-/*
- * 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
package jalview.io;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignViewport;
+import jalview.api.AlignExportSettingI;
+import jalview.datamodel.AlignmentExportData;
+import jalview.exceptions.NoFileSelectedException;
import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
-import jalview.gui.SequenceRenderer;
+import jalview.gui.IProgressIndicator;
import jalview.util.MessageManager;
-import java.awt.Color;
-import java.awt.Font;
-import java.io.PrintWriter;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.Objects;
-public class HTMLOutput
+public abstract class HTMLOutput implements Runnable
{
- AlignViewport av;
+ protected AlignmentPanel ap;
- SequenceRenderer sr;
+ protected long pSessionId;
- jalview.renderer.seqfeatures.FeatureRenderer fr;
+ protected IProgressIndicator pIndicator;
- Color color;
+ protected File generatedFile;
- public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
- FeatureRenderer fr1)
+ public HTMLOutput(AlignmentPanel ap)
{
- this.av = ap.av;
- this.sr = sr;
-
- fr = new FeatureRenderer(ap);
- fr.transferSettings(fr1);
-
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
- new String[] { "html" }, new String[] { "HTML files" },
- "HTML files");
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_as_html"));
- chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ if (ap != null)
{
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
-
- try
- {
- PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
- choice));
- out.println("<HTML>");
- out.println("<style type=\"text/css\">");
- out.println("<!--");
- out.print("td {font-family: \"" + av.getFont().getFamily()
- + "\", \"" + av.getFont().getName() + "\", mono; "
- + "font-size: " + av.getFont().getSize() + "px; ");
-
- if (av.getFont().getStyle() == Font.BOLD)
- {
- out.print("font-weight: BOLD; ");
- }
-
- if (av.getFont().getStyle() == Font.ITALIC)
- {
- out.print("font-style: italic; ");
- }
-
- out.println("text-align: center; }");
-
- out.println("-->");
- out.println("</style>");
- out.println("<BODY>");
-
- if (av.getWrapAlignment())
- {
- drawWrappedAlignment(out);
- }
- else
- {
- drawUnwrappedAlignment(out);
- }
-
- out.println("\n</body>\n</html>");
- out.close();
- jalview.util.BrowserLauncher.openURL("file:///" + choice);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ this.ap = ap;
+ this.pIndicator = ap.alignFrame;
}
}
- void drawUnwrappedAlignment(PrintWriter out)
+ public String getBioJSONData()
{
- out.println("<table border=\"1\"><tr><td>\n");
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
-
- // ////////////
- SequenceI seq;
- AlignmentI alignment = av.getAlignment();
-
- // draws the top row, the measure rule
- out.println("<tr><td colspan=\"6\"></td>");
-
- int i = 0;
+ return getBioJSONData(null);
+ }
- for (i = 10; i < (alignment.getWidth() - 10); i += 10)
+ public String getBioJSONData(AlignExportSettingI exportSettings)
+ {
+ if (!isEmbedData())
{
- out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
+ return null;
}
-
- out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i
- + "<br>|</td>");
- out.println("</tr>");
-
- for (i = 0; i < alignment.getHeight(); i++)
+ if (exportSettings == null)
{
- seq = alignment.getSequenceAt(i);
-
- String id = seq.getDisplayId(av.getShowJVSuffix());
-
- out.println("<tr><td nowrap>" + id + " </td>");
-
- for (int res = 0; res < seq.getLength(); res++)
+ exportSettings = new AlignExportSettingI()
{
- if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
+ @Override
+ public boolean isExportHiddenSequences()
{
- color = sr.getResidueBoxColour(seq, res);
+ return true;
+ }
- color = fr.findFeatureColour(color, seq, res);
+ @Override
+ public boolean isExportHiddenColumns()
+ {
+ return true;
}
- else
+
+ @Override
+ public boolean isExportAnnotations()
{
- color = Color.white;
+ return true;
}
- if (color.getRGB() < -1)
+ @Override
+ public boolean isExportFeatures()
{
- out.println("<td bgcolor=\"#"
- + jalview.util.Format.getHexString(color) + "\">"
- + seq.getCharAt(res) + "</td>");
+ return true;
}
- else
+
+ @Override
+ public boolean isExportGroups()
{
- out.println("<td>" + seq.getCharAt(res) + "</td>");
+ return true;
}
- }
- out.println("</tr>");
+ @Override
+ public boolean isCancelled()
+ {
+ return false;
+ }
+ };
}
-
- // ////////////
- out.println("</table>");
- out.println("</td></tr></table>");
+ AlignmentExportData exportData = jalview.gui.AlignFrame
+ .getAlignmentForExport(FileFormat.Json,
+ ap.getAlignViewport(), exportSettings);
+ String bioJSON = new FormatAdapter(ap, exportData.getSettings())
+ .formatSequences(FileFormat.Json, exportData.getAlignment(),
+ exportData.getOmitHidden(), exportData
+ .getStartEndPostions(), ap.getAlignViewport()
+ .getColumnSelection());
+ return bioJSON;
}
- void drawWrappedAlignment(PrintWriter out)
+ /**
+ * Read a template file content as string
+ *
+ * @param file
+ * - the file to be read
+ * @return File content as String
+ * @throws IOException
+ */
+ public static String readFileAsString(File file) throws IOException
{
- // //////////////////////////////////
- // / How many sequences and residues can we fit on a printable page?
