/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
-import jalview.appletgui.TreePanel;\r
+import jalview.appletgui.FeatureSettings;\r
\r
\r
/**\r
*/\r
public class JalviewLite extends Applet\r
{\r
+\r
+ ///////////////////////////////////////////\r
+ //The following public methods maybe called\r
+ //externally, eg via javascript in HTML page\r
+\r
+ public String getSelectedSequences()\r
+ {\r
+ StringBuffer result = new StringBuffer("");\r
+\r
+ if(initialAlignFrame.viewport.getSelectionGroup()!=null)\r
+ {\r
+ SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().\r
+ getSequencesInOrder(\r
+ initialAlignFrame.viewport.getAlignment());\r
+\r
+ for (int i = 0; i < seqs.length; i++)\r
+ result.append(seqs[i].getName() + "¬");\r
+ }\r
+\r
+ return result.toString();\r
+ }\r
+\r
+ public String getAlignment(String format)\r
+ {\r
+ return getAlignment(format, "true");\r
+ }\r
+\r
+ public String getAlignment(String format, String suffix)\r
+ {\r
+ try\r
+ {\r
+ boolean seqlimits = suffix.equalsIgnoreCase("true");\r
+\r
+ String reply = new AppletFormatAdapter().formatSequences(format,\r
+ currentAlignFrame.viewport.getAlignment(), seqlimits);\r
+ return reply;\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ return "Error retrieving alignment in " + format + " format. ";\r
+ }\r
+ }\r
+\r
+ public void loadAnnotation(String annotation)\r
+ {\r
+ if (new AnnotationFile().readAnnotationFile(\r
+ currentAlignFrame.getAlignViewport().getAlignment(), annotation,\r
+ AppletFormatAdapter.PASTE))\r
+ {\r
+ currentAlignFrame.alignPanel.fontChanged();\r
+ currentAlignFrame.alignPanel.setScrollValues(0, 0);\r
+ }\r
+ else\r
+ {\r
+ currentAlignFrame.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);\r
+ }\r
+ }\r
+\r
+ public String getFeatures(String format)\r
+ {\r
+ return currentAlignFrame.outputFeatures(false, format);\r
+ }\r
+\r
+ public String getAnnotation()\r
+ {\r
+ return currentAlignFrame.outputAnnotations(false);\r
+ }\r
+\r
+ public void loadAlignment(String text, String title)\r
+ {\r
+ Alignment al = null;\r
+ String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);\r
+ try{\r
+ al = new AppletFormatAdapter().readFile(text,\r
+ AppletFormatAdapter.PASTE,\r
+ format);\r
+ if (al.getHeight() > 0)\r
+ new AlignFrame(al, this, title, false);\r
+ }catch(java.io.IOException ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ ////////////////////////////////////////////////\r
+ ////////////////////////////////////////////////\r
+\r
+\r
+\r
static int lastFrameX = 200;\r
static int lastFrameY = 200;\r
boolean fileFound = true;\r
\r
//The currentAlignFrame is static, it will change\r
//if and when the user selects a new window\r
- static AlignFrame currentAlignFrame;\r
+ public static AlignFrame currentAlignFrame;\r
\r
//This is the first frame to be displayed, and does not change\r
AlignFrame initialAlignFrame;\r
\r
file = getParameter("file");\r
\r
+ if(file==null)\r
+ {\r
+ //Maybe the sequences are added as parameters\r
+ StringBuffer data = new StringBuffer("PASTE");\r
+ int i=1;\r
+ while( (file=getParameter("sequence"+i))!=null)\r
+ {\r
+ data.append(file.toString()+"\n");\r
+ i++;\r
+ }\r
+ if(data.length()>5)\r
+ file = data.toString();\r
+ }\r
+\r
final JalviewLite applet = this;\r
if(getParameter("embedded")!=null\r
&& getParameter("embedded").equalsIgnoreCase("true"))\r
{\r
embedded = true;\r
- LoadingThread loader = new LoadingThread(file,\r
- AppletFormatAdapter.URL,\r
- applet);\r
+ LoadingThread loader = new LoadingThread(file, applet);\r
loader.start();\r
}\r
else if (file != null)\r
public void actionPerformed(ActionEvent e)\r
{\r
LoadingThread loader = new LoadingThread(file,\r
- AppletFormatAdapter.URL,\r
applet);\r
loader.start();\r
}\r
\r
String format = new jalview.io.IdentifyFile().Identify(args[0],AppletFormatAdapter.FILE);\r
\r
- SequenceI[] sequences = null;\r
