X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHTMLOutput.java;h=e4dc83e9d35912535e26518c3aeba827f38e93e3;hb=48b79dd91c3d96b84a1a74aa0217c7c32c3107ef;hp=b42547a1b3213e5a17efcdf280ef6d0ad0833835;hpb=8a55dd77f109200c28f35d1c1d33da72982381a3;p=jalview.git diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java index b42547a..e4dc83e 100755 --- a/src/jalview/io/HTMLOutput.java +++ b/src/jalview/io/HTMLOutput.java @@ -1,78 +1,398 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program 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 2 + * of the License, or (at your option) any later version. + * + * This program 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 this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.io; -import jalview.gui.*; -import jalview.datamodel.*; -import jalview.schemes.*; -import java.awt.*; -import javax.swing.*; import java.io.*; -import java.util.*; +import java.awt.*; + +import jalview.datamodel.*; +import jalview.gui.*; +import jalview.schemes.*; public class HTMLOutput { - SequenceRenderer sr = new SequenceRenderer(); + AlignViewport av; + SequenceRenderer sr; + Color color; - public HTMLOutput(AlignmentI alignment, ColourSchemeI cs) + public HTMLOutput(AlignViewport av) { - Color color; - JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY); + this.av = av; + sr = new SequenceRenderer(av); + + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. + getProperty( + "LAST_DIRECTORY"), new String[] + {"html"}, + new String[] + {"HTML files"}, "HTML files"); + + chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Save as HTML"); chooser.setToolTipText("Save"); + int value = chooser.showSaveDialog(null); - if(value == JFileChooser.APPROVE_OPTION) + + if (value == JalviewFileChooser.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)); + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); + + try + { + PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter( + choice)); out.println(""); out.println(""); out.println(""); - out.println(""); + } - jalview.util.BrowserLauncher.openURL( choice ); + if (endRes < al.getWidth()) + { + out.println(""); } - catch(Exception ex){} } + + out.println("

\n"); - out.println("\n"); + if (av.getWrapAlignment()) + { + drawWrappedAlignment(out); + } + else + { + drawUnwrappedAlignment(out); + } + + out.println("\n\n"); + out.close(); + jalview.util.BrowserLauncher.openURL("file:///" + choice); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + } + + void drawUnwrappedAlignment(PrintWriter out) + { + out.println("

\n"); + out.println( + "\n"); + + ////////////// + SequenceGroup[] groups; + SequenceI seq; + ColourSchemeI cs = null; + AlignmentI alignment = av.getAlignment(); + String r; + String g; + String b; + + // draws the top row, the measure rule + out.println(""); + + int i = 0; + + for (i = 10; i < (alignment.getWidth() - 10); i += 10) + { + out.println(""); + } + + out.println(""); + out.println(""); - ////////////// - for (int i = 0; i < alignment.getHeight(); i++) + for (i = 0; i < alignment.getHeight(); i++) + { + seq = alignment.getSequenceAt(i); + groups = alignment.findAllGroups(seq); + + if (av.getShowFullId()) + { + out.println(""); + } + else + { + out.println(""); + } + + for (int res = 0; res < seq.getLength(); res++) + { + cs = av.getGlobalColourScheme(); + + if (groups != null) { - SequenceI seq = alignment.getSequenceAt(i); - out.println(""); - for (int res = 0; res < seq.getLength(); res++) + for (int k = 0; k < groups.length; k++) { - color = sr.getResidueBoxColour(cs, seq, res); - - if(color.getRGB()<-1) + if ( (groups[k].getStartRes() <= res) && + (groups[k].getEndRes() >= res)) { - out.println(""); + cs = groups[k].cs; + + break; } - else - out.println(""); + } + } + color = sr.getResidueBoxColour(cs, seq, res); + + if (color.getRGB() < -1) + { + out.println(""); + } + else + { + out.println(""); + } + } + + out.println(""); + } + + ////////////// + out.println("

	" + i + " \|			" + i + + " \|
" + seq.getDisplayId() + + "
" + seq.getName() + + "
"+seq.getName()+"	"+seq.getCharAt(res)+"	"+seq.getCharAt(res)+"	" + + seq.getCharAt(res) + "	" + seq.getCharAt(res) + "

"); + out.println("

"); + } + + void drawWrappedAlignment(PrintWriter out) + { + //////////////////////////////////// + /// How many sequences and residues can we fit on a printable page? + AlignmentI al = av.getAlignment(); + SequenceGroup[] groups; + SequenceI seq; + ColourSchemeI cs = null; + String r; + String g; + String b; + + out.println("

\n"); + out.println( + "\n"); + + for (int startRes = 0; startRes < al.getWidth(); + startRes += av.getChunkWidth()) + { + int endRes = startRes + av.getChunkWidth(); + + if (endRes > al.getWidth()) + { + endRes = al.getWidth(); + } + + out.println(""); + out.println(""); + + for (int i = startRes + 10; i < endRes; i += 10) + { + out.println(""); + } + + // out.println(""); + out.println(""); + + for (int s = 0; s < al.getHeight(); s++) + { + out.println(""); + seq = al.getSequenceAt(s); + groups = al.findAllGroups(seq); + + if (av.getShowFullId()) + { + out.println(""); + } + else + { + out.println(""); + } + + for (int res = startRes; res < endRes; res++) + { + cs = av.getGlobalColourScheme(); + + if (groups != null) + { + for (int k = 0; k < groups.length; k++) + { + if ( (groups[k].getStartRes() <= res) && + (groups[k].getEndRes() >= res)) + { + cs = groups[k].cs; + + break; + } + } } - out.println(""); + 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(""); + } + else + { + out.println(""); + } } - ////////////// - out.println("

	" + i + " \|	" + i + + // " \|
" + seq.getDisplayId() + + "	" + seq.getName() + + "
" + + seq.getCharAt(res) + "	" + seq.getCharAt(res) + "

"); - out.println("

\n\n"); - out.close(); + out.println("

"); + out.println(""); } + public static String getImageMapHTML() + { + return new String( + "\n" + +"\n" + +"\n" + +"\n" + +"\n" + +"

\n" + +"\n"); + } }