BioJS viewer

From 961eec1363ddc5f0f5a08b9063a7a2a9b1c9d2bd Mon Sep 17 00:00:00 2001 From: Charles Ofoegbu Date: Thu, 30 Oct 2014 10:35:04 +0000 Subject: [PATCH] JAL-1541 BioJs MSA Viewer export option implementation --- .gitignore | 1 + resources/templates/BioJSTemplate.txt | 59 +++++++++++++++++++++ src/jalview/gui/AlignFrame.java | 54 +++++++++++++++++++ src/jalview/io/BioJsHTMLOutput.java | 91 +++++++++++++++++++++++++++++++++ src/jalview/jbgui/GAlignFrame.java | 22 +++++++- 5 files changed, 226 insertions(+), 1 deletion(-) create mode 100644 resources/templates/BioJSTemplate.txt create mode 100644 src/jalview/io/BioJsHTMLOutput.java diff --git a/.gitignore b/.gitignore index 9841761..c47ff62 100644 --- a/.gitignore +++ b/.gitignore @@ -3,4 +3,5 @@ /classes .externalToolBuilders/Jalview Release indices [Builder].launch /.DS_Store +.DS_Store /.com.apple.timemachine.supported diff --git a/resources/templates/BioJSTemplate.txt b/resources/templates/BioJSTemplate.txt new file mode 100644 index 0000000..324ecfe --- /dev/null +++ b/resources/templates/BioJSTemplate.txt @@ -0,0 +1,59 @@ + +

BioJS viewer

+ + + + + + + + + + + + +

press "Run with JS"

+ + + + + + + \ No newline at end of file diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index d9c0c6a..a9eeb12 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -53,6 +53,7 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; +import jalview.io.BioJsHTMLOutput; import jalview.io.FeaturesFile; import jalview.io.FileLoader; import jalview.io.FormatAdapter; @@ -377,7 +378,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt .getKeyCode() <= KeyEvent.VK_NUMPAD9)) && Character.isDigit(evt.getKeyChar())) + { alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + } switch (evt.getKeyCode()) { @@ -389,32 +392,48 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_DOWN: if (evt.isAltDown() || !viewport.cursorMode) + { moveSelectedSequences(false); + } if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(0, 1); + } break; case KeyEvent.VK_UP: if (evt.isAltDown() || !viewport.cursorMode) + { moveSelectedSequences(true); + } if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(0, -1); + } break; case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) + { slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); + } else + { alignPanel.seqPanel.moveCursor(-1, 0); + } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) + { slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); + } else + { alignPanel.seqPanel.moveCursor(1, 0); + } break; case KeyEvent.VK_SPACE: @@ -551,14 +570,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) + { viewport.firePropertyChange("alignment", null, viewport .getAlignment().getSequences()); + } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) + { viewport.firePropertyChange("alignment", null, viewport .getAlignment().getSequences()); + } break; } } @@ -1207,6 +1230,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); } + @Override + public void bioJSMenuItem_actionPerformed(ActionEvent e) + { + new BioJsHTMLOutput(alignPanel, + alignPanel.seqPanel.seqCanvas.getSequenceRenderer(), + alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + } public void createImageMap(File file, String image) { alignPanel.makePNGImageMap(file, image); @@ -1458,7 +1488,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void undoMenuItem_actionPerformed(ActionEvent e) { if (viewport.historyList.empty()) + { return; + } CommandI command = (CommandI) viewport.historyList.pop(); viewport.redoList.push(command); command.undoCommand(getViewAlignments()); @@ -1611,37 +1643,53 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, for (int i = 0; i < viewport.getAlignment().getHeight(); i++) { if (!sg.contains(viewport.getAlignment().getSequenceAt(i))) + { invertGroup.add(viewport.getAlignment().getSequenceAt(i)); + } } SequenceI[] seqs1 = sg.toArray(new SequenceI[0]); SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; for (int i = 0; i < invertGroup.size(); i++) + { seqs2[i] = (SequenceI) invertGroup.elementAt(i); + } SlideSequencesCommand ssc; if (right) + { ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, viewport.getGapCharacter()); + } else + { ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, viewport.getGapCharacter()); + } int groupAdjustment = 0; if (ssc.getGapsInsertedBegin() && right) { if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(size, 0); + } else + { groupAdjustment = size; + } } else if (!ssc.getGapsInsertedBegin() && !right) { if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(-size, 0); + } else + { groupAdjustment = -size; + } } if (groupAdjustment != 0) @@ -1662,7 +1710,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (!appendHistoryItem) + { addHistoryItem(ssc); + } repaint(); } @@ -1997,7 +2047,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { AlignmentAnnotation sann[] = sequences[i].getAnnotation(); if (sann == null) + { continue; + } for (int avnum = 0; avnum < alview.length; avnum++) { if (alview[avnum] != alignment) @@ -4643,7 +4695,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (ds.getSequences() == null || !ds.getSequences().contains( sprods[s].getDatasetSequence())) + { ds.addSequence(sprods[s].getDatasetSequence()); + } sprods[s].updatePDBIds(); } Alignment al = new Alignment(sprods); diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java new file mode 100644 index 0000000..5a236dc --- /dev/null +++ b/src/jalview/io/BioJsHTMLOutput.java @@ -0,0 +1,91 @@ +package jalview.io; + +import static java.nio.file.Files.readAllBytes; +import static java.nio.file.Paths.get; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignViewport; +import jalview.gui.AlignmentPanel; +import jalview.gui.FeatureRenderer; +import jalview.gui.SequenceRenderer; +import jalview.util.MessageManager; + +import java.io.IOException; +import java.io.PrintWriter; + +public class BioJsHTMLOutput +{ + private AlignViewport av; + private FeatureRenderer fr; + + public BioJsHTMLOutput(AlignmentPanel ap, SequenceRenderer sr, + FeatureRenderer fr1) + { + System.out.println("BioJs working as expected so far"); + 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 + { + StringBuilder bioJsData = new StringBuilder(); + int count = 0; + for (SequenceI seq : alignment.getSequences()) + { + bioJsData.append("seqOnFly.push({seq:'" + seq.getSequenceAsString() + + "', name:'" + seq.getName() + "', id:" + ++count + "});"); + } + String bioJSTemplate = new String( + readAllBytes(get("resources/templates/BioJSTemplate.txt"))); + + return bioJSTemplate.replaceAll("#sequenceData#", bioJsData.toString()); + } + + +} + diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index afb0dc1..741c124 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -210,6 +210,8 @@ public class GAlignFrame extends JInternalFrame JMenuItem createPNG = new JMenuItem(); + JMenuItem createBioJS = new JMenuItem(); + protected JMenuItem font = new JMenuItem(); public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); @@ -1118,6 +1120,19 @@ public class GAlignFrame extends JInternalFrame htmlMenuItem_actionPerformed(e); } }); + + // TODO uncomment when supported by MassageManager + // createBioJS.setText(MessageManager.getString("label.biojs_html_export")); + createBioJS.setText("BioJS"); + createBioJS.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + bioJSMenuItem_actionPerformed(e); + } + }); + overviewMenuItem.setText(MessageManager .getString("label.overview_window")); overviewMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -1497,7 +1512,6 @@ public class GAlignFrame extends JInternalFrame font_actionPerformed(e); } }); - seqLimits.setText(MessageManager .getString("label.show_sequence_limits")); seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true)); @@ -2225,6 +2239,7 @@ public class GAlignFrame extends JInternalFrame jMenu2.add(htmlMenuItem); jMenu2.add(epsFile); jMenu2.add(createPNG); + jMenu2.add(createBioJS); addSequenceMenu.add(addFromFile); addSequenceMenu.add(addFromText); addSequenceMenu.add(addFromURL); @@ -2455,6 +2470,11 @@ public class GAlignFrame extends JInternalFrame { } + protected void bioJSMenuItem_actionPerformed(ActionEvent e) + { + + } + protected void closeMenuItem_actionPerformed(boolean b) { } -- 1.7.10.2