+ Alignment al = null;\r
try{\r
- sequences = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format);\r
+ al = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format);\r
}catch(java.io.IOException ex)\r
{\r
ex.printStackTrace();\r
}\r
- if ( (sequences != null) && (sequences.length > 0))\r
+ if ( (al != null) && (al.getHeight() > 0))\r
{\r
- AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]);\r
+ AlignFrame af = new AlignFrame(al, null, args[0], false);\r
af.statusBar.setText("Successfully loaded file " + args[0]);\r
}\r
}\r
{\r
public void windowClosing(WindowEvent e)\r
{\r
+ if(frame instanceof AlignFrame)\r
+ ((AlignFrame)frame).closeMenuItem_actionPerformed();\r
if(currentAlignFrame == frame)\r
{\r
currentAlignFrame = null;\r
frame.setVisible(true);\r
}\r
\r
- public String getSelectedSequences()\r
- {\r
- StringBuffer result = new StringBuffer("");\r
-\r
- if(initialAlignFrame.viewport.getSelectionGroup()!=null)\r
- {\r
- SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().\r
- getSequencesInOrder(\r
- initialAlignFrame.viewport.getAlignment());\r
-\r
- for (int i = 0; i < seqs.length; i++)\r
- result.append(seqs[i].getName() + "¬");\r
- }\r
-\r
- return result.toString();\r
- }\r
-\r
- public String getAlignment(String format)\r
- {\r
- return getAlignment(format, "true");\r
- }\r
-\r
- public String getAlignment(String format, String suffix)\r
- {\r
- try\r
- {\r
- boolean seqlimits = suffix.equalsIgnoreCase("true");\r
\r
- String reply = new AppletFormatAdapter().formatSequences(format,\r
- currentAlignFrame.viewport.getAlignment().getSequences(), seqlimits);\r
- return reply;\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- return "Error retrieving alignment in " + format + " format. ";\r
- }\r
- }\r
\r
/**\r
* This paints the background surrounding the "Launch Jalview button"\r
{\r
g.setColor(Color.black);\r
g.setFont(new Font("Arial", Font.BOLD, 24));\r
- g.drawString("Jalview Applet", 50, this.size().height/2 -30);\r
- g.drawString("Loading Data...", 50, this.size().height/2);\r
+ g.drawString("Jalview Applet", 50, this.getSize().height/2 -30);\r
+ g.drawString("Loading Data...", 50, this.getSize().height/2);\r
}\r
\r
\r
JalviewLite applet;\r
\r
public LoadingThread(String _file,\r
- String _protocol,\r
JalviewLite _applet)\r
{\r
file = _file;\r
- if(inArchive(file))\r
+ if(file.startsWith("PASTE"))\r
+ {\r
+ file = file.substring(5);\r
+ protocol = AppletFormatAdapter.PASTE;\r
+ }\r
+ else if(inArchive(file))\r
protocol = AppletFormatAdapter.CLASSLOADER;\r
else\r
- protocol = _protocol;\r
-\r
+ {\r
+ file = addProtocol(file);\r
+ protocol = AppletFormatAdapter.URL;\r
+ }\r
format = new jalview.io.IdentifyFile().Identify(file, protocol);\r
applet = _applet;\r
}\r
\r
public void run()\r
{\r
- SequenceI[] sequences = null;\r
+ Alignment al = null;\r
try{\r
- sequences = new AppletFormatAdapter().readFile(file, protocol,\r
+ al = new AppletFormatAdapter().readFile(file, protocol,\r
format);\r
}catch(java.io.IOException ex)\r
{\r
ex.printStackTrace();\r
}\r
- if ((sequences != null) && (sequences.length > 0))\r
+ if ((al != null) && (al.getHeight() > 0))\r
{\r
- currentAlignFrame = new AlignFrame(new Alignment(sequences),\r
- applet, file);\r
+ currentAlignFrame = new AlignFrame(al,\r
+ applet,\r
+ file,\r
+ embedded);\r
\r
- initialAlignFrame = currentAlignFrame;\r
+ if(protocol==jalview.io.AppletFormatAdapter.PASTE)\r
+ currentAlignFrame.setTitle("Sequences from "+getDocumentBase());\r
\r
- if (embedded)\r
- currentAlignFrame.setEmbedded();\r
+ initialAlignFrame = currentAlignFrame;\r
\r
currentAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
\r
\r
- String treeFile = applet.getParameter("treeFile");\r
+ String treeFile = applet.getParameter("tree");\r
+ if(treeFile==null)\r
+ treeFile = applet.getParameter("treeFile");\r
+\r
if (treeFile != null)\r
