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Merge branch 'develop' into features/filetypeEnum
[jalview.git]
/
src
/
jalview
/
bin
/
Jalview.java
diff --git
a/src/jalview/bin/Jalview.java
b/src/jalview/bin/Jalview.java
index
3294c26
..
1ab837f
100755
(executable)
--- a/
src/jalview/bin/Jalview.java
+++ b/
src/jalview/bin/Jalview.java
@@
-28,8
+28,11
@@
import jalview.gui.Desktop;
import jalview.gui.PromptUserConfig;
import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
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.FileLoader;
-import jalview.io.FormatAdapter;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
@@
-344,7
+347,9
@@
public class Jalview
BioJsHTMLOutput.updateBioJS();
}
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
FileLoader fileLoader = new FileLoader(!headless);
Vector<String> getFeatures = null; // vector of das source nicknames to
// fetch
@@
-377,13
+382,13
@@
public class Jalview
{
try
{
{
try
{
- String viprotocol = AppletFormatAdapter
+ DataSourceType viprotocol = AppletFormatAdapter
.checkProtocol(vamsasImport);
.checkProtocol(vamsasImport);
- if (viprotocol == jalview.io.FormatAdapter.FILE)
+ if (viprotocol == DataSourceType.FILE)
{
inSession = desktop.vamsasImport(new File(vamsasImport));
}
{
inSession = desktop.vamsasImport(new File(vamsasImport));
}
- else if (viprotocol == FormatAdapter.URL)
+ else if (viprotocol == DataSourceType.URL)
{
inSession = desktop.vamsasImport(new URL(vamsasImport));
}
{
inSession = desktop.vamsasImport(new URL(vamsasImport));
}
@@
-472,7
+477,13
@@
public class Jalview
protocol = AppletFormatAdapter.checkProtocol(file);
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);
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
@@
-617,17
+628,17
@@
public class Jalview
String imageName = "unnamed.png";
while (aparser.getSize() > 1)
{
String imageName = "unnamed.png";
while (aparser.getSize() > 1)
{
- format = aparser.nextValue();
+ String outputFormat = aparser.nextValue();
file = 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;
}
{
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();
{
File imageFile = new File(file);
imageName = imageFile.getName();
@@
-635,7
+646,7
@@
public class Jalview
System.out.println("Creating SVG image: " + file);
continue;
}
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();
{
File imageFile = new File(file);
imageName = imageFile.getName();
@@
-643,13
+654,13
@@
public class Jalview
System.out.println("Creating HTML image: " + file);
continue;
}
System.out.println("Creating HTML image: " + 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;
}
{
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: "
{
File outputFile = new File(file);
System.out.println("Creating EPS file: "
@@
-698,20
+709,26
@@
public class Jalview
jalview.bin.Cache.removeProperty("STARTUP_FILE");
}
jalview.bin.Cache.removeProperty("STARTUP_FILE");
}
- protocol = "File";
+ protocol = DataSourceType.FILE;
if (file.indexOf("http:") > -1)
{
if (file.indexOf("http:") > -1)
{
- protocol = "URL";
+ protocol = DataSourceType.URL;
}
if (file.endsWith(".jar"))
{
}
if (file.endsWith(".jar"))
{
- format = "Jalview";
+ format = FileFormat.Jalview;
}
else
{
}
else
{
- format = new IdentifyFile().identify(file, protocol);
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e)
+ {
+ // TODO what?
+ }
}
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
}
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,