X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlSvgOutput.java;h=4b66f810045d578dfbfc5b50ce37815d306977ef;hb=refs%2Fheads%2Ffeatures%2Fr2_11_2_alphafold%2FJAL-2349_JAL-3855;hp=e60824a6e668112f4c8367b9933f930d48c62c9a;hpb=e60cacff9260c47c12cf34a7e191678cfc97d265;p=jalview.git

diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index e60824a..4b66f81 100644
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -20,8 +20,9 @@
  */
 package jalview.io;
 
+import jalview.bin.Cache;
 import jalview.gui.AlignmentPanel;
-import jalview.gui.HTMLOptions;
+import jalview.gui.LineartOptions;
 import jalview.gui.OOMWarning;
 import jalview.math.AlignmentDimension;
 import jalview.util.MessageManager;
@@ -31,137 +32,24 @@ import java.awt.print.PrinterException;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.util.concurrent.atomic.AtomicBoolean;
 
 import org.jfree.graphics2d.svg.SVGGraphics2D;
 import org.jfree.graphics2d.svg.SVGHints;
 
 public class HtmlSvgOutput extends HTMLOutput
 {
-
-  private File generatedFile;
-
   public HtmlSvgOutput(AlignmentPanel ap)
   {
-    super(ap);
-  }
-
-  @Override
-  public void exportHTML(String file)
-  {
-    exportStarted();
-    try
-    {
-      if (file == null)
-      {
-        file = getOutputFile();
-      }
-      generatedFile = new File(file);
-    } catch (Exception e)
-    {
-      setProgressMessage(MessageManager.formatMessage(
-              "info.error_creating_file", "HTML"));
-      e.printStackTrace();
-      return;
-    }
-    new Thread()
-    {
-      @Override
-      public void run()
-      {
-        try
-        {
-          setProgressMessage(null);
-          setProgressMessage(MessageManager.formatMessage(
-                  "status.exporting_alignment_as_x_file", "HTML"));
-          AlignmentDimension aDimension = ap.getAlignmentDimension();
-          SVGGraphics2D idPanelGraphics = new SVGGraphics2D(
-                  aDimension.getWidth(),
-                  aDimension.getHeight());
-          SVGGraphics2D alignPanelGraphics = new SVGGraphics2D(
-                  aDimension.getWidth(),
-                  aDimension.getHeight());
-
-          String renderStyle = jalview.bin.Cache.getDefault(
-                  "HTML_RENDERING", "Prompt each time");
-
-          // If we need to prompt, and if the GUI is visible then
-          // Prompt for rendering style
-          if (renderStyle.equalsIgnoreCase("Prompt each time")
-                  && !isHeadless())
-          {
-            HTMLOptions svgOption = new HTMLOptions();
-            renderStyle = svgOption.getValue();
-
-            if (renderStyle == null || svgOption.cancelled)
-            {
-              setProgressMessage(MessageManager.formatMessage(
-                      "status.cancelled_image_export_operation", "HTML"));
-              return;
-            }
-          }
-
-          if (renderStyle.equalsIgnoreCase("Lineart"))
-          {
-            idPanelGraphics.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
-                    SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
-            alignPanelGraphics.setRenderingHint(
-                    SVGHints.KEY_DRAW_STRING_TYPE,
-                    SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
-          }
-          if (ap.av.getWrapAlignment())
-          {
-            printWrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
-                    alignPanelGraphics);
-          }
-          else
-          {
-          printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
- idPanelGraphics, alignPanelGraphics);
-          }
-
-          String idPanelSvgData = idPanelGraphics.getSVGDocument();
-          String alignPanelSvgData = alignPanelGraphics.getSVGDocument();
-          String jsonData = getBioJSONData();
-          String htmlData = getHtml(idPanelSvgData, alignPanelSvgData, jsonData,
- ap.av.getWrapAlignment());
-          FileOutputStream out = new FileOutputStream(generatedFile);
-          out.write(htmlData.getBytes());
-          out.flush();
-          out.close();
-          exportCompleted();
-        } catch (OutOfMemoryError err)
-        {
-          System.out.println("########################\n"
-                  + "OUT OF MEMORY " + generatedFile + "\n"
-                  + "########################");
-          new OOMWarning("Creating Image for " + generatedFile, err);
-        } catch (Exception e)
-        {
-          e.printStackTrace();
-          setProgressMessage(MessageManager.formatMessage(
-                  "info.error_creating_file", "HTML"));
-        }
-        setProgressMessage(MessageManager.formatMessage(
-                "status.export_complete", "HTML"));
-      }
-    }.start();
-
-  }
-
-
-  static JalviewFileChooser getHTMLChooser()
-  {
-    return new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            new String[] { "html" },
-            new String[] { "Hypertext Markup Language" },
-            "Hypertext Markup Language");
+    super(ap, "HTML");
   }
 
