X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=src%2Fjalview%2Fjsdev%2FGenericFileAdapter.java;fp=src%2Fjalview%2Fjsdev%2FGenericFileAdapter.java;h=f112ebfd1608eee7f35202dff25d690e43b4fd36;hp=4bafd3111c3026b29e2d9adabec4f96ecf5bba06;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/src/jalview/jsdev/GenericFileAdapter.java b/src/jalview/jsdev/GenericFileAdapter.java
index 4bafd31..f112ebf 100644
--- a/src/jalview/jsdev/GenericFileAdapter.java
+++ b/src/jalview/jsdev/GenericFileAdapter.java
@@ -1,130 +1,130 @@
-package jalview.jsdev;
-
-import jalview.datamodel.AlignmentI;
-import jalview.io.AlignFile;
-import jalview.io.FileParse;
-
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.lang.reflect.Constructor;
-import java.lang.reflect.InvocationTargetException;
-import java.net.URL;
-
-import javajs.J2SIgnoreImport;
-/**
- * A class to open files via reflection so that their classes are only loaded as necessary
- * 
- * note: not all file openers have corresponding String inFile and FileParse
- * source options. Why not?
- * 
- * note: Pileupfile does not have a capital "F"; the method below requires that,
- * so if that file name gets changed, so too does the reflection code here.
- * 
- * @author Bob Hanson
- * 
- */
-
-@J2SIgnoreImport({java.io.FileReader.class})
-abstract public class GenericFileAdapter extends AlignFile {
-
-	/**
-	 * inFileOrSource class type
-	 * 
-	 * @param inFileOrSource
-	 *          type will determine constructor -- [], [AlignmentI],
-	 *          [inFile,type], or [source]
-	 * @param type
-	 * @param fileName
-	 * @return
-	 */
-	public static AlignFile getFile(String fileType, Object... params) {
-		Class<?> cl = null;
-		try {
-			cl = Class.forName("jalview.io." + fileType);
-		} catch (ClassNotFoundException e) {
-			System.err.println("did not find file jalview.io." + fileType);
-			return null;
-		}
-		Constructor<?> m;
-		Throwable ex = null;
-		try {
-			switch (params.length) {
-			case 0:
-				return (AlignFile) cl.newInstance();
-			case 1:
-				m = (params[0] instanceof FileParse ? cl
-						.getConstructor(FileParse.class) : cl
-						.getConstructor(AlignmentI.class));
-				break;
-			case 2:
-				m = cl.getConstructor(String.class, String.class);
-				break;
-			default:
-				return null;
-			}
-			return (AlignFile) m.newInstance(params);
-		} catch (InstantiationException e) {
-			ex = e;
-		} catch (IllegalAccessException e) {
-			ex = e;
-		} catch (NoSuchMethodException e) {
-			ex = e;
-		} catch (SecurityException e) {
-			ex = e;
-		} catch (IllegalArgumentException e) {
-			ex = e;
-		} catch (InvocationTargetException e) {
-			ex = e;
-		}
-		if (ex != null) {
-			System.err.println("Error in GenericFileAdapter: " + ex);
-			/**
-			 * @j2sNative
-			 * 
-			 *            alert(ex)
-			 * 
-			 */
-			{
-				ex.printStackTrace();
-			}
-		}
-		return null;
-	}
-
-	/**
-	 * Determines whether or not we have a JavaScript applet.
