\r
import java.awt.*;\r
import java.awt.event.*;\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
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], false);\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
\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
+ currentAlignFrame = new AlignFrame(al,\r
applet,\r
file,\r
embedded);\r
if(param !=null && param.equalsIgnoreCase("true"))\r
{\r
currentAlignFrame.viewport.showSequenceFeatures(true);\r
- currentAlignFrame.featureSettings_actionPerformed();\r
+ new FeatureSettings(currentAlignFrame.alignPanel);\r
}\r
\r
param = getParameter("annotations");\r
\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
- 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
git://source.jalview.org / jalview.git / blobdiff