-package jalview.jsdev;\r
-\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.io.AlignFile;\r
-import jalview.io.FileParse;\r
-\r
-import java.io.BufferedReader;\r
-import java.io.FileReader;\r
-import java.io.IOException;\r
-import java.io.InputStreamReader;\r
-import java.lang.reflect.Constructor;\r
-import java.lang.reflect.InvocationTargetException;\r
-import java.net.URL;\r
-\r
-import javajs.J2SIgnoreImport;\r
-/**\r
- * A class to open files via reflection so that their classes are only loaded as necessary\r
- * \r
- * note: not all file openers have corresponding String inFile and FileParse\r
- * source options. Why not?\r
- * \r
- * note: Pileupfile does not have a capital "F"; the method below requires that,\r
- * so if that file name gets changed, so too does the reflection code here.\r
- * \r
- * @author Bob Hanson\r
- * \r
- */\r
-\r
-@J2SIgnoreImport({java.io.FileReader.class})\r
-abstract public class GenericFileAdapter extends AlignFile {\r
-\r
- /**\r
- * inFileOrSource class type\r
- * \r
- * @param inFileOrSource\r
- * type will determine constructor -- [], [AlignmentI],\r
- * [inFile,type], or [source]\r
- * @param type\r
- * @param fileName\r
- * @return\r
- */\r
- public static AlignFile getFile(String fileType, Object... params) {\r
- Class<?> cl = null;\r
- try {\r
- cl = Class.forName("jalview.io." + fileType);\r
- } catch (ClassNotFoundException e) {\r
- System.err.println("did not find file jalview.io." + fileType);\r
- return null;\r
- }\r
- Constructor<?> m;\r
- Throwable ex = null;\r
- try {\r
- switch (params.length) {\r
- case 0:\r
- return (AlignFile) cl.newInstance();\r
- case 1:\r
- m = (params[0] instanceof FileParse ? cl\r
- .getConstructor(FileParse.class) : cl\r
- .getConstructor(AlignmentI.class));\r
- break;\r
- case 2:\r
- m = cl.getConstructor(String.class, String.class);\r
- break;\r
- default:\r
- return null;\r
- }\r
- return (AlignFile) m.newInstance(params);\r
- } catch (InstantiationException e) {\r
- ex = e;\r
- } catch (IllegalAccessException e) {\r
- ex = e;\r
- } catch (NoSuchMethodException e) {\r
- ex = e;\r
- } catch (SecurityException e) {\r
- ex = e;\r
- } catch (IllegalArgumentException e) {\r
- ex = e;\r
- } catch (InvocationTargetException e) {\r
- ex = e;\r
- }\r
- if (ex != null) {\r
- System.err.println("Error in GenericFileAdapter: " + ex);\r
- /**\r
- * @j2sNative\r
- * \r
- * alert(ex)\r
- * \r
- */\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- return null;\r
- }\r
-\r
- /**\r
- * Determines whether or not we have a JavaScript applet.\r
- * \r
- * @return\r
- */\r
- public static boolean isJS() {\r
- /**\r
- * @j2sNative \r
- * \r
- * return true;\r
- * \r
- */\r
- {\r
- return false;\r
- } \r
- }\r
-\r
- /**\r
- * opens a file for line-oriented reading via File() or URL()\r
- * \r
- * @param fileName\r
- * @param forceURL\r
- * @return\r
- * @throws IOException\r
- */\r
- public static BufferedReader getReader(String fileName, boolean forceURL) throws IOException {\r
- if (!forceURL && !isJS())\r
- return new BufferedReader(new FileReader(fileName)); \r
- if (fileName.indexOf("//") < 0)\r
- fileName = "file://" + fileName;\r
- return new BufferedReader(new InputStreamReader(new URL(fileName).openStream()));\r
- }\r
- \r
-\r
-}\r
+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()));
+ }
+
+ public final static String TCOFFEE_SCORE = "TCoffeeScore";
+ public static final int Phylip_FILE = 1;
+ public static final String Phylip_FILE_EXT = "phy";
+ public static final String Phylip_FILE_DESC = "PHYLIP";
+ public static final int JSON_FILE = 2;
+ public static final String JSON_FILE_EXT = "json";
+ public static final String JSON_FILE_DESC = "JSON";
+ public static final int Html_FILE = 3;
+ public static final String Html_FILE_EXT = "html";
+ public static final String Html_FILE_DESC = "HTML";
+
+
+}
git://source.jalview.org / jalviewjs.git / blobdiff