-  public int printUnwrapped(int pwidth, int pheight, int pi, Graphics... pg)
+  public int printUnwrapped(int pwidth, int pheight, int pi,
+          Graphics idGraphics, Graphics alignmentGraphics)
           throws PrinterException
   {
-    return ap.printUnwrapped(pwidth, pheight, pi, pg);
+    return ap.printUnwrapped(pwidth, pheight, pi, idGraphics,
+            alignmentGraphics);
   }
 
   public int printWrapped(int pwidth, int pheight, int pi, Graphics... pg)
@@ -170,17 +58,20 @@ public class HtmlSvgOutput extends HTMLOutput
     return ap.printWrappedAlignment(pwidth, pheight, pi, pg[0]);
   }
 
-  private String getHtml(String titleSvg, String alignmentSvg,
-          String jsonData, boolean wrapped)
+  String getHtml(String titleSvg, String alignmentSvg, String jsonData,
+          boolean wrapped)
   {
     StringBuilder htmlSvg = new StringBuilder();
     htmlSvg.append("<html>\n");
     if (jsonData != null)
     {
-      htmlSvg.append("<button onclick=\"javascipt:openJalviewUsingCurrentUrl();\">Launch in Jalview</button> &nbsp;");
-      htmlSvg.append("<input type=\"submit\" value=\"View raw BioJSON Data\" onclick=\"jQuery.facebox({ div:'#seqData' }); return false;\" />");
-      htmlSvg.append("<div style=\"display: none;\" name=\"seqData\" id=\"seqData\" >"
-              + jsonData + "</div>");
+      htmlSvg.append(
+              "<button onclick=\"javascipt:openJalviewUsingCurrentUrl();\">Launch in Jalview</button> &nbsp;");
+      htmlSvg.append(
+              "<input type=\"submit\" value=\"View raw BioJSON Data\" onclick=\"jQuery.facebox({ div:'#seqData' }); return false;\" />");
+      htmlSvg.append(
+              "<div style=\"display: none;\" name=\"seqData\" id=\"seqData\" >"
+                      + jsonData + "</div>");
       htmlSvg.append("<br/>&nbsp;");
     }
     htmlSvg.append("\n<style type=\"text/css\"> "
@@ -193,74 +84,80 @@ public class HtmlSvgOutput extends HTMLOutput
     if (jsonData != null)
     {
       // facebox style sheet for displaying raw BioJSON data
-      htmlSvg.append("#facebox { position: absolute;  top: 0;   left: 0; z-index: 100; text-align: left; }\n"
-              + "#facebox .popup{ position:relative; border:3px solid rgba(0,0,0,0); -webkit-border-radius:5px;"
-              + "-moz-border-radius:5px; border-radius:5px; -webkit-box-shadow:0 0 18px rgba(0,0,0,0.4); -moz-box-shadow:0 0 18px rgba(0,0,0,0.4);"
-              + "box-shadow:0 0 18px rgba(0,0,0,0.4); }\n"
-              + "#facebox .content { display:table; width: 98%; padding: 10px; background: #fff; -webkit-border-radius:4px; -moz-border-radius:4px;"
-              + " border-radius:4px; }\n"
-              + "#facebox .content > p:first-child{ margin-top:0; }\n"
-              + "#facebox .content > p:last-child{ margin-bottom:0; }\n"
-              + "#facebox .close{ position:absolute; top:5px; right:5px; padding:2px; background:#fff; }\n"
-              + "#facebox .close img{ opacity:0.3; }\n"
-              + "#facebox .close:hover img{ opacity:1.0; }\n"
-              + "#facebox .loading { text-align: center; }\n"
-              + "#facebox .image { text-align: center;}\n"
-              + "#facebox img { border: 0;  margin: 0; }\n"
