X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=db43a3f7bf1a17bcd2eca81f6249ab2450566b7f;hb=25aaaa87042b3f507ad4348120df7dd073182759;hp=6e2ec8c05f9d9f2e4a022a282ac85156fc7e4983;hpb=50ff87bdae1829a7a7471ec393142ae659b40a11;p=jalview.git diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java index 6e2ec8c..db43a3f 100644 --- a/src/jalview/io/BioJsHTMLOutput.java +++ b/src/jalview/io/BioJsHTMLOutput.java @@ -1,86 +1,222 @@ package jalview.io; -import static java.nio.file.Files.readAllBytes; -import static java.nio.file.Paths.get; +import jalview.api.FeaturesDisplayedI; import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.exceptions.NoFileSelectedException; import jalview.gui.AlignViewport; import jalview.gui.AlignmentPanel; import jalview.gui.FeatureRenderer; -import jalview.gui.SequenceRenderer; import jalview.json.binding.v1.BioJsAlignmentPojo; +import jalview.json.binding.v1.BioJsFeaturePojo; import jalview.json.binding.v1.BioJsSeqPojo; +import jalview.schemes.ColourSchemeProperty; import jalview.util.MessageManager; +import java.awt.Color; +import java.io.BufferedReader; import java.io.IOException; +import java.io.InputStreamReader; import java.io.PrintWriter; - -import org.json.simple.parser.ParseException; +import java.net.URL; +import java.util.ArrayList; import com.json.JSONException; -public class BioJsHTMLOutput { - private AlignViewport av; - private FeatureRenderer fr; - - public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr, FeatureRenderer fr1) { - this.av = ap.av; - this.fr = new FeatureRenderer(ap); - fr.transferSettings(fr1); - exportAsBioJsHtml(); - } - - private void exportAsBioJsHtml() { - try { - JalviewFileChooser jvFileChooser = getJalviewFileChooserOption(); - int fileChooserOpt = jvFileChooser.showSaveDialog(null); - if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION) { - jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser.getSelectedFile().getParent()); - String selectedFile = jvFileChooser.getSelectedFile().getPath(); - String generartedBioJs = generateBioJsAlignmentData(av.getAlignment()); - PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(selectedFile)); - out.print(generartedBioJs); - out.close(); - jalview.util.BrowserLauncher.openURL("file:///" + selectedFile); - } - } catch (Exception ex) { - ex.printStackTrace(); - } - } - - private JalviewFileChooser getJalviewFileChooserOption() { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { "html" }, new String[] { "HTML files" }, "HTML files"); - chooser.setFileView(new JalviewFileView()); - - // TODO uncomment when supported by MassageManager - chooser.setDialogTitle(MessageManager.getString("label.save_as_biojs_html")); - chooser.setDialogTitle("save as BioJs HTML"); - chooser.setToolTipText(MessageManager.getString("action.save")); - - return chooser; - } - - private String generateBioJsAlignmentData(AlignmentI alignment) throws IOException, JSONException { - BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo(); - int count = 0; - for (SequenceI seq : alignment.getSequences()) { - StringBuilder name = new StringBuilder(); - name.append(seq.getName()).append("/").append(seq.getStart()).append("-").append(seq.getEnd()); - bjsAlignment.getSeqs().add(new BioJsSeqPojo(String.valueOf(++count), name.toString(), seq.getSequenceAsString())); - } - - // Taylor - // av.getGlobalColourScheme().; - String seqs = new com.json.JSONObject(bjsAlignment).getString("seqs"); - String bioJSTemplate = new String(readAllBytes(get("resources/templates/BioJSTemplate.txt"))); - - // av.get - // fr. - return bioJSTemplate.replaceAll("#sequenceData#", seqs).replaceAll("#scheme#", "zappo"); - } - - public static void main(String[] args) throws IOException, ParseException { - - } +public class BioJsHTMLOutput +{ + private AlignViewport av; + + private jalview.api.FeatureRenderer fr; + + private String globalColorScheme; + + private FeaturesDisplayedI displayedFeatures; + + private String jalviewVersion; + + private String webStartLaunchServletUrl = "http://www.jalview.org/services/launchApp"; + + public BioJsHTMLOutput(AlignmentPanel