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