-	 * 
-	 * @return
-	 */
-	public static boolean isJS() {
-  	/**
-  	 * @j2sNative 
-  	 * 
-  	 * return true;
-  	 * 
-  	 */
-  	{
-  		return false;
-  	} 
-	}
-
-	/**
-	 * opens a file for line-oriented reading via File() or URL()
-	 * 
-	 * @param fileName
-	 * @param forceURL
-	 * @return
-	 * @throws IOException
-	 */
-	public static BufferedReader getReader(String fileName, boolean forceURL) throws IOException {
-  	if (!forceURL && !isJS())
-  		return new BufferedReader(new FileReader(fileName));		
-		if (fileName.indexOf("//") < 0)
-			fileName = "file://" + fileName;
-    return new BufferedReader(new InputStreamReader(new URL(fileName).openStream()));
-	}
-	
-
-}
+package jalview.jsdev;
+
+import jalview.datamodel.AlignmentI;
+import jalview.io.AlignFile;
+import jalview.io.FileParse;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.lang.reflect.Constructor;
+import java.lang.reflect.InvocationTargetException;
+import java.net.URL;
+
+import javajs.J2SIgnoreImport;
+/**
+ * A class to open files via reflection so that their classes are only loaded as necessary
+ * 
+ * note: not all file openers have corresponding String inFile and FileParse
+ * source options. Why not?
+ * 
+ * note: Pileupfile does not have a capital "F"; the method below requires that,
+ * so if that file name gets changed, so too does the reflection code here.
+ * 
+ * @author Bob Hanson
+ * 
+ */
+
+@J2SIgnoreImport({java.io.FileReader.class})
+abstract public class GenericFileAdapter extends AlignFile {
+
+	/**
+	 * inFileOrSource class type
+	 * 
+	 * @param inFileOrSource
+	 *          type will determine constructor -- [], [AlignmentI],
+	 *          [inFile,type], or [source]
+	 * @param type
+	 * @param fileName
+	 * @return
+	 */
+	public static AlignFile getFile(String fileType, Object... params) {
+		Class<?> cl = null;
+		try {
+			cl = Class.forName("jalview.io." + fileType);
+		} catch (ClassNotFoundException e) {
+			System.err.println("did not find file jalview.io." + fileType);
+			return null;
+		}
+		Constructor<?> m;
+		Throwable ex = null;
+		try {
+			switch (params.length) {
+			case 0:
+				return (AlignFile) cl.newInstance();
+			case 1:
+				m = (params[0] instanceof FileParse ? cl
+						.getConstructor(FileParse.class) : cl
+						.getConstructor(AlignmentI.class));
+				break;
+			case 2:
+				m = cl.getConstructor(String.class, String.class);
+				break;
+			default:
+				return null;
+			}
+			return (AlignFile) m.newInstance(params);
+		} catch (InstantiationException e) {
+			ex = e;
+		} catch (IllegalAccessException e) {
+			ex = e;
+		} catch (NoSuchMethodException e) {
+			ex = e;
+		} catch (SecurityException e) {
+			ex = e;
+		} catch (IllegalArgumentException e) {
+			ex = e;
+		} catch (InvocationTargetException e) {
+			ex = e;
+		}
+		if (ex != null) {
+			System.err.println("Error in GenericFileAdapter: " + ex);
+			/**
+			 * @j2sNative
+			 * 
+			 *            alert(ex)
+			 * 
+			 */
+			{
+				ex.printStackTrace();
+			}
+		}
+		return null;
+	}
+
+	/**
+	 * Determines whether or not we have a JavaScript applet.
+	 * 
+	 * @return
+	 */
+	public static boolean isJS() {
+  	/**
+  	 * @j2sNative 
+  	 * 
+  	 * return true;
+  	 * 
+  	 */
+  	{
+  		return false;
+  	} 
+	}
+
+	/**
+	 * opens a file for line-oriented reading via File() or URL()
+	 * 
+	 * @param fileName
+	 * @param forceURL
+	 * @return
+	 * @throws IOException
+	 */
+	public static BufferedReader getReader(String fileName, boolean forceURL) throws IOException {
+  	if (!forceURL && !isJS())
+  		return new BufferedReader(new FileReader(fileName));		
+		if (fileName.indexOf("//") < 0)
+			fileName = "file://" + fileName;
+    return new BufferedReader(new InputStreamReader(new URL(fileName).openStream()));
+	}
+	
+
+}