- AlignmentI al = av.getAlignment();
- SequenceI seq;
- String r;
- String g;
- String b;
-
- out.println("<table border=\"1\"><tr><td>\n");
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
-
- for (int startRes = 0; startRes < al.getWidth(); startRes += av
- .getWrappedWidth())
+ InputStreamReader isReader = null;
+ BufferedReader buffReader = null;
+ StringBuilder sb = new StringBuilder();
+ Objects.requireNonNull(file, "File must not be null!");
+ @SuppressWarnings("deprecation")
+ URL url = file.toURL();
+ if (url != null)
{
- int endRes = startRes + av.getWrappedWidth();
-
- if (endRes > al.getWidth())
- {
- endRes = al.getWidth();
- }
-
- if (av.getScaleAboveWrapped())
+ try
{
- out.println("<tr>");
-
- if (av.getScaleLeftWrapped())
+ isReader = new InputStreamReader(url.openStream());
+ buffReader = new BufferedReader(isReader);
+ String line;
+ String lineSeparator = System.getProperty("line.separator");
+ while ((line = buffReader.readLine()) != null)
{
- out.println("<td colspan=\"7\"> </td>");
+ sb.append(line).append(lineSeparator);
}
- else
- {
- out.println("<td colspan=\"6\"> </td>");
- }
-
- for (int i = startRes + 10; i < endRes; i += 10)
- {
- out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
- }
-
- out.println("</tr>");
- }
-
- int startPos, endPos;
- for (int s = 0; s < al.getHeight(); s++)
+
+ } catch (Exception ex)
{
- out.println("<tr>");
- seq = al.getSequenceAt(s);
-
- startPos = seq.findPosition(startRes);
- endPos = seq.findPosition(endRes) - 1;
-
- String id = seq.getDisplayId(av.getShowJVSuffix());
-
- out.println("<td nowrap>" + id + " </td>");
-
- if (av.getScaleLeftWrapped())
- {
- if (startPos > seq.getEnd() || endPos == 0)
- {
- out.println("<td nowrap> </td>");
- }
- else
- {
- out.println("<td nowrap>" + startPos + " </td>");
- }
- }
-
- for (int res = startRes; res < endRes; res++)
- {
- if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
- {
- color = sr.getResidueBoxColour(seq, res);
-
- color = fr.findFeatureColour(color, seq, res);
- }
- else
- {
- color = Color.white;
- }
-
- if (color.getRGB() < -1)
- {
- out.println("<td bgcolor=\"#"
- + jalview.util.Format.getHexString(color) + "\">"
- + seq.getCharAt(res) + "</td>");
- }
- else
- {
- out.println("<td>" + seq.getCharAt(res) + "</td>");
- }
-
- }
-
- if (av.getScaleRightWrapped()
- && endRes < startRes + av.getWrappedWidth())
+ ex.printStackTrace();
+ } finally
+ {
+ if (isReader != null)
{
- out.println("<td colspan=\""
- + (startRes + av.getWrappedWidth() - endRes) + "\">"
- + " </td>");
+ isReader.close();
}
-
- if (av.getScaleRightWrapped() && startPos < endPos)
+
+ if (buffReader != null)
{
- out.println("<td nowrap> " + endPos + " </td>");
+ buffReader.close();
}
-
- out.println("</tr>");
- }
-
- if (endRes < al.getWidth())
- {
- out.println("<tr><td height=\"5\"></td></tr>");
}
}
-
- out.println("</table>");
- out.println("</table>");
+ return sb.toString();
}
public static String getImageMapHTML()
+ "initToolTips(); //--></script>\n");
}
-}
+
+ public String getOutputFile() throws NoFileSelectedException
+ {
+ String selectedFile = null;
+ if (pIndicator != null && !isHeadless())
+ {
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "status.waiting_for_user_to_select_output_file", "HTML"),
+ pSessionId);
+ }
+
+ JalviewFileChooser jvFileChooser = new JalviewFileChooser("html",
+ "HTML files");
+ jvFileChooser.setFileView(new JalviewFileView());
+
+ 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());
+ selectedFile = jvFileChooser.getSelectedFile().getPath();
+ }
+ else
+ {
+ throw new NoFileSelectedException("No file was selected.");
+ }
+ return selectedFile;
+ }
+
+ protected void setProgressMessage(String message)
+ {
+ if (pIndicator != null && !isHeadless())
+ {
+ pIndicator.setProgressBar(message, pSessionId);
+ }
+ else
+ {
+ System.out.println(message);
+ }
+ }
+
+ /**
+ * 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())
+ {
+ try
+ {
+ jalview.util.BrowserLauncher
+ .openURL("file:///" + getExportedFile());
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ /**
+ * if this answers true then BioJSON data will be embedded to the exported
+ * HTML file otherwise it won't be embedded.
+ *
+ * @return
+ */
+ public abstract boolean isEmbedData();
+
+ /**
+ * if this answers true then the generated HTML file is opened for viewing in
+ * a browser after its generation otherwise it won't be opened in a browser
+ *
+ * @return
+ */
+ public abstract boolean isLaunchInBrowserAfterExport();
+
+ /**
+ * handle to the generated HTML file
+ *
+ * @return
+ */
+ public abstract File getExportedFile();
+
+ /**
+ * This is the main method to handle the HTML generation.
+ *
+ * @param outputFile
+ * the file path of the generated HTML
+ */
+ public abstract void exportHTML(String outputFile);
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff