+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+*/\r
package jalview.io;\r
\r
-import jalview.gui.*;\r
import jalview.datamodel.*;\r
+\r
+import jalview.gui.*;\r
+\r
import jalview.schemes.*;\r
+\r
import java.awt.*;\r
-import javax.swing.*;\r
+\r
import java.io.*;\r
+\r
import java.util.*;\r
\r
+import javax.swing.*;\r
\r
-public class HTMLOutput\r
-{\r
- AlignViewport av;\r
- SequenceRenderer sr;\r
- Color color;\r
-\r
- public HTMLOutput(AlignViewport av)\r
- {\r
- this.av = av;\r
- sr = new SequenceRenderer(av);\r
- JalviewFileChooser chooser = new JalviewFileChooser(\r
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
- new String[]{"html"},\r
- new String[]{"HTML files"},\r
- "HTML files");\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save as HTML");\r
- chooser.setToolTipText("Save");\r
- int value = chooser.showSaveDialog(null);\r
- if(value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());\r
- try{\r
- PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(choice));\r
- out.println("<HTML>");\r
- out.println("<style type=\"text/css\">");\r
- out.println("<!--");\r
- out.print("td {font-family: \""+av.getFont().getFamily()+"\", \""+av.getFont().getName()+ "\", mono; "\r
- +"font-size: "+av.getFont().getSize()+"px; ");\r
-\r
-\r
- if (av.getFont().getStyle() == Font.BOLD)\r
- out.print("font-weight: BOLD; ");\r
-\r
- if (av.getFont().getStyle() == Font.ITALIC)\r
- out.print("font-style: italic; ");\r
-\r
- out.println("text-align: center; }");\r
-\r
- out.println("-->");\r
- out.println("</style>");\r
- out.println("<BODY>");\r
-\r
-\r
- if(av.getWrapAlignment())\r
- drawWrappedAlignment(out);\r
- else\r
- drawUnwrappedAlignment(out);\r
-\r
- out.println("\n</body>\n</html>");\r
- out.close();\r
- jalview.util.BrowserLauncher.openURL( "file:///"+choice );\r
- }\r
- catch(Exception ex){ex.printStackTrace();}\r
- }\r
- }\r
-\r
- void drawUnwrappedAlignment(PrintWriter out)\r
- {\r
-\r
- out.println("<table border=\"1\"><tr><td>\n");\r
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
-\r
-\r
- //////////////\r
- SequenceGroup [] groups;\r
- SequenceI seq;\r
- ColourSchemeI cs = null;\r
- AlignmentI alignment = av.getAlignment();\r
- String r,g,b;\r
-\r
- // draws the top row, the measure rule\r
- out.println("<tr><td colspan=\"6\"></td>");\r
- int i=0;\r
- for(i=10; i<alignment.getWidth()-10; i+=10)\r
- out.println("<td colspan=\"9\">"+i+"<br>|</td><td></td>");\r
-\r
- out.println("<td colspan=\"3\"></td><td colspan=\"3\">"+i+"<br>|</td>");\r
- out.println("</tr>");\r
-\r
- for (i = 0; i < alignment.getHeight(); i++)\r
- {\r
- seq = alignment.getSequenceAt(i);\r
- groups = alignment.findAllGroups( seq );\r
- if(av.getShowFullId())\r
- out.println("<tr><td nowrap>"+seq.getDisplayId()+" </td>");\r
- else\r
- out.println("<tr><td nowrap>"+seq.getName()+" </td>");\r
-\r
-\r
-\r
- for (int res = 0; res < seq.getLength(); res++)\r
- {\r
- cs = av.getGlobalColourScheme();\r
-\r
- if(groups!=null)\r
- {\r
- for (int k = 0; k < groups.length; k++)\r
- if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)\r
- {\r
- cs = groups[k].cs;\r
- break;\r
- }\r
- }\r
-\r
-\r
- color = sr.getResidueBoxColour(cs, seq, res);\r
-\r
- if(color.getRGB()<-1)\r
- {\r
- r = Integer.toHexString(color.getRed());\r
- if(r.length()<2)\r
- r = "0"+r;\r
- g = Integer.toHexString(color.getGreen());\r
- if(g.length()<2)\r
- g = "0"+g;\r
- b = Integer.toHexString(color.getBlue());\r
- if(b.length()<2)\r
- b = "0"+b;\r
- out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");\r
- }\r
- else\r
- out.println("<td>"+seq.getCharAt(res)+"</td>");\r
\r
- }\r
+public class HTMLOutput {\r
+ AlignViewport av;\r
+ SequenceRenderer sr;\r
+ Color color;\r
+\r
+ public HTMLOutput(AlignViewport av) {\r
+ this.av = av;\r
+ sr = new SequenceRenderer(av);\r