{\r
try\r
\r
if (fin.getTree() != null)\r
{\r
- TreePanel tp = null;\r
- tp = new TreePanel(currentAlignFrame.viewport,\r
- currentAlignFrame.viewport.getAlignment().getSequences(),\r
- fin, "FromFile", treeFile);\r
- addFrame(tp, treeFile, 600, 500);\r
- currentAlignFrame.addTreeMenuItem(tp, treeFile);\r
+ currentAlignFrame.loadTree(fin, treeFile);\r
}\r
}\r
catch (Exception ex)\r
if( !inArchive(param) )\r
param = addProtocol( param );\r
\r
- currentAlignFrame.parseFeaturesFile(param);\r
+ currentAlignFrame.parseFeaturesFile(param, protocol);\r
+ }\r
+\r
+ param = getParameter("showFeatureSettings");\r
+ if(param !=null && param.equalsIgnoreCase("true"))\r
+ {\r
+ currentAlignFrame.viewport.showSequenceFeatures(true);\r
+ new FeatureSettings(currentAlignFrame.alignPanel);\r
}\r
\r
param = getParameter("annotations");\r
if( !inArchive(param) )\r
param = addProtocol( param );\r
\r
- new AnnotationReader().readAnnotationFile(\r
+ new AnnotationFile().readAnnotationFile(\r
currentAlignFrame.viewport.getAlignment(),\r
- param);\r
+ param,\r
+ protocol);\r
\r
currentAlignFrame.alignPanel.fontChanged();\r
+ currentAlignFrame.alignPanel.setScrollValues(0,0);\r
+\r
+ }\r
+\r
+ param = getParameter("jnetfile");\r
+ if (param != null)\r
+ {\r
+ try\r
+ {\r
+ if (inArchive(param))\r
+ protocol = AppletFormatAdapter.CLASSLOADER;\r
+ else\r
+ {\r
+ protocol = AppletFormatAdapter.URL;\r
+ param = addProtocol(param);\r
+ }\r
+\r
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(\r
+ param, protocol);\r
+ new JnetAnnotationMaker().add_annotation(predictions,\r
+ currentAlignFrame.viewport.getAlignment(),\r
+ 0,false); // do not add sequence profile from concise output\r
+ currentAlignFrame.alignPanel.fontChanged();\r
+ currentAlignFrame.alignPanel.setScrollValues(0, 0);\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
+ }\r
}\r
\r
\r
- String pdbfile = applet.getParameter("PDBFILE");\r
- if(pdbfile!=null)\r
+ param = getParameter("PDBFILE");\r
+ if(param!=null)\r
{\r
- if( inArchive(pdbfile) )\r
+ if( inArchive(param) )\r
protocol = AppletFormatAdapter.CLASSLOADER;\r
else\r
{\r
protocol = AppletFormatAdapter.URL;\r
- pdbfile = addProtocol(pdbfile);\r
+ param = addProtocol(param);\r
}\r
\r
String sequence = applet.getParameter("PDBSEQ");\r
\r
if(sequence!=null)\r
{\r
- new MCview.AppletPDBViewer(pdbfile, protocol,\r
+ new MCview.AppletPDBViewer(param, protocol,\r
(Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),\r
currentAlignFrame.getSeqcanvas());\r
}\r
\r
}\r
+\r
+ int gIndex = 1;\r
+ param = getParameter("SEQUENCE_GROUP"+gIndex);\r
+ if(param!=null)\r
+ do{\r
+ new AnnotationFile().readAnnotationFile(\r
+ currentAlignFrame.viewport.getAlignment(),\r
+ "JALVIEW_ANNOTATION\nSEQUENCE_GROUP\t"+param,\r
+ AppletFormatAdapter.PASTE);\r
+ gIndex++;\r
+ param = applet.getParameter("SEQUENCE_GROUP"+gIndex);\r
+ currentAlignFrame.alignPanel.repaint();\r
+ }while(param!=null);\r
+\r
+ gIndex = 1;\r
+ param = getParameter("PROPERTIES" + gIndex);\r
+ if (param != null)\r
+ do\r
+ {\r
+ new AnnotationFile().readAnnotationFile(\r
+ currentAlignFrame.viewport.getAlignment(),\r
+ "JALVIEW_ANNOTATION\nPROPERTIES\t" + param,\r
+ AppletFormatAdapter.PASTE);\r
+ gIndex++;\r
+ param = applet.getParameter("PROPERTIES" + gIndex);\r
+ currentAlignFrame.alignPanel.repaint();\r
+ }\r
+ while (param != null);\r
}\r
else\r
{\r
*/\r
boolean inArchive(String file)\r
{\r
- return ( getClass().getResourceAsStream("/" + file) != null );\r
+ //This might throw a security exception in certain browsers\r
+ //Netscape Communicator for instance.\r
+ try{\r
+ return (getClass().getResourceAsStream("/" + file) != null);\r
+ }catch(Exception ex)\r
+ {\r
+ System.out.println("Exception checking resources: "+file+" "+ex);\r
+ return false;\r
+ }\r
}\r
\r
String addProtocol(String file)\r
git://source.jalview.org / jalview.git / blobdiff