X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHTMLOutput.java;h=711c46588159abc563486352a0db455d2d0e3f14;hb=94ca0419cc7afa75b3c51917a8beaf46a7c05540;hp=7988182beaba5b4076a2936b0374c4e5e1fc10e8;hpb=54e2b67f5548b7f009fda7059b86e6b430448576;p=jalview.git
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
old mode 100755
new mode 100644
index 7988182..711c465
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -1,106 +1,366 @@
-package jalview.io;
-
-import jalview.gui.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import java.awt.*;
-import javax.swing.*;
-import java.io.*;
-import java.util.*;
-
-
-public class HTMLOutput
-{
-
-
- public HTMLOutput(AlignViewport av)
- {
- SequenceRenderer sr = new SequenceRenderer(av);
- Color color;
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
- chooser.setDialogTitle("Save as HTML");
- chooser.setToolTipText("Save");
- int value = chooser.showSaveDialog(null);
- if(value == JFileChooser.APPROVE_OPTION)
- {
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.LAST_DIRECTORY = choice;
- try{
- PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(choice));
- out.println("");
- out.println("");
- out.println("
");
- out.println("\n");
- out.println("\n");
-
-
- //////////////
- SequenceGroup group;
- SequenceI seq;
- ColourSchemeI cs;
- AlignmentI alignment = av.getAlignment();
- String r,g,b;
- for (int i = 0; i < alignment.getHeight(); i++)
- {
- seq = alignment.getSequenceAt(i);
- group = alignment.findGroup( seq );
- out.println(""+seq.getDisplayId()+" | ");
- for (int res = 0; res < seq.getLength(); res++)
- {
- if(group!=null && group.getStartRes()<=res && group.getEndRes()>=res)
- cs = group.cs;
- else
- cs = av.getGlobalColourScheme();
-
-
- color = sr.getResidueBoxColour(cs, seq, res);
-
- if(color.getRGB()<-1)
- {
- r = Integer.toHexString(color.getRed());
- if(r.length()<2)
- r = "0"+r;
- g = Integer.toHexString(color.getGreen());
- if(g.length()<2)
- g = "0"+g;
- b = Integer.toHexString(color.getBlue());
- if(b.length()<2)
- b = "0"+b;
- out.println(""+seq.getCharAt(res)+" | ");
- }
- else
- out.println(""+seq.getCharAt(res)+" | ");
-
- }
-
- out.println(" ");
- }
- //////////////
- out.println(" ");
- out.println(" |
\n\n");
-
- out.close();
-
- jalview.util.BrowserLauncher.openURL( choice );
- }
- catch(Exception ex){ex.printStackTrace();}
- }
- }
-
-
-}
+/*
+ * 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 java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.Objects;
+
+import jalview.api.AlignExportSettingsI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignExportSettingsAdapter;
+import jalview.datamodel.AlignmentExportData;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.IProgressIndicator;
+import jalview.io.exceptions.ImageOutputException;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
+import jalview.util.MessageManager;
+
+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;
+
+ protected File generatedFile;
+
+ 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)
+ {
+ this.ap = ap;
+ this.pIndicator = ap.alignFrame;
+ this.description = desc;
+ this.pSessionId = IdUtils.newId(IdType.PROGRESS);
+ }
+
+ /**
+ * 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;
+ }
+ if (_bioJson == null)
+ {
+ 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());
+ }
+
+ return _bioJson;
+ }
+
+ /**
+ * 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
+ {
+ 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)
+ {
+ try
+ {
+ isReader = new InputStreamReader(url.openStream());
+ buffReader = new BufferedReader(isReader);
+ String line;
+ String lineSeparator = System.getProperty("line.separator");
+ while ((line = buffReader.readLine()) != null)
+ {
+ sb.append(line).append(lineSeparator);
+ }
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } finally
+ {
+ if (isReader != null)
+ {
+ isReader.close();
+ }
+
+ if (buffReader != null)
+ {
+ buffReader.close();
+ }
+ }
+ }
+ return sb.toString();
+ }
+
+ public static String getImageMapHTML()
+ {
+ return new String("\n" + "\n"
+ + "\n" + "\n" + "\n"
+ + "\n"
+ + "\n");
+
+ }
+
+ /**
+ * Prompts the user to choose an output file and returns the file path, or
+ * null on Cancel
+ *
+ * @return
+ */
+ public String getOutputFile()
+ {
+ String selectedFile = null;
+
+ // 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_html"));
+ jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
+
+ int fileChooserOpt = jvFileChooser.showSaveDialog(null);
+ if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
+ {
+ Cache.setProperty("LAST_DIRECTORY",
+ jvFileChooser.getSelectedFile().getParent());
+ selectedFile = jvFileChooser.getSelectedFile().getPath();
+ }
+
+ return selectedFile;
+ }
+
+ protected void setProgressMessage(String message)
+ {
+ if (pIndicator != null && !isHeadless())
+ {
+ pIndicator.setProgressBar(message, pSessionId);
+ }
+ else
+ {
+ jalview.bin.Console.outPrintln(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 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 File getExportedFile()
+ {
+ return generatedFile;
+ }
+
+ public void exportHTML(String outputFile) throws ImageOutputException
+ {
+ exportHTML(outputFile, null);
+ }
+
+ public void exportHTML(String outputFile, String renderer)
+ throws ImageOutputException
+ {
+ 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;
+ }
+ if (Jalview.isHeadlessMode())
+ {
+ this.run(renderer);
+ }
+ else
+ {
+ new Thread(this).start();
+ }
+
+ }
+
+ /**
+ * Answers a short description of the image format suitable for display in
+ * messages
+ *
+ * @return
+ */
+ protected final String getDescription()
+ {
+ return description;
+ }
+
+ // used to pass an option such as render to run
+ public abstract void run(String string) throws ImageOutputException;
+}
\ No newline at end of file