-              + "#facebox_overlay { position: fixed; top: 0px; left: 0px; height:100%; width:100%; }\n"
-              + ".facebox_hide { z-index:-100; }\n"
-              + ".facebox_overlayBG { background-color: #000;  z-index: 99;  }");
+      htmlSvg.append(
+              "#facebox { position: absolute;  top: 0;   left: 0; z-index: 100; text-align: left; }\n"
+                      + "#facebox .popup{ position:relative; border:3px solid rgba(0,0,0,0); -webkit-border-radius:5px;"
+                      + "-moz-border-radius:5px; border-radius:5px; -webkit-box-shadow:0 0 18px rgba(0,0,0,0.4); -moz-box-shadow:0 0 18px rgba(0,0,0,0.4);"
+                      + "box-shadow:0 0 18px rgba(0,0,0,0.4); }\n"
+                      + "#facebox .content { display:table; width: 98%; padding: 10px; background: #fff; -webkit-border-radius:4px; -moz-border-radius:4px;"
+                      + " border-radius:4px; }\n"
+                      + "#facebox .content > p:first-child{ margin-top:0; }\n"
+                      + "#facebox .content > p:last-child{ margin-bottom:0; }\n"
+                      + "#facebox .close{ position:absolute; top:5px; right:5px; padding:2px; background:#fff; }\n"
+                      + "#facebox .close img{ opacity:0.3; }\n"
+                      + "#facebox .close:hover img{ opacity:1.0; }\n"
+                      + "#facebox .loading { text-align: center; }\n"
+                      + "#facebox .image { text-align: center;}\n"
+                      + "#facebox img { border: 0;  margin: 0; }\n"
+                      + "#facebox_overlay { position: fixed; top: 0px; left: 0px; height:100%; width:100%; }\n"
+                      + ".facebox_hide { z-index:-100; }\n"
+                      + ".facebox_overlayBG { background-color: #000;  z-index: 99;  }");
     }
     htmlSvg.append("</style>");
     if (!wrapped)
     {
-    htmlSvg.append("<div class=\"main-container\" \n>");
-    htmlSvg.append("<div class=\"titlex\">\n");
-    htmlSvg.append("<div class=\"sub-category-container\"> \n");
-    htmlSvg.append(titleSvg);
-    htmlSvg.append("</div>");
-    htmlSvg.append("</div>\n\n<!-- ========================================================================================== -->\n\n");
-    htmlSvg.append("<div class=\"align\" >");
-    htmlSvg.append(
-            "<div class=\"sub-category-container\"> <div style=\"overflow-x: scroll;\">")
-            .append(alignmentSvg).append("</div></div>").append("</div>");
-    htmlSvg.append("</div>");
+      htmlSvg.append("<div class=\"main-container\" \n>");
+      htmlSvg.append("<div class=\"titlex\">\n");
+      htmlSvg.append("<div class=\"sub-category-container\"> \n");
+      htmlSvg.append(titleSvg);
+      htmlSvg.append("</div>");
+      htmlSvg.append(
+              "</div>\n\n<!-- ========================================================================================== -->\n\n");
+      htmlSvg.append("<div class=\"align\" >");
+      htmlSvg.append(
+              "<div class=\"sub-category-container\"> <div style=\"overflow-x: scroll;\">")
+              .append(alignmentSvg).append("</div></div>").append("</div>");
+      htmlSvg.append("</div>");
 
