import jalview.gui.PromptUserConfig;
import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
import java.io.PrintWriter;
import java.net.MalformedURLException;
import java.net.URI;
+import java.net.URISyntaxException;
import java.net.URL;
import java.security.AllPermission;
import java.security.CodeSource;
BioJsHTMLOutput.updateBioJS();
}
- String file = null, protocol = null, format = null, data = null;
+ String file = null, data = null;
+ FileFormatI format = null;
+ DataSourceType protocol = null;
FileLoader fileLoader = new FileLoader(!headless);
Vector<String> getFeatures = null; // vector of das source nicknames to
// fetch
{
try
{
- String viprotocol = AppletFormatAdapter
+ DataSourceType viprotocol = AppletFormatAdapter
.checkProtocol(vamsasImport);
- if (viprotocol == jalview.io.FormatAdapter.FILE)
+ if (viprotocol == DataSourceType.FILE)
{
inSession = desktop.vamsasImport(new File(vamsasImport));
}
- else if (viprotocol == FormatAdapter.URL)
+ else if (viprotocol == DataSourceType.URL)
{
inSession = desktop.vamsasImport(new URL(vamsasImport));
}
protocol = AppletFormatAdapter.checkProtocol(file);
- format = new IdentifyFile().identify(file, protocol);
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e1)
+ {
+ // TODO ?
+ }
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
{
data.replaceAll("%20", " ");
- ColourSchemeI cs = ColourSchemeProperty.getColour(af
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(af
.getViewport().getAlignment(), data);
- if (cs == null)
- {
- UserColourScheme ucs = new UserColourScheme("white");
- ucs.parseAppletParameter(data);
- cs = ucs;
- }
- else
+ if (cs != null)
{
System.out.println("CMD [-color " + data
+ "] executed successfully!");
String imageName = "unnamed.png";
while (aparser.getSize() > 1)
{
- format = aparser.nextValue();
+ String outputFormat = aparser.nextValue();
file = aparser.nextValue();
- if (format.equalsIgnoreCase("png"))
+ if (outputFormat.equalsIgnoreCase("png"))
{
af.createPNG(new File(file));
imageName = (new File(file)).getName();
System.out.println("Creating PNG image: " + file);
continue;
}
- else if (format.equalsIgnoreCase("svg"))
+ else if (outputFormat.equalsIgnoreCase("svg"))
{
File imageFile = new File(file);
imageName = imageFile.getName();
System.out.println("Creating SVG image: " + file);
continue;
}
- else if (format.equalsIgnoreCase("html"))
+ else if (outputFormat.equalsIgnoreCase("html"))
{
File imageFile = new File(file);
imageName = imageFile.getName();
HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.generateHtmlSvgOutput(new File(file));
+ htmlSVG.exportHTML(file);
System.out.println("Creating HTML image: " + file);
continue;
}
- else if (format.equalsIgnoreCase("biojsmsa"))
+ else if (outputFormat.equalsIgnoreCase("biojsmsa"))
{
- BioJsHTMLOutput.updateBioJS();
+ if (file == null)
+ {
+ System.err.println("The output html file must not be null");
+ return;
+ }
try
{
- Thread.sleep(1500);
- } catch (InterruptedException e)
+ BioJsHTMLOutput
+ .refreshVersionInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
{
e.printStackTrace();
}
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel, af);
- bjs.exportJalviewAlignmentAsBioJsHtmlFile(file);
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(file);
System.out.println("Creating BioJS MSA Viwer HTML file: "
+ file);
continue;
}
- else if (format.equalsIgnoreCase("imgMap"))
+ else if (outputFormat.equalsIgnoreCase("imgMap"))
{
af.createImageMap(new File(file), imageName);
System.out.println("Creating image map: " + file);
continue;
}
- else if (format.equalsIgnoreCase("eps"))
+ else if (outputFormat.equalsIgnoreCase("eps"))
{
File outputFile = new File(file);
System.out.println("Creating EPS file: "
jalview.bin.Cache.removeProperty("STARTUP_FILE");
}
- protocol = "File";
+ protocol = DataSourceType.FILE;
if (file.indexOf("http:") > -1)
{
- protocol = "URL";
+ protocol = DataSourceType.URL;
}
if (file.endsWith(".jar"))
{
- format = "Jalview";
+ format = FileFormat.Jalview;
}
else
{
- format = new IdentifyFile().identify(file, protocol);
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e)
+ {
+ // TODO what?
+ }
}
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,