X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fcom%2Fstevesoft%2Fpat%2FRegexReader.java;fp=src%2Fcom%2Fstevesoft%2Fpat%2FRegexReader.java;h=6475dfecdef71cbb7d4a28909e83daad19ac1b61;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=0ff33e395245327d936be4591fb310d575ce0837;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

diff --git a/src/com/stevesoft/pat/RegexReader.java b/src/com/stevesoft/pat/RegexReader.java
index 0ff33e3..6475dfe 100755
--- a/src/com/stevesoft/pat/RegexReader.java
+++ b/src/com/stevesoft/pat/RegexReader.java
@@ -8,6 +8,7 @@
 package com.stevesoft.pat;
 
 import java.io.*;
+
 import com.stevesoft.pat.wrap.*;
 
 /** This class allows you to replace the text in strings
@@ -15,8 +16,10 @@ import com.stevesoft.pat.wrap.*;
     this freedom... using Regex.perlCode("s{.*}{x}s")
     as your pattern will result in loading the entire
     contents of the Reader into memory.
-    */
-public class RegexReader extends Reader {
+ */
+public class RegexReader
+    extends Reader
+{
   RBuffer rb = new RBuffer(new StringBuffer());
   PartialBuffer wrap = new PartialBuffer(rb.sb);
   boolean moreToRead = true;
@@ -24,185 +27,259 @@ public class RegexReader extends Reader {
   Replacer rp;
 
   // the buffer size
-  int nmax = 2*1024;
+  int nmax = 2 * 1024;
 