-    htmlSvg.append("<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
-            + "<script language=\"JavaScript\" type=\"text/javascript\"  src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n"
-            + "<script>\n"
-            + "var subCatContainer = $(\".sub-category-container\");\n"
-            + "subCatContainer.scroll(\nfunction() {\n"
-            + "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
+      htmlSvg.append(
+              "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
+                      + "<script language=\"JavaScript\" type=\"text/javascript\"  src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n"
+                      + "<script>\n"
+                      + "var subCatContainer = $(\".sub-category-container\");\n"
+                      + "subCatContainer.scroll(\nfunction() {\n"
+                      + "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
 
-    htmlSvg.append("</script>\n");
+      htmlSvg.append("</script>\n");
     }
     else
     {
-      htmlSvg.append("<div>\n")
-              .append(alignmentSvg).append("</div>");
-      htmlSvg.append("<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
-              + "<script language=\"JavaScript\" type=\"text/javascript\"  src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n");
-
+      htmlSvg.append("<div>\n").append(alignmentSvg).append("</div>");
+      htmlSvg.append(
+              "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
+                      + "<script language=\"JavaScript\" type=\"text/javascript\"  src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n");
     }
 
     // javascript for launching file in Jalview
-
     htmlSvg.append("<script language=\"JavaScript\">\n");
     htmlSvg.append("function openJalviewUsingCurrentUrl(){\n");
-    htmlSvg.append("    var json = JSON.parse(document.getElementById(\"seqData\").innerHTML);\n");
-    htmlSvg.append("    var jalviewVersion = json['appSettings'].version;\n");
+    htmlSvg.append(
+            "    var json = JSON.parse(document.getElementById(\"seqData\").innerHTML);\n");
+    htmlSvg.append(
+            "    var jalviewVersion = json['appSettings'].version;\n");
     htmlSvg.append("    var url = json['appSettings'].webStartUrl;\n");
-    htmlSvg.append("    var myForm = document.createElement(\"form\");\n\n");
+    htmlSvg.append(
+            "    var myForm = document.createElement(\"form\");\n\n");
     htmlSvg.append("    var heap = document.createElement(\"input\");\n");
     htmlSvg.append("    heap.setAttribute(\"name\", \"jvm-max-heap\") ;\n");
     htmlSvg.append("    heap.setAttribute(\"value\", \"2G\");\n\n");
     htmlSvg.append("    var target = document.createElement(\"input\");\n");
     htmlSvg.append("    target.setAttribute(\"name\", \"open\");\n");
     htmlSvg.append("    target.setAttribute(\"value\", document.URL);\n\n");
-    htmlSvg.append("    var jvVersion = document.createElement(\"input\");\n");
+    htmlSvg.append(
+            "    var jvVersion = document.createElement(\"input\");\n");
     htmlSvg.append("    jvVersion.setAttribute(\"name\", \"version\") ;\n");
-    htmlSvg.append("    jvVersion.setAttribute(\"value\", jalviewVersion);\n\n");
+    htmlSvg.append(
+            "    jvVersion.setAttribute(\"value\", jalviewVersion);\n\n");
     htmlSvg.append("    myForm.action = url;\n");
     htmlSvg.append("    myForm.appendChild(heap);\n");
     htmlSvg.append("    myForm.appendChild(target);\n");
@@ -270,9 +167,9 @@ public class HtmlSvgOutput extends HTMLOutput
     htmlSvg.append("    document.body.removeChild(myForm);\n");
     htmlSvg.append("}\n");
 
