X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=89c01679f49945c95ee43c145bc819f0f776e06c;hb=3ab14ac58b3829f6f83353eb3e600cf9152d83bc;hp=331e7f53acd348d834572fd50ee2756dca94cd89;hpb=285388369aa586c03977a409a11d44b2ee17be16;p=jalview.git diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index 331e7f5..89c0167 100755 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* Copyright (C) 2006 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 @@ -28,7 +28,7 @@ import java.applet.*; import java.awt.*; import java.awt.event.*; -import jalview.appletgui.TreePanel; +import jalview.appletgui.FeatureSettings; /** @@ -39,13 +39,109 @@ import jalview.appletgui.TreePanel; */ public class JalviewLite extends Applet { + + /////////////////////////////////////////// + //The following public methods maybe called + //externally, eg via javascript in HTML page + + 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"); + } + + public String getAlignment(String format, String suffix) + { + try + { + boolean seqlimits = suffix.equalsIgnoreCase("true"); + + String reply = new AppletFormatAdapter().formatSequences(format, + currentAlignFrame.viewport.getAlignment(), seqlimits); + return reply; + } + catch (Exception ex) + { + ex.printStackTrace(); + return "Error retrieving alignment in " + format + " format. "; + } + } + + public void loadAnnotation(String annotation) + { + if (new AnnotationFile().readAnnotationFile( + currentAlignFrame.getAlignViewport().getAlignment(), annotation, + AppletFormatAdapter.PASTE)) + { + currentAlignFrame.alignPanel.fontChanged(); + currentAlignFrame.alignPanel.setScrollValues(0, 0); + } + else + { + currentAlignFrame.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE); + } + } + + public String getFeatures(String format) + { + return currentAlignFrame.outputFeatures(false, format); + } + + public String getAnnotation() + { + return currentAlignFrame.outputAnnotations(false); + } + + public void loadAlignment(String text, String title) + { + Alignment al = null; + String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE); + try{ + al = new AppletFormatAdapter().readFile(text, + AppletFormatAdapter.PASTE, + format); + if (al.getHeight() > 0) + new AlignFrame(al, this, title, false); + }catch(java.io.IOException ex) + { + ex.printStackTrace(); + } + } + + //////////////////////////////////////////////// + //////////////////////////////////////////////// + + + static int lastFrameX = 200; static int lastFrameY = 200; boolean fileFound = true; String file = "No file"; Button launcher = new Button("Start Jalview"); - static AlignFrame currentAlignFrame; + //The currentAlignFrame is static, it will change + //if and when the user selects a new window + public static AlignFrame currentAlignFrame; + + //This is the first frame to be displayed, and does not change + AlignFrame initialAlignFrame; + boolean embedded = false; @@ -81,28 +177,28 @@ public class JalviewLite extends Applet this.setBackground(new Color(r, g, b)); + file = getParameter("file"); - param = getParameter("features"); - if(param!=null) + if(file==null) { - if(param.indexOf("://")==-1) - param = getCodeBase() + param; + //Maybe the sequences are added as parameters + StringBuffer data = new StringBuffer("PASTE"); + int i=1; + while( (file=getParameter("sequence"+i))!=null) + { + data.append(file.toString()+"\n"); + i++; + } + if(data.length()>5) + file = data.toString(); } - final String featuresFile = param; - - file = getParameter("file"); - if(file.indexOf("://")==-1) - file = getCodeBase() + file; final JalviewLite applet = this; if(getParameter("embedded")!=null && getParameter("embedded").equalsIgnoreCase("true")) { embedded = true; - LoadingThread loader = new LoadingThread(file, - "URL", - featuresFile, - applet); + LoadingThread loader = new LoadingThread(file, applet); loader.start(); } else if (file != null) @@ -114,8 +210,6 @@ public class JalviewLite extends Applet public void actionPerformed(ActionEvent e) { LoadingThread loader = new LoadingThread(file, - "URL", - featuresFile, applet); loader.start(); } @@ -137,12 +231,18 @@ 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); - if ( (sequences != null) && (sequences.length > 0)) + Alignment al = null; + try{ + al = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format); + }catch(java.io.IOException ex) + { + ex.printStackTrace(); + } + if ( (al != null) && (al.getHeight() > 0)) { - AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]); + AlignFrame af = new AlignFrame(al, null, args[0], false); af.statusBar.setText("Successfully loaded file " + args[0]); } } @@ -168,12 +268,14 @@ public class JalviewLite extends Applet { public void windowClosing(WindowEvent e) { + if(frame instanceof AlignFrame) + ((AlignFrame)frame).closeMenuItem_actionPerformed(); if(currentAlignFrame == frame) { currentAlignFrame = null; } lastFrameX -=40; - lastFrameY-=40; + lastFrameY -=40; frame.setMenuBar(null); frame.dispose(); } @@ -187,27 +289,7 @@ public class JalviewLite extends Applet frame.setVisible(true); } - public String getAlignment(String format) - { - return getAlignment(format, "true"); - } - public String getAlignment(String format, String suffix) - { - try - { - boolean seqlimits = suffix.equalsIgnoreCase("true"); - - String reply = new AppletFormatAdapter().formatSequences(format, - currentAlignFrame.viewport.getAlignment().getSequences(), seqlimits); - return reply; - } - catch (Exception ex) - { - ex.printStackTrace(); - return "Error retrieving alignment in " + format + " format. "; - } - } /** * This paints the background surrounding the "Launch Jalview button" @@ -231,8 +313,8 @@ public class JalviewLite extends Applet { 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); + g.drawString("Jalview Applet", 50, this.getSize().height/2 -30); + g.drawString("Loading Data...", 50, this.getSize().height/2); } @@ -243,55 +325,76 @@ public class JalviewLite extends Applet String file; String protocol; String format; - String featuresFile; JalviewLite applet; - public LoadingThread(String file, - String protocol, - String features, - JalviewLite applet) + public LoadingThread(String _file, + JalviewLite _applet) { - this.file = file; - this.protocol = protocol; - format = jalview.io.IdentifyFile.Identify(file, "URL"); - featuresFile = features; - this.applet = applet; + file = _file; + if(file.startsWith("PASTE")) + { + file = file.substring(5); + protocol = AppletFormatAdapter.PASTE; + } + else 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); - - if ((sequences != null) && (sequences.length > 0)) + Alignment al = null; + try{ + al = new AppletFormatAdapter().readFile(file, protocol, + format); + }catch(java.io.IOException ex) { - currentAlignFrame = new AlignFrame(new Alignment(sequences), - applet, file); - if (embedded) - currentAlignFrame.setEmbedded(); + ex.printStackTrace(); + } + if ((al != null) && (al.getHeight() > 0)) + { + currentAlignFrame = new AlignFrame(al, + applet, + file, + embedded); + + if(protocol==jalview.io.AppletFormatAdapter.PASTE) + currentAlignFrame.setTitle("Sequences from "+getDocumentBase()); + + initialAlignFrame = currentAlignFrame; currentAlignFrame.statusBar.setText("Successfully loaded file " + file); - if (featuresFile != null) - currentAlignFrame.parseFeaturesFile(featuresFile); - String treeFile = applet.getParameter("treeFile"); + String treeFile = applet.getParameter("tree"); + if(treeFile==null) + treeFile = applet.getParameter("treeFile"); + if (treeFile != null) { try { - jalview.io.NewickFile fin = new jalview.io.NewickFile(applet. - getCodeBase() + treeFile, "URL"); + 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) { - TreePanel tp = null; - tp = new TreePanel(currentAlignFrame.viewport, - currentAlignFrame.viewport.getAlignment().getSequences(), - fin, "FromFile", applet.getCodeBase() + treeFile); - addFrame(tp, treeFile, 600, 500); - currentAlignFrame.addTreeMenuItem(tp, treeFile); + currentAlignFrame.loadTree(fin, treeFile); } } catch (Exception ex) @@ -300,18 +403,80 @@ public class JalviewLite extends Applet } } + 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.viewport.showSequenceFeatures(true); + new FeatureSettings(currentAlignFrame.alignPanel); + } - String pdbfile = applet.getParameter("PDBFILE"); - if(pdbfile!=null) + param = getParameter("annotations"); + if (param != null) + { + if( !inArchive(param) ) + param = addProtocol( param ); + + new AnnotationFile().readAnnotationFile( + currentAlignFrame.viewport.getAlignment(), + param, + protocol); + + 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(); + } + } + + + param = getParameter("PDBFILE"); + if(param!=null) { - if(pdbfile.indexOf("://")==-1) - pdbfile = getCodeBase() + pdbfile; + if( inArchive(param) ) + protocol = AppletFormatAdapter.CLASSLOADER; + else + { + protocol = AppletFormatAdapter.URL; + param = addProtocol(param); + } String sequence = applet.getParameter("PDBSEQ"); if(sequence!=null) { - new MCview.AppletPDBViewer(pdbfile, "URL", + new MCview.AppletPDBViewer(param, protocol, (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence), currentAlignFrame.getSeqcanvas()); } @@ -325,5 +490,32 @@ 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; + } + } }