+\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[] { "html" },\r
+ new String[] { "HTML files" }, "HTML files");\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save as HTML");\r
+ chooser.setToolTipText("Save");\r
+\r
+ int value = chooser.showSaveDialog(null);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION) {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+\r
+ try {\r
+ PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
+ choice));\r
+ out.println("<HTML>");\r
+ out.println("<style type=\"text/css\">");\r
+ out.println("<!--");\r
+ out.print("td {font-family: \"" + av.getFont().getFamily() +\r
+ "\", \"" + av.getFont().getName() + "\", mono; " +\r
+ "font-size: " + av.getFont().getSize() + "px; ");\r
+\r
+ if (av.getFont().getStyle() == Font.BOLD) {\r
+ out.print("font-weight: BOLD; ");\r
+ }\r
+\r
+ if (av.getFont().getStyle() == Font.ITALIC) {\r
+ out.print("font-style: italic; ");\r
+ }\r
\r
- out.println("</tr>");\r
+ out.println("text-align: center; }");\r
+\r
+ out.println("-->");\r
+ out.println("</style>");\r
+ out.println("<BODY>");\r
+\r
+ if (av.getWrapAlignment()) {\r
+ drawWrappedAlignment(out);\r
+ } else {\r
+ drawUnwrappedAlignment(out);\r
+ }\r
+\r
+ out.println("\n</body>\n</html>");\r
+ out.close();\r
+ jalview.util.BrowserLauncher.openURL("file:///" + choice);\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
}\r
- //////////////\r
- out.println("</table>");\r
- out.println("</td></tr></table>");\r
-\r
- }\r
-\r
- void drawWrappedAlignment(PrintWriter out)\r
- {\r
- ////////////////////////////////////\r
- /// How many sequences and residues can we fit on a printable page?\r
- AlignmentI al = av.getAlignment();\r
- SequenceGroup [] groups;\r
- SequenceI seq;\r
- ColourSchemeI cs = null;\r
- String r,g,b;\r
-\r
- out.println("<table border=\"1\"><tr><td>\n");\r
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
-\r
- for(int startRes=0; startRes<al.getWidth(); startRes+=av.getChunkWidth())\r
- {\r
-\r
- int endRes = startRes+av.getChunkWidth();\r
- if(endRes>al.getWidth())\r
- endRes = al.getWidth();\r
-\r
- out.println("<tr>");\r
- out.println("<td colspan=\"6\"> </td>");\r
- for (int i = startRes+10; i < endRes; i += 10)\r
- out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
-\r
- // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
- // "<br>|</td>");\r
- out.println("</tr>");\r
-\r
-\r
-\r
- for (int s = 0; s < al.getHeight(); s++)\r
- {\r
- out.println("<tr>");\r
- seq = al.getSequenceAt(s);\r
- groups = al.findAllGroups( seq );\r
- if(av.getShowFullId())\r
- out.println("<td nowrap>"+seq.getDisplayId()+" </td>");\r
- else\r
- out.println("<td nowrap>"+seq.getName()+" </td>");\r
-\r
- for (int res = startRes; res < endRes; res++)\r
- {\r
+\r
+ void drawUnwrappedAlignment(PrintWriter out) {\r
+ out.println("<table border=\"1\"><tr><td>\n");\r
+ out.println(\r
+ "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
+\r
+ //////////////\r
+ SequenceGroup[] groups;\r
+ SequenceI seq;\r
+ ColourSchemeI cs = null;\r
+ AlignmentI alignment = av.getAlignment();\r
+ String r;\r
+ String g;\r
+ String b;\r
+\r
+ // draws the top row, the measure rule\r
+ out.println("<tr><td colspan=\"6\"></td>");\r
+\r
+ int i = 0;\r
+\r
+ for (i = 10; i < (alignment.getWidth() - 10); i += 10)\r
+ out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
+\r
+ out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
+ "<br>|</td>");\r
+ out.println("</tr>");\r
+\r
+ for (i = 0; i < alignment.getHeight(); i++) {\r
+ seq = alignment.getSequenceAt(i);\r
+ groups = alignment.findAllGroups(seq);\r
+\r
+ if (av.getShowFullId()) {\r
+ out.println("<tr><td nowrap>" + seq.getDisplayId() +\r
+ " </td>");\r
+ } else {\r
+ out.println("<tr><td nowrap>" + seq.getName() +\r
+ " </td>");\r
+ }\r
+\r
+ for (int res = 0; res < seq.getLength(); res++) {\r
