X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=373e9163c8d827b32406645d42da7a073b15b122;hb=ec187a3251292293356cc9ee42f90d5c7d5a3a78;hp=d5801df3fbfb2e05fb5f354fb9750d5978c5bbaa;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index d5801df..373e916 100755 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -44,7 +44,14 @@ public class JalviewLite extends Applet String file = "No file"; Button launcher = new Button("Start Jalview"); - AlignFrame currentAlignFrame; + //The currentAlignFrame is static, it will change + //if and when the user selects a new window + static AlignFrame currentAlignFrame; + + //This is the first frame to be displayed, and does not change + AlignFrame initialAlignFrame; + + boolean embedded = false; /** @@ -79,33 +86,25 @@ public class JalviewLite extends Applet this.setBackground(new Color(r, g, b)); + file = getParameter("file"); - param = getParameter("features"); - if(param!=null) + final JalviewLite applet = this; + if(getParameter("embedded")!=null + && getParameter("embedded").equalsIgnoreCase("true")) { - if(param.indexOf("://")==-1) - param = getCodeBase() + param; + embedded = true; + LoadingThread loader = new LoadingThread(file, applet); + loader.start(); } - final String featuresFile = param; - - file = getParameter("file"); - final JalviewLite applet = this; - if (file != null) + else if (file != null) { add(launcher); - if(file.indexOf("://")==-1) - file = getCodeBase() + file; launcher.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - String format = jalview.io.IdentifyFile.Identify(file, - "URL"); LoadingThread loader = new LoadingThread(file, - "URL", - format, - featuresFile, applet); loader.start(); } @@ -127,12 +126,18 @@ public class JalviewLite extends Applet System.exit(1); } - String format = jalview.io.IdentifyFile.Identify(args[0],"File"); - SequenceI[] sequences = new AppletFormatAdapter().readFile(args[0], "File", format); + String format = new jalview.io.IdentifyFile().Identify(args[0],AppletFormatAdapter.FILE); + SequenceI[] sequences = null; + try{ + sequences = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format); + }catch(java.io.IOException ex) + { + ex.printStackTrace(); + } if ( (sequences != null) && (sequences.length > 0)) { - AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]); + AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0], false); af.statusBar.setText("Successfully loaded file " + args[0]); } } @@ -158,14 +163,42 @@ public class JalviewLite extends Applet { public void windowClosing(WindowEvent e) { + if(currentAlignFrame == frame) + { + currentAlignFrame = null; + } lastFrameX -=40; - lastFrameY-=40; + lastFrameY -=40; + frame.setMenuBar(null); frame.dispose(); } + public void windowActivated(WindowEvent e) + { + if(frame instanceof AlignFrame) + currentAlignFrame = (AlignFrame)frame; + } + }); frame.setVisible(true); } + public String getSelectedSequences() + { + StringBuffer result = new StringBuffer(""); + + if(initialAlignFrame.viewport.getSelectionGroup()!=null) + { + SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup(). + getSequencesInOrder( + initialAlignFrame.viewport.getAlignment()); + + for (int i = 0; i < seqs.length; i++) + result.append(seqs[i].getName() + "¬"); + } + + return result.toString(); + } + public String getAlignment(String format) { return getAlignment(format, "true"); @@ -182,9 +215,9 @@ public class JalviewLite extends Applet return reply; } catch (Exception ex) - {ex.printStackTrace(); + { + ex.printStackTrace(); return "Error retrieving alignment in " + format + " format. "; - } } @@ -206,6 +239,15 @@ public class JalviewLite extends Applet g.drawString("Jalview can't open file", 5, 15); g.drawString("\"" + file + "\"", 5, 30); } + else if(embedded) + { + g.setColor(Color.black); + g.setFont(new Font("Arial", Font.BOLD, 24)); + g.drawString("Jalview Applet", 50, this.size().height/2 -30); + g.drawString("Loading Data...", 50, this.size().height/2); + } + + } class LoadingThread extends Thread @@ -213,51 +255,148 @@ public class JalviewLite extends Applet String file; String protocol; String format; - String featuresFile; JalviewLite applet; - public LoadingThread(String file, - String protocol, - String format, - String features, - JalviewLite