ap, + FeatureRenderer fr1) + { + + jalviewVersion = jalview.bin.Cache.getProperty("VERSION"); + webStartLaunchServletUrl = jalview.bin.Cache.getDefault( + "www.jalview.org", "http://www.jalview.org") + + "/services/launchApp"; + if (ap != null) + { + this.av = ap.av; + this.globalColorScheme = ColourSchemeProperty.getColourName(av + .getGlobalColourScheme()); + this.fr = ap.cloneFeatureRenderer(); + displayedFeatures = av.getFeaturesDisplayed(); + } + } + + private void exportJalviewAlignmentAsBioJsHtmlFile() + { + try + { + String outputFile = getOutputFile(); + String jalviewAlignmentJson = getJalviewAlignmentAsJsonString(av + .getAlignment()); + String bioJSTemplateString = getBioJsTemplateAsString(this); + String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString + .replaceAll( +"#sequenceData#", jalviewAlignmentJson) + .toString(); + + PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter( + outputFile)); + out.print(generatedBioJsWithJalviewAlignmentAsJson); + out.flush(); + out.close(); + jalview.util.BrowserLauncher.openURL("file:///" + outputFile); + } catch (NoFileSelectedException ex) + { + // do noting if no file was selected + } catch (Exception e) + { + e.printStackTrace(); + } + } + + public String getOutputFile() throws NoFileSelectedException + { + String selectedFile = null; + JalviewFileChooser jvFileChooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] + { "html" }, new String[] + { "HTML files" }, "HTML files"); + jvFileChooser.setFileView(new JalviewFileView()); + + // TODO uncomment when supported by MassageManager + jvFileChooser.setDialogTitle(MessageManager + .getString("label.save_as_biojs_html")); + jvFileChooser.setDialogTitle("save as BioJs 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; + } + + public String getJalviewAlignmentAsJsonString(AlignmentI alignment) + throws IOException, JSONException + { + BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo(); + + bjsAlignment.setGlobalColorScheme(getGlobalColorScheme()); + bjsAlignment.setJalviewVersion(jalviewVersion); + bjsAlignment.setWebStartUrl(webStartLaunchServletUrl); + + int count = 0; + for (SequenceI seq : alignment.getSequences()) + { + StringBuilder name = new StringBuilder(); + name.append(seq.getName()).append("/").append(seq.getStart()) + .append("-").append(seq.getEnd()); + + BioJsSeqPojo seqPojo = new BioJsSeqPojo(); + seqPojo.setId(String.valueOf(++count)); + seqPojo.setEnd(seq.getEnd()); + seqPojo.setStart(seq.getStart()); + seqPojo.setName(name.toString()); + seqPojo.setSeq(seq.getSequenceAsString()); + + SequenceFeature[] seqFeatures = seq.getDatasetSequence() + .getSequenceFeatures(); + if (seqFeatures != null) + { + ArrayList bjsSeqFeatures = new ArrayList(); + for (SequenceFeature sf : seqFeatures) + { + if (displayedFeatures != null + && displayedFeatures.isVisible(sf.getType())) + { + + // TODO: translate graduated/complex colourschemes to biojs model + String featureColour = jalview.util.Format.getHexString(fr + .findFeatureColour(Color.white, seq, + seq.findIndex(sf.getBegin()))); + BioJsFeaturePojo bjsFeature = new BioJsFeaturePojo(); + bjsFeature.setFillColor(featureColour); + bjsFeature.setXstart(seq.findIndex(sf.getBegin()) - 1); + bjsFeature.setXend(seq.findIndex(sf.getEnd())); + bjsFeature.setText(sf.getType()); + bjsSeqFeatures.add(bjsFeature); + } + } + seqPojo.setFeatures(bjsSeqFeatures); + } + bjsAlignment.getSeqs().add(seqPojo); + } + + return new com.json.JSONObject(bjsAlignment).toString() + .replaceAll("xstart", "xStart").replaceAll("xend", "xEnd"); + } + + public static String getBioJsTemplateAsString(Object currentObj) + throws IOException + { + InputStreamReader isReader = null; + BufferedReader buffReader = null; + StringBuilder sb = new StringBuilder(); + URL url = currentObj.getClass().getResource( + "/templates/BioJSTemplate.txt"); + 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 String getGlobalColorScheme() + { + return globalColorScheme; + } + + public void setGlobalColorScheme(String globalColorScheme) + { + this.globalColorScheme = globalColorScheme; + } }