cs = av.getGlobalColourScheme();\r
- if(groups!=null)\r
- {\r
- for (int k = 0; k < groups.length; k++)\r
- if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)\r
- {\r
- cs = groups[k].cs;\r
- break;\r
- }\r
- }\r
+\r
+ if (groups != null) {\r
+ for (int k = 0; k < groups.length; k++)\r
+ if ((groups[k].getStartRes() <= res) &&\r
+ (groups[k].getEndRes() >= res)) {\r
+ cs = groups[k].cs;\r
+\r
+ break;\r
+ }\r
+ }\r
\r
color = sr.getResidueBoxColour(cs, seq, res);\r
\r
- if(color.getRGB()<-1)\r
- {\r
- r = Integer.toHexString(color.getRed());\r
- if(r.length()<2)\r
- r = "0"+r;\r
- g = Integer.toHexString(color.getGreen());\r
- if(g.length()<2)\r
- g = "0"+g;\r
- b = Integer.toHexString(color.getBlue());\r
- if(b.length()<2)\r
- b = "0"+b;\r
- out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");\r
+ if (color.getRGB() < -1) {\r
+ out.println("<td bgcolor=\"#" +\r
+ jalview.util.Format.getHexString(color) + "\">" +\r
+ seq.getCharAt(res) + "</td>");\r
+ } else {\r
+ out.println("<td>" + seq.getCharAt(res) + "</td>");\r
+ }\r
+ }\r
+\r
+ out.println("</tr>");\r
+ }\r
+\r
+ //////////////\r
+ out.println("</table>");\r
+ out.println("</td></tr></table>");\r
+ }\r
+\r
+ void drawWrappedAlignment(PrintWriter out) {\r
+ ////////////////////////////////////\r
+ /// How many sequences and residues can we fit on a printable page?\r
+ AlignmentI al = av.getAlignment();\r
+ SequenceGroup[] groups;\r
+ SequenceI seq;\r
+ ColourSchemeI cs = null;\r
+ String r;\r
+ String g;\r
+ String b;\r
+\r
+ out.println("<table border=\"1\"><tr><td>\n");\r
+ out.println(\r
+ "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
+\r
+ for (int startRes = 0; startRes < al.getWidth();\r
+ startRes += av.getChunkWidth()) {\r
+ int endRes = startRes + av.getChunkWidth();\r
+\r
+ if (endRes > al.getWidth()) {\r
+ endRes = al.getWidth();\r
+ }\r
+\r
+ out.println("<tr>");\r
+ out.println("<td colspan=\"6\"> </td>");\r
+\r
+ for (int i = startRes + 10; i < endRes; i += 10)\r
+ out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
+\r
+ // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
+ // "<br>|</td>");\r
+ out.println("</tr>");\r
+\r
+ for (int s = 0; s < al.getHeight(); s++) {\r
+ out.println("<tr>");\r
+ seq = al.getSequenceAt(s);\r
+ groups = al.findAllGroups(seq);\r
+\r
+ if (av.getShowFullId()) {\r
+ out.println("<td nowrap>" + seq.getDisplayId() +\r
+ " </td>");\r
+ } else {\r
+ out.println("<td nowrap>" + seq.getName() +\r
+ " </td>");\r
}\r
- else\r
- out.println("<td>"+seq.getCharAt(res)+"</td>");\r
\r
- }\r
+ for (int res = startRes; res < endRes; res++) {\r
+ cs = av.getGlobalColourScheme();\r
\r
- out.println("</tr>");\r
+ if (groups != null) {\r
+ for (int k = 0; k < groups.length; k++)\r
+ if ((groups[k].getStartRes() <= res) &&\r
+ (groups[k].getEndRes() >= res)) {\r
+ cs = groups[k].cs;\r
\r
- }\r
- if(endRes<al.getWidth())\r
- out.println("<tr><td height=\"5\"></td></tr>");\r
+ break;\r
+ }\r
+ }\r
\r
+ color = sr.getResidueBoxColour(cs, seq, res);\r
\r
+ if (color.getRGB() < -1) {\r
+ r = Integer.toHexString(color.getRed());\r
\r
- }\r
+ if (r.length() < 2) {\r
+ r = "0" + r;\r
+ }\r
\r
- out.println("</table>");\r
- out.println("</table>");\r
+ g = Integer.toHexString(color.getGreen());\r
\r
+ if (g.length() < 2) {\r
+ g = "0" + g;\r
+ }\r
\r
+ b = Integer.toHexString(color.getBlue());\r
\r
- }\r
+ if (b.length() < 2) {\r
+ b = "0" + b;\r
+ }\r
\r
+ out.println("<td bgcolor=\"#" + r + g + b + "\">" +\r
+ seq.getCharAt(res) + "</td>");\r
+ } else {\r
+ out.println("<td>" + seq.getCharAt(res) + "</td>");\r
+ }\r
+ }\r
+\r
+ out.println("</tr>");\r
+ }\r
\r
+ if (endRes < al.getWidth()) {\r
+ out.println("<tr><td height=\"5\"></td></tr>");\r
+ }\r
+ }\r
+\r
+ out.println("</table>");\r
+ out.println("</table>");\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff