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Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.io

File HtmlSvgOutput.java

 

Coverage histogram

../../img/srcFileCovDistChart8.png
20% of files have more coverage

Code metrics

14
99
10
1
318
259
22
0.22
9.9
10
2.2

Classes

Class Line # Actions
HtmlSvgOutput 40 99 22
0.764227676.4%
 

Contributing tests

No tests hitting this source file were found.

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.io;
22   
23    import jalview.bin.Cache;
24    import jalview.gui.AlignmentPanel;
25    import jalview.gui.LineartOptions;
26    import jalview.gui.OOMWarning;
27    import jalview.math.AlignmentDimension;
28    import jalview.util.MessageManager;
29   
30    import java.awt.Graphics;
31    import java.awt.print.PrinterException;
32    import java.io.File;
33    import java.io.FileOutputStream;
34    import java.io.IOException;
35    import java.util.concurrent.atomic.AtomicBoolean;
36   
37    import org.jfree.graphics2d.svg.SVGGraphics2D;
38    import org.jfree.graphics2d.svg.SVGHints;
39   
 
40    public class HtmlSvgOutput extends HTMLOutput
41    {
 
42  1 toggle public HtmlSvgOutput(AlignmentPanel ap)
43    {
44  1 super(ap, "HTML");
45    }
46   
 
47  1 toggle public int printUnwrapped(int pwidth, int pheight, int pi,
48    Graphics idGraphics, Graphics alignmentGraphics)
49    throws PrinterException
50    {
51  1 return ap.printUnwrapped(pwidth, pheight, pi, idGraphics,
52    alignmentGraphics);
53    }
54   
 
55  0 toggle public int printWrapped(int pwidth, int pheight, int pi, Graphics... pg)
56    throws PrinterException
57    {
58  0 return ap.printWrappedAlignment(pwidth, pheight, pi, pg[0]);
59    }
60   
 