applet) + public LoadingThread(String _file, + JalviewLite _applet) { - this.file = file; - this.protocol = protocol; - this.format = format; - featuresFile = features; - this.applet = applet; + file = _file; + if(inArchive(file)) + protocol = AppletFormatAdapter.CLASSLOADER; + else + { + file = addProtocol(file); + protocol = AppletFormatAdapter.URL; + } + format = new jalview.io.IdentifyFile().Identify(file, protocol); + applet = _applet; } public void run() { SequenceI[] sequences = null; - sequences = new AppletFormatAdapter().readFile(file, protocol, format); - + try{ + sequences = new AppletFormatAdapter().readFile(file, protocol, + format); + }catch(java.io.IOException ex) + { + ex.printStackTrace(); + } if ((sequences != null) && (sequences.length > 0)) { - currentAlignFrame = new AlignFrame(new Alignment(sequences), - applet, file); - currentAlignFrame.statusBar.setText("Successfully loaded file " + file); + currentAlignFrame = new AlignFrame(new Alignment(sequences), + applet, + file, + embedded); + + + initialAlignFrame = currentAlignFrame; + + currentAlignFrame.statusBar.setText("Successfully loaded file " + file); + + + String treeFile = applet.getParameter("treeFile"); + if (treeFile != null) + { + try + { + if(inArchive(treeFile)) + protocol = AppletFormatAdapter.CLASSLOADER; + else + { + protocol = AppletFormatAdapter.URL; + treeFile = addProtocol(treeFile); + } + + jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, protocol); + + fin.parse(); + + if (fin.getTree() != null) + { + currentAlignFrame.loadTree(fin, treeFile); + } + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + + String param = getParameter("features"); + if (param != null) + { + if( !inArchive(param) ) + param = addProtocol( param ); + + currentAlignFrame.parseFeaturesFile(param, protocol); + } + + param = getParameter("showFeatureSettings"); + if(param !=null && param.equalsIgnoreCase("true")) + { + currentAlignFrame.featureSettings_actionPerformed(); + } + + param = getParameter("annotations"); + if (param != null) + { + if( !inArchive(param) ) + param = addProtocol( param ); + + new AnnotationFile().readAnnotationFile( + currentAlignFrame.viewport.getAlignment(), + param); + + currentAlignFrame.alignPanel.fontChanged(); + currentAlignFrame.alignPanel.setScrollValues(0,0); + + } + + param = getParameter("jnetfile"); + if (param != null) + { + try + { + if (inArchive(param)) + protocol = AppletFormatAdapter.CLASSLOADER; + else + { + protocol = AppletFormatAdapter.URL; + param = addProtocol(param); + } + + jalview.io.JPredFile predictions = new jalview.io.JPredFile( + param, protocol); + new JnetAnnotationMaker().add_annotation(predictions, + currentAlignFrame.viewport.getAlignment(), + 0,false); // do not add sequence profile from concise output + currentAlignFrame.alignPanel.fontChanged(); + currentAlignFrame.alignPanel.setScrollValues(0, 0); + } catch (Exception ex) { + ex.printStackTrace(); + } + } - if(featuresFile!=null) - currentAlignFrame.parseFeaturesFile(featuresFile); String pdbfile = applet.getParameter("PDBFILE"); if(pdbfile!=null) { - if(pdbfile.indexOf("://")==-1) - pdbfile = getCodeBase() + pdbfile; + if( inArchive(pdbfile) ) + protocol = AppletFormatAdapter.CLASSLOADER; + else + { + protocol = AppletFormatAdapter.URL; + pdbfile = addProtocol(pdbfile); + } String sequence = applet.getParameter("PDBSEQ"); if(sequence!=null) { - new MCview.AppletPDBViewer(pdbfile, "URL", + new MCview.AppletPDBViewer(pdbfile, protocol, (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence), currentAlignFrame.getSeqcanvas()); - - } } @@ -269,5 +408,32 @@ public class JalviewLite extends Applet repaint(); } } + + /** + * Discovers whether the given file is in the Applet Archive + * @param file String + * @return boolean + */ + boolean inArchive(String file) + { + //This might throw a security exception in certain browsers + //Netscape Communicator for instance. + try{ + return (getClass().getResourceAsStream("/" + file) != null); + }catch(Exception ex) + { + System.out.println("Exception checking resources: "+file+" "+ex); + return false; + } + } + + String addProtocol(String file) + { + if (file.indexOf("://") == -1) + file = getCodeBase() + file; + + return file; + } + } }