X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FHTMLOutput.java;h=bebfd280c90be0cb5a8ae3efca3303222f80beb8;hb=f47ded5b8b48d6372cd1ef8f49e1a630dcadfbdb;hp=a37d8a2f8b76de7750632bf3318624a2d07b6f1b;hpb=61464a7627562c55f28357cb6eeb68eb734961b7;p=jalview.git
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
old mode 100755
new mode 100644
index a37d8a2..bebfd28
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -1,106 +1,336 @@
-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.getName()+" | ");
- 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 jalview.api.AlignExportSettingI;
+import jalview.datamodel.AlignmentExportData;
+import jalview.exceptions.NoFileSelectedException;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.IProgressIndicator;
+import jalview.util.MessageManager;
+
+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 abstract class HTMLOutput implements Runnable
+{
+ protected AlignmentPanel ap;
+
+ protected long pSessionId;
+
+ protected IProgressIndicator pIndicator;
+
+ protected File generatedFile;
+
+ public HTMLOutput(AlignmentPanel ap)
+ {
+ if (ap != null)
+ {
+ this.ap = ap;
+ this.pIndicator = ap.alignFrame;
+ }
+ }
+
+ public String getBioJSONData()
+ {
+ return getBioJSONData(null);
+ }
+
+ public String getBioJSONData(AlignExportSettingI exportSettings)
+ {
+ if (!isEmbedData())
+ {
+ return null;
+ }
+ if (exportSettings == null)
+ {
+ exportSettings = new AlignExportSettingI()
+ {
+ @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;
+ }
+ };
+ }
+ 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()
+ .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");
+
+ }
+
+ 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