61  1 toggle String getHtml(String titleSvg, String alignmentSvg,
62    String jsonData, boolean wrapped)
63    {
64  1 StringBuilder htmlSvg = new StringBuilder();
65  1 htmlSvg.append("<html>\n");
66  1 if (jsonData != null)
67    {
68  1 htmlSvg.append(
69    "<button onclick=\"javascipt:openJalviewUsingCurrentUrl();\">Launch in Jalview</button> &nbsp;");
70  1 htmlSvg.append(
71    "<input type=\"submit\" value=\"View raw BioJSON Data\" onclick=\"jQuery.facebox({ div:'#seqData' }); return false;\" />");
72  1 htmlSvg.append(
73    "<div style=\"display: none;\" name=\"seqData\" id=\"seqData\" >"
74    + jsonData + "</div>");
75  1 htmlSvg.append("<br/>&nbsp;");
76    }
77  1 htmlSvg.append("\n<style type=\"text/css\"> "
78    + "div.parent{ width:100%;<!-- overflow: auto; -->}\n"
79    + "div.titlex{ width:11%; float: left; }\n"
80    + "div.align{ width:89%; float: right; }\n"
81    + "div.main-container{ border: 2px solid blue; border: 2px solid blue; width: 99%; min-height: 99%; }\n"
82    + ".sub-category-container {overflow-y: scroll; overflow-x: hidden; width: 100%; height: 100%;}\n"
83    + "object {pointer-events: none;}");
84  1 if (jsonData != null)
85    {
86    // facebox style sheet for displaying raw BioJSON data
87  1 htmlSvg.append(
88    "#facebox { position: absolute; top: 0; left: 0; z-index: 100; text-align: left; }\n"
89    + "#facebox .popup{ position:relative; border:3px solid rgba(0,0,0,0); -webkit-border-radius:5px;"
90    + "-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);"
91    + "box-shadow:0 0 18px rgba(0,0,0,0.4); }\n"
92    + "#facebox .content { display:table; width: 98%; padding: 10px; background: #fff; -webkit-border-radius:4px; -moz-border-radius:4px;"
93    + " border-radius:4px; }\n"
94    + "#facebox .content > p:first-child{ margin-top:0; }\n"
95    + "#facebox .content > p:last-child{ margin-bottom:0; }\n"
96    + "#facebox .close{ position:absolute; top:5px; right:5px; padding:2px; background:#fff; }\n"
97    + "#facebox .close img{ opacity:0.3; }\n"
98    + "#facebox .close:hover img{ opacity:1.0; }\n"
99    + "#facebox .loading { text-align: center; }\n"
100    + "#facebox .image { text-align: center;}\n"
101    + "#facebox img { border: 0; margin: 0; }\n"
102    + "#facebox_overlay { position: fixed; top: 0px; left: 0px; height:100%; width:100%; }\n"
103    + ".facebox_hide { z-index:-100; }\n"
104    + ".facebox_overlayBG { background-color: #000; z-index: 99; }");
105    }
106  1 htmlSvg.append("</style>");
107  1 if (!wrapped)
108    {
109  1 htmlSvg.append("<div class=\"main-container\" \n>");
110  1 htmlSvg.append("<div class=\"titlex\">\n");
111  1 htmlSvg.append("<div class=\"sub-category-container\"> \n");
112  1 htmlSvg.append(titleSvg);
113  1 htmlSvg.append("</div>");
114  1 htmlSvg.append(
115    "</div>\n\n<!-- ========================================================================================== -->\n\n");
116  1 htmlSvg.append("<div class=\"align\" >");
117  1 htmlSvg.append(
118    "<div class=\"sub-category-container\"> <div style=\"overflow-x: scroll;\">")
119    .append(alignmentSvg).append("</div></div>").append("</div>");
120  1 htmlSvg.append("</div>");
121   
122  1 htmlSvg.append(
123    "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
124    + "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n"
125    + "<script>\n"
126    + "var subCatContainer = $(\".sub-category-container\");\n"
127    + "subCatContainer.scroll(\nfunction() {\n"
128    + "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
129   
130  1 htmlSvg.append("</script>\n");
131    }
132    else
133    {
134  0 htmlSvg.append("<div>\n").append(alignmentSvg).append("</div>");
135  0 htmlSvg.append(
136    "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
137    + "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n");
138    }
139   
140    // javascript for launching file in Jalview
141  1 htmlSvg.append("<script language=\"JavaScript\">\n");
142  1 htmlSvg.append("function openJalviewUsingCurrentUrl(){\n");
143  1 htmlSvg.append(
144    " var json = JSON.parse(document.getElementById(\"seqData\").innerHTML);\n");
145  1 htmlSvg.append(
146    " var jalviewVersion = json['appSettings'].version;\n");
147  1 htmlSvg.append(" var url = json['appSettings'].webStartUrl;\n");
148  1 htmlSvg.append(
149    " var myForm = document.createElement(\"form\");\n\n");
150  1 htmlSvg.append(" var heap = document.createElement(\"input\");\n");
151  1 htmlSvg.append(" heap.setAttribute(\"name\", \"jvm-max-heap\") ;\n");
152  1 htmlSvg.append(" heap.setAttribute(\"value\", \"2G\");\n\n");
153  1 htmlSvg.append(" var target = document.createElement(\"input\");\n");
154  1 htmlSvg.append(" target.setAttribute(\"name\", \"open\");\n");
155  1 htmlSvg.append(" target.setAttribute(\"value\", document.URL);\n\n");
156  1 htmlSvg.append(
157    " var jvVersion = document.createElement(\"input\");\n");
158  1 htmlSvg.append(" jvVersion.setAttribute(\"name\", \"version\") ;\n");
159  1 htmlSvg.append(
160    " jvVersion.setAttribute(\"value\", jalviewVersion);\n\n");
161  1 htmlSvg.append(" myForm.action = url;\n");
162  1 htmlSvg.append(" myForm.appendChild(heap);\n");
163  1 htmlSvg.append(" myForm.appendChild(target);\n");
164  1 htmlSvg.append(" myForm.appendChild(jvVersion);\n");
165  1 htmlSvg.append(" document.body.appendChild(myForm);\n");
166  1 htmlSvg.append(" myForm.submit() ;\n");
167  1 htmlSvg.append(" document.body.removeChild(myForm);\n");
168  1 htmlSvg.append("}\n");
169   
170  1 if (jsonData != null)
171    {
172    // JQuery FaceBox for displaying raw BioJSON data");
173  1 File faceBoxJsFile = new File("examples/javascript/facebox-1.3.js");
174  1 try
175    {
176  1 htmlSvg.append(HTMLOutput.readFileAsString(faceBoxJsFile));
177    } catch (IOException e)
178    {
179  0 e.printStackTrace();
180    }
181    }
182   
183  1 htmlSvg.append("</script>\n");
184  1 htmlSvg.append("</html>");
185  1 return htmlSvg.toString();
186    }
187   
 
188  1 toggle @Override
189    public boolean isEmbedData()
190    {
191  1 return Boolean.valueOf(
192    jalview.bin.Cache.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
193    }
194   
 
195  1 toggle @Override
196    public boolean isLaunchInBrowserAfterExport()
197    {
198  1 return true;
199    }
200   
 
201  1 toggle @Override
202    public void run()
203    {
204  1 try
205    {
206  1 String renderStyle = Cache.getDefault("HTML_RENDERING",
207    "Prompt each time");
208  1 AtomicBoolean textOption = new AtomicBoolean(
209    !"Lineart".equals(renderStyle));
210   
211    /*
212    * configure the action to run on OK in the dialog
213    */
214  1 Runnable okAction = new Runnable()
215    {
 
216  0 toggle @Override
217    public void run()
218    {
219  0 doOutput(textOption.get());
220    }
221    };
222   
223    /*
224    * Prompt for character rendering style if preference is not set
225    */
226  1 if (renderStyle.equalsIgnoreCase("Prompt each time") && !isHeadless())
227    {
228  0 LineartOptions svgOption = new LineartOptions("HTML", textOption);
229  0 svgOption.setResponseAction(1, new Runnable()
230    {
 
231  0 toggle @Override
232    public void run()
233    {
234  0 setProgressMessage(MessageManager.formatMessage(
235    "status.cancelled_image_export_operation",
236    getDescription()));
237    }
238    });
239  0 svgOption.setResponseAction(0, okAction);
240  0 svgOption.showDialog();
241    /* no code here - JalviewJS cannot execute it */
242    }
243    else
244    {
245    /*
246    * else (if preference set) just do the export action
247    */
248  1 doOutput(textOption.get());
249    }
250    } catch (OutOfMemoryError err)
251    {
252  0 System.out.println("########################\n" + "OUT OF MEMORY "
253    + generatedFile + "\n" + "########################");
254  0 new OOMWarning("Creating Image for " + generatedFile, err);
255    } catch (Exception e)
256    {
257  0 e.printStackTrace();
258  0 setProgressMessage(MessageManager
259    .formatMessage("info.error_creating_file", getDescription()));
260    }
261    }
262   
263    /**
264    * Builds and writes the image to the file specified by field
265    * <code>generatedFile</code>
266    *
267    * @param textCharacters
268    * true for Text character rendering, false for Lineart
269    */
 
270  1 toggle protected void doOutput(boolean textCharacters)
271    {
272  1 try
273    {
274  1 AlignmentDimension aDimension = ap.getAlignmentDimension();
275  1 SVGGraphics2D idPanelGraphics = new SVGGraphics2D(
276    aDimension.getWidth(), aDimension.getHeight());
277  1 SVGGraphics2D alignPanelGraphics = new SVGGraphics2D(
278    aDimension.getWidth(), aDimension.getHeight());
279  1 if (!textCharacters) // Lineart selected
280    {
281  0 idPanelGraphics.setRenderingHint(
282    SVGHints.KEY_DRAW_STRING_TYPE,
283    SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
284  0 alignPanelGraphics.setRenderingHint(
285    SVGHints.KEY_DRAW_STRING_TYPE,
286    SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
287    }
288  1 if (ap.av.getWrapAlignment())
289    {
290  0 printWrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
291    alignPanelGraphics);
292    }
293    else
294    {
295  1 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
296    0, idPanelGraphics, alignPanelGraphics);
297    }
298   
299  1 String idPanelSvgData = idPanelGraphics.getSVGDocument();
300  1 String alignPanelSvgData = alignPanelGraphics.getSVGDocument();
301  1 String jsonData = getBioJSONData();
302  1 String htmlData = getHtml(idPanelSvgData, alignPanelSvgData,
303    jsonData, ap.av.getWrapAlignment());
304  1 FileOutputStream out = new FileOutputStream(generatedFile);
305  1 out.write(htmlData.getBytes());
306  1 out.flush();
307  1 out.close();
308  1 setProgressMessage(MessageManager
309    .formatMessage("status.export_complete", getDescription()));
310  1 exportCompleted();
311    } catch (Exception e)
312    {
313  0 e.printStackTrace();
314  0 setProgressMessage(MessageManager
315    .formatMessage("info.error_creating_file", getDescription()));
316    }
317    }
318    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.