X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=89c01679f49945c95ee43c145bc819f0f776e06c;hb=3ab14ac58b3829f6f83353eb3e600cf9152d83bc;hp=a0c7c2d1af63a8953221a07d3c9c6bf391004f24;hpb=4fc3b9ce0764a3f25846dc89de98577394862f49;p=jalview.git diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index a0c7c2d..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 @@ -28,6 +28,7 @@ import java.applet.*; import java.awt.*; import java.awt.event.*; +import jalview.appletgui.FeatureSettings; /** @@ -38,6 +39,96 @@ import java.awt.event.*; */ 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; @@ -46,7 +137,7 @@ public class JalviewLite extends Applet //The currentAlignFrame is static, it will change //if and when the user selects a new window - static AlignFrame currentAlignFrame; + public static AlignFrame currentAlignFrame; //This is the first frame to be displayed, and does not change AlignFrame initialAlignFrame; @@ -88,6 +179,20 @@ public class JalviewLite extends Applet file = getParameter("file"); + if(file==null) + { + //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 JalviewLite applet = this; if(getParameter("embedded")!=null && getParameter("embedded").equalsIgnoreCase("true")) @@ -128,16 +233,16 @@ public class JalviewLite extends Applet String format = new jalview.io.IdentifyFile().Identify(args[0],AppletFormatAdapter.FILE); - SequenceI[] sequences = null; + Alignment al = null; try{ - sequences = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format); + al = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format); }catch(java.io.IOException ex) { ex.printStackTrace(); } - if ( (sequences != null) && (sequences.length > 0)) + if ( (al != null) && (al.getHeight() > 0)) { - AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0], false); + AlignFrame af = new AlignFrame(al, null, args[0], false); af.statusBar.setText("Successfully loaded file " + args[0]); } } @@ -163,6 +268,8 @@ public class JalviewLite extends Applet { public void windowClosing(WindowEvent e) { + if(frame instanceof AlignFrame) + ((AlignFrame)frame).closeMenuItem_actionPerformed(); if(currentAlignFrame == frame) { currentAlignFrame = null; @@ -182,44 +289,7 @@ public class JalviewLite extends Applet 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"); - } - - 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" @@ -243,8 +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); } @@ -261,7 +331,12 @@ public class JalviewLite extends Applet JalviewLite _applet) { file = _file; - if(inArchive(file)) + if(file.startsWith("PASTE")) + { + file = file.substring(5); + protocol = AppletFormatAdapter.PASTE; + } + else if(inArchive(file)) protocol = AppletFormatAdapter.CLASSLOADER; else { @@ -274,28 +349,33 @@ public class JalviewLite extends Applet public void run() { - SequenceI[] sequences = null; + Alignment al = null; try{ - sequences = new AppletFormatAdapter().readFile(file, protocol, + al = new AppletFormatAdapter().readFile(file, protocol, format); }catch(java.io.IOException ex) { ex.printStackTrace(); } - if ((sequences != null) && (sequences.length > 0)) + if ((al != null) && (al.getHeight() > 0)) { - currentAlignFrame = new AlignFrame(new Alignment(sequences), + 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); - String treeFile = applet.getParameter("treeFile"); + String treeFile = applet.getParameter("tree"); + if(treeFile==null) + treeFile = applet.getParameter("treeFile"); + if (treeFile != null) { try @@ -329,13 +409,14 @@ public class JalviewLite extends Applet if( !inArchive(param) ) param = addProtocol( param ); - currentAlignFrame.parseFeaturesFile(param); + currentAlignFrame.parseFeaturesFile(param, protocol); } param = getParameter("showFeatureSettings"); if(param !=null && param.equalsIgnoreCase("true")) { - currentAlignFrame.featureSettings_actionPerformed(); + currentAlignFrame.viewport.showSequenceFeatures(true); + new FeatureSettings(currentAlignFrame.alignPanel); } param = getParameter("annotations"); @@ -346,7 +427,8 @@ public class JalviewLite extends Applet new AnnotationFile().readAnnotationFile( currentAlignFrame.viewport.getAlignment(), - param); + param, + protocol); currentAlignFrame.alignPanel.fontChanged(); currentAlignFrame.alignPanel.setScrollValues(0,0); @@ -379,22 +461,22 @@ public class JalviewLite extends Applet } - String pdbfile = applet.getParameter("PDBFILE"); - if(pdbfile!=null) + param = getParameter("PDBFILE"); + if(param!=null) { - if( inArchive(pdbfile) ) + if( inArchive(param) ) protocol = AppletFormatAdapter.CLASSLOADER; else { protocol = AppletFormatAdapter.URL; - pdbfile = addProtocol(pdbfile); + param = addProtocol(param); } String sequence = applet.getParameter("PDBSEQ"); if(sequence!=null) { - new MCview.AppletPDBViewer(pdbfile, protocol, + new MCview.AppletPDBViewer(param, protocol, (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence), currentAlignFrame.getSeqcanvas()); }