needed for applet search

[jalview.git] / src / com / stevesoft / pat / wrap / RandomAccessFileWrap.java

diff --git a/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java b/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java
new file mode 100755 (executable)
index 0000000..23782ad
--- /dev/null
+++ b/src/com/stevesoft/pat/wrap/RandomAccessFileWrap.java
@@ -0,0 +1,116 @@
+//\r
+// This software is now distributed according to\r
+// the Lesser Gnu Public License.  Please see\r
+// http://www.gnu.org/copyleft/lesser.txt for\r
+// the details.\r
+//    -- Happy Computing!\r
+//\r
+package com.stevesoft.pat.wrap;\r
+\r
+import com.stevesoft.pat.*;\r
+import java.io.*;\r
+\r
+/** Provides a wrapper for a RandomAccessFile so that it\r
+    can be searched by Regex. */\r
+public class RandomAccessFileWrap implements StringLike {\r
+\r
+    long offset = 0;\r
+    public void setOffset(long o) {\r
+      offset = o;\r
+      i0 = iend = 0;\r
+    }\r
+    public long getOffset() {\r
+      return offset;\r
+    }\r
+    RandomAccessFile raf;\r
+    int i0=0,iend=0;\r
+    byte[] buf = new byte[1024];\r
+\r
+    public int getBufferSize() {\r
+      return buf.length;\r
+    }\r
+\r
+    public void setBufferSize(int bs) {\r
+      buf = new byte[bs];\r
+      i0 = iend = 0;\r
+    }\r
+\r
+    public RandomAccessFileWrap(String file) throws IOException {\r
+        this.raf = new RandomAccessFile(file,"r");\r
+    }\r
+    public RandomAccessFileWrap(RandomAccessFile raf) {\r
+        this.raf = raf;\r
+    }\r
+\r
+    public char charAt(int i) {\r
+        if(i >= i0 && i < iend)\r
+            return (char)buf[i-i0];\r
+\r
+        try {\r
+            i0 = i-5;\r
+            //if(i0+offset<0) i0=(int)(-offset);\r
+            if(i0<0) i0=0;\r
+            raf.seek(i0+offset);\r
+            iend = i0+raf.read(buf,0,buf.length);\r
+\r
+            if(i >= i0 && i < iend)\r
+                return (char)buf[i-i0];\r
+        } catch(Throwable t) {}\r
+\r
+        throw new ArrayIndexOutOfBoundsException("Out of bounds for file:"+\r
+          " i="+i+\r
+          ", Final Buffer: i0="+i0+\r
+          " iend="+iend);\r
+    }\r
+\r
+    public String toString() { throw new Error("Not implemented"); }\r
+    public int length() {\r
+      try {\r
+        long len = raf.length()-offset;\r
+        if(len > Integer.MAX_VALUE)\r
+          return Integer.MAX_VALUE;\r
+        return (int)len;\r
+      } catch(IOException ioe) {\r
+        return 0;\r
+      }\r
+    }\r
+    public String substring(int i1,int i2) {\r
+        StringBuffer sb = new StringBuffer();\r
+        for(int i=i1;i<i2;i++)\r
+            sb.append(charAt(i));\r
+        return sb.toString();\r
+    }\r
+    public Object unwrap() { return raf; }\r
+\r
+    public static void main(String[] files) throws IOException {\r
+      for(int i=0;i<files.length;i++) {\r
+        RandomAccessFileWrap fw =\r
+          new RandomAccessFileWrap(new RandomAccessFile(files[i],"r"));\r
+        Regex r = new Regex("toString\\(\\) *(?@{})");\r
+        r.setGFlag(true);\r
+        r.optimize();\r
+        System.out.print(files[i]+" ");\r
+        int j=0;\r
+        do {\r
+          if(r.searchFrom(fw,j)) {\r
+            System.out.println("Matched at index: "+\r
+             r.matchedFrom());\r
+            j=r.matchedTo();\r
+          } else\r
+            System.out.println("not found");\r
+          System.out.println(r.stringMatched());\r
+        } while(r.didMatch());\r
+      }\r
+    }\r
+\r
+    public BasicStringBufferLike newStringBufferLike() {\r
+      return new StringBufferWrap();\r
+    }\r
+\r
+    public int indexOf(char c) {\r
+      for(int i=0;i<length();i++)\r
+        if(charAt(i)==c)\r
+          return i;\r
+      return -1;\r
+    }\r
+}\r