-    // jquery facebox for displaying raw BioJSON data");
     if (jsonData != null)
     {
+      // JQuery FaceBox for displaying raw BioJSON data");
       File faceBoxJsFile = new File("examples/javascript/facebox-1.3.js");
       try
       {
@@ -291,8 +188,8 @@ public class HtmlSvgOutput extends HTMLOutput
   @Override
   public boolean isEmbedData()
   {
-    return Boolean.valueOf(jalview.bin.Cache.getDefault(
-            "EXPORT_EMBBED_BIOJSON", "true"));
+    return Boolean
+            .valueOf(Cache.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
   }
 
   @Override
@@ -302,8 +199,118 @@ public class HtmlSvgOutput extends HTMLOutput
   }
 
   @Override
-  public File getExportedFile()
+  public void run()
   {
-    return generatedFile;
+    try
+    {
+      String renderStyle = Cache.getDefault("HTML_RENDERING",
+              "Prompt each time");
+      AtomicBoolean textOption = new AtomicBoolean(
+              !"Lineart".equals(renderStyle));
+
+      /*
+       * configure the action to run on OK in the dialog
+       */
+      Runnable okAction = new Runnable()
+      {
+        @Override
+        public void run()
+        {
+          doOutput(textOption.get());
+        }
+      };
+
+      /*
+       * Prompt for character rendering style if preference is not set
+       */
+      if (renderStyle.equalsIgnoreCase("Prompt each time") && !isHeadless())
+      {
+        LineartOptions svgOption = new LineartOptions("HTML", textOption);
+        svgOption.setResponseAction(1, new Runnable()
+        {
+          @Override
+          public void run()
+          {
+            setProgressMessage(MessageManager.formatMessage(
+                    "status.cancelled_image_export_operation",
+                    getDescription()));
+          }
+        });
+        svgOption.setResponseAction(0, okAction);
+        svgOption.showDialog();
+        /* no code here - JalviewJS cannot execute it */
+      }
+      else
+      {
+        /*
+         * else (if preference set) just do the export action
+         */
+        doOutput(textOption.get());
+      }
+    } catch (OutOfMemoryError err)
+    {
+      System.out.println("########################\n" + "OUT OF MEMORY "
+              + generatedFile + "\n" + "########################");
+      new OOMWarning("Creating Image for " + generatedFile, err);
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+      setProgressMessage(MessageManager
+              .formatMessage("info.error_creating_file", getDescription()));
+    }
+  }
+
+  /**
+   * Builds and writes the image to the file specified by field
+   * <code>generatedFile</code>
+   * 
+   * @param textCharacters
+   *          true for Text character rendering, false for Lineart
+   */
+  protected void doOutput(boolean textCharacters)
+  {
+    try
+    {
+      AlignmentDimension aDimension = ap.getAlignmentDimension();
+      SVGGraphics2D idPanelGraphics = new SVGGraphics2D(
+              aDimension.getWidth(), aDimension.getHeight());
+      SVGGraphics2D alignPanelGraphics = new SVGGraphics2D(
+              aDimension.getWidth(), aDimension.getHeight());
+      if (!textCharacters) // Lineart selected
+      {
+        idPanelGraphics.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+                SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
+        alignPanelGraphics.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+                SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
+      }
+      if (ap.av.getWrapAlignment())
+      {
+        printWrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+                alignPanelGraphics);
+      }
+      else
+      {
+        printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+                idPanelGraphics, alignPanelGraphics);
+      }
+
+      String idPanelSvgData = idPanelGraphics.getSVGDocument();
+      String alignPanelSvgData = alignPanelGraphics.getSVGDocument();
+      String jsonData = getBioJSONData();
+      String htmlData = getHtml(idPanelSvgData, alignPanelSvgData, jsonData,
+              ap.av.getWrapAlignment());
+      FileOutputStream out = new FileOutputStream(generatedFile);
+      out.write(htmlData.getBytes());
+      out.flush();
+      out.close();
+      setProgressMessage(MessageManager
+              .formatMessage("status.export_complete", getDescription()));
+      exportCompleted();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+      setProgressMessage(MessageManager
+              .formatMessage("info.error_creating_file", getDescription()));
+    }
   }
 }