4c37610dc373b9b3349e5c0915c6eddda2efe31;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..e7054c7
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -20,12 +20,15 @@
*/
package jalview.io;
-import jalview.api.AlignExportSettingI;
+import jalview.api.AlignExportSettingsI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignExportSettingsAdapter;
import jalview.datamodel.AlignmentExportData;
-import jalview.exceptions.NoFileSelectedException;
import jalview.gui.AlignmentPanel;
import jalview.gui.IProgressIndicator;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.io.BufferedReader;
import java.io.File;
@@ -34,83 +37,65 @@ 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;
+ /*
+ * key for progress or status messages
+ */
protected long pSessionId;
+ /*
+ * (optional) place to write progress messages to
+ */
protected IProgressIndicator pIndicator;
- private boolean headless;
-
protected File generatedFile;
- public HTMLOutput(AlignmentPanel ap)
+ String _bioJson = null;
+
+ private String description;
+
+ /**
+ * Constructor given an alignment panel (which should not be null)
+ *
+ * @param ap
+ * @param desc
+ */
+ public HTMLOutput(AlignmentPanel ap, String desc)
{
- if (ap != null)
- {
- this.ap = ap;
- this.pIndicator = ap.alignFrame;
- }
+ this.ap = ap;
+ this.pIndicator = ap.alignFrame;
+ this.description = desc;
+ this.pSessionId = System.currentTimeMillis();
}
-
+ /**
+ * Gets the BioJSON data as a string, with lazy evaluation (first time called
+ * only). If the output format is configured not to embed BioJSON, returns
+ * null.
+ *
+ * @return
+ */
public String getBioJSONData()
{
if (!isEmbedData())
{
return null;
}
- AlignExportSettingI exportSettings = new AlignExportSettingI()
+ if (_bioJson == null)
{
- @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;
- }
+ AlignExportSettingsI options = new AlignExportSettingsAdapter(true);
+ AlignmentExportData exportData = ap.getAlignViewport()
+ .getAlignExportData(options);
+ _bioJson = new FormatAdapter(ap, options).formatSequences(
+ FileFormat.Json, exportData.getAlignment(),
+ exportData.getOmitHidden(), exportData.getStartEndPostions(),
+ ap.getAlignViewport().getAlignment().getHiddenColumns());
+ }
- };
- 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());
- return bioJSON;
+ return _bioJson;
}
/**
@@ -141,7 +126,7 @@ public abstract class HTMLOutput
{
sb.append(line).append(lineSeparator);
}
-
+
} catch (Exception ex)
{
ex.printStackTrace();
@@ -151,7 +136,7 @@ public abstract class HTMLOutput
{
isReader.close();
}
-
+
if (buffReader != null)
{
buffReader.close();
@@ -163,132 +148,92 @@ 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
+ /**
+ * Prompts the user to choose an output file and returns the file path, or
+ * null on Cancel
+ *
+ * @return
+ */
+ public String getOutputFile()
{
String selectedFile = null;
- if (pIndicator != null && !headless)
- {
- 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" },
+ // TODO: JAL-3048 generate html rendered view (requires SvgGraphics and/or
+ // Jalview HTML rendering system- probably not required for Jalview-JS)
+ 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());
+ 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;
}
protected void setProgressMessage(String message)
{
- if (pIndicator != null && !headless)
+ if (pIndicator != null && !Jalview.isHeadlessMode())
{
pIndicator.setProgressBar(message, pSessionId);
}
@@ -299,39 +244,17 @@ public abstract class HTMLOutput
}
/**
- * Answers true if HTML export is invoke in headless mode or false otherwise
- *
- * @return
- */
- protected boolean isHeadless()
- {
- return System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true");
- }
-
- /**
- * This method provides implementation of consistent behaviour which should
- * occur before a HTML file export. It MUST be called at the start of the
- * exportHTML() method implementation.
- */
- protected void exportStarted()
- {
- pSessionId = System.currentTimeMillis();
- }
-
- /**
* This method provides implementation of consistent behaviour which should
* occur after a HTML file export. It MUST be called at the end of the
* exportHTML() method implementation.
*/
protected void exportCompleted()
{
- if (isLaunchInBrowserAfterExport() && !isHeadless())
+ if (isLaunchInBrowserAfterExport() && !Jalview.isHeadlessMode())
{
try
{
- jalview.util.BrowserLauncher
- .openURL("file:///" + getExportedFile());
+ Platform.openURL("file:///" + getExportedFile());
} catch (IOException e)
{
e.printStackTrace();
@@ -360,13 +283,51 @@ public abstract class HTMLOutput
*
* @return
*/
- public abstract File getExportedFile();
+ public File getExportedFile()
+ {
+ return generatedFile;
+ }
+
+ public void exportHTML(String outputFile)
+ {
+ setProgressMessage(MessageManager.formatMessage(
+ "status.exporting_alignment_as_x_file", getDescription()));
+ try
+ {
+ if (outputFile == null)
+ {
+ /*
+ * prompt for output file
+ */
+ outputFile = getOutputFile();
+ if (outputFile == null)
+ {
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation",
+ getDescription()));
+ return;
+ }
+ }
+ generatedFile = new File(outputFile);
+ } catch (Exception e)
+ {
+ setProgressMessage(MessageManager
+ .formatMessage("info.error_creating_file", getDescription()));
+ e.printStackTrace();
+ return;
+ }
+ new Thread(this).start();
+
+ }
/**
- * This is the main method to handle the HTML generation.
+ * Answers a short description of the image format suitable for display in
+ * messages
*
- * @param outputFile
- * the file path of the generated HTML
+ * @return
*/
- public abstract void exportHTML(String outputFile);
-}
+ protected final String getDescription()
+ {
+ return description;
+ }
+}
\ No newline at end of file