-  public RegexReader(Regex rex,Reader r) {
+  public RegexReader(Regex rex, Reader r)
+  {
     this.r = r;
     rp = rex.getReplacer();
   }
-  public RegexReader(Transformer tex,Reader r) {
+
+  public RegexReader(Transformer tex, Reader r)
+  {
     this.r = r;
     rp = tex.getReplacer();
   }
-  public void reset() throws IOException {
+
+  public void reset()
+      throws IOException
+  {
     r.reset();
     rb = new RBuffer(new StringBuffer());
     wrap = new PartialBuffer(rb.sb);
     moreToRead = true;
   }
-  void readData() throws IOException {
+
+  void readData()
+      throws IOException
+  {
     int c;
     int n = 0;
-    while( (c = r.read()) != -1) {
-      rb.sb.append((char)c);
-      if(n++ > nmax)
+    while ( (c = r.read()) != -1)
+    {
+      rb.sb.append( (char) c);
+      if (n++ > nmax)
+      {
         break;
+      }
     }
-    if(c == -1 && n == 0) {
+    if (c == -1 && n == 0)
+    {
       moreToRead = false;
       wrap.allowOverRun = false;
     }
   }
-  void getMoreData() throws IOException {
-    while(rb.pos >= rb.epos) {
+
+  void getMoreData()
+      throws IOException
+  {
+    while (rb.pos >= rb.epos)
+    {
       wrap.overRun = false;
-      if(rb.next != null) {
-	rb = rb.next;
-      } else if(rb.done) {
+      if (rb.next != null)
+      {
+        rb = rb.next;
+      }
+      else if (rb.done)
+      {
         break;
-      } else if(rb.epos >= rb.sb.length()
-	     && rb.epos > nmax) {
-	rb.pos = 1;
-	rb.epos = 1;
-	rb.sb.setLength(1);
-	readData();
-      } else if(rb.epos >= rb.sb.length()
-	     && moreToRead) {
+      }
+      else if (rb.epos >= rb.sb.length()
+               && rb.epos > nmax)
+      {
+        rb.pos = 1;
+        rb.epos = 1;
+        rb.sb.setLength(1);
+        readData();
+      }
+      else if (rb.epos >= rb.sb.length()
+               && moreToRead)
+      {
         readData();
-      } else if(rp.getRegex().matchAt(wrap,rb.epos)) {
-	if(wrap.overRun) {
-	  readData();
-	} else {
-	  StringBufferWrap sbw = new StringBufferWrap();
-	  StringBufferLike sbl = new StringBufferLike(sbw);
-	  /*
-          ReplaceRule rr = rex.getReplaceRule();
-	  while(rr != null) {
-	    rr.apply(sbl,rex);
-	    rr = rr.next;
-	  }
-	  */
-	  Regex rex = rp.getRegex();
-	  int npos = rex.matchedTo();
-	  rp.setBuffer(sbl);
-	  rp.setSource(wrap);
-	  rp.setPos(npos);
-	  rp.apply(rex,rex.getReplaceRule());
-	  int opos = rb.epos;
-	  RBuffer rb2 = new RBuffer((StringBuffer)sbw.unwrap());
-	  rb2.epos = rb2.sb.length();
-	  RBuffer rb3 = new RBuffer(rb.sb);
-
-	  rb.next = rb2;
-	  rb2.next = rb3;
-
-	  if(npos == opos) {
-	    rb3.epos = npos+1;
-	    if(rb3.epos > rb3.sb.length()) {
-	      if(rb.pos >= rb.epos)
-	        rb = rb.next;
-	      rb3.pos = rb3.epos = 0;
-	      rb3.done = true;
-	      //break;
-	    }
+      }
+      else if (rp.getRegex().matchAt(wrap, rb.epos))
+      {
+        if (wrap.overRun)
+        {
+          readData();
+        }
+        else
+        {
+          StringBufferWrap sbw = new StringBufferWrap();
+          StringBufferLike sbl = new StringBufferLike(sbw);
+          /*
+                 ReplaceRule rr = rex.getReplaceRule();
+              while(rr != null) {
+            rr.apply(sbl,rex);
+            rr = rr.next;
+              }
+           */
+          Regex rex = rp.getRegex();
+          int npos = rex.matchedTo();
+          rp.setBuffer(sbl);
+          rp.setSource(wrap);
+          rp.setPos(npos);
+          rp.apply(rex, rex.getReplaceRule());
+          int opos = rb.epos;
+          RBuffer rb2 = new RBuffer( (StringBuffer) sbw.unwrap());
+          rb2.epos = rb2.sb.length();
+          RBuffer rb3 = new RBuffer(rb.sb);
+
+          rb.next = rb2;
+          rb2.next = rb3;
+
+          if (npos == opos)
+          {
+            rb3.epos = npos + 1;
+            if (rb3.epos > rb3.sb.length())
+            {
+              if (rb.pos >= rb.epos)
+              {
+                rb = rb.next;
+              }
+              rb3.pos = rb3.epos = 0;
+              rb3.done = true;
+              //break;
+            }
             rb3.pos = npos;
-	  } else {
-	    rb3.pos = rb3.epos = npos;
-	  }
+          }
+          else
+          {
+            rb3.pos = rb3.epos = npos;
+          }
 
         }
-      } else {
-	if(wrap.overRun) {
-	  readData();
-        } else if(rb.epos<rb.sb.length()) {
-	  rb.epos++;
-        } else {
-	  break;
-	}
+      }
+      else
+      {
+        if (wrap.overRun)
+        {
+          readData();
+        }
+        else if (rb.epos < rb.sb.length())
+        {
+          rb.epos++;
+        }
+        else
+        {
+          break;
+        }
       }
     }
   }
-  public int read() throws IOException {
-    if(rb.pos >= rb.epos) {
+
+  public int read()
+      throws IOException
+  {
+    if (rb.pos >= rb.epos)
+    {
       getMoreData();
-      if(rb.pos >= rb.epos)
+      if (rb.pos >= rb.epos)
+      {
         return -1;
+      }
     }
     //System.out.println(rb);
     return rb.sb.charAt(rb.pos++);
   }
-  public int read(char[] buf,int off,int len)
-    throws IOException
+
+  public int read(char[] buf, int off, int len)
+      throws IOException
   {
     int c = -1;
-    int end = off+len;
-    for(int i=off;i<end;i++) {
+    int end = off + len;
+    for (int i = off; i < end; i++)
+    {
       c = read();
-      if(c < 0) {
-	if(i == off)
-	  return -1;
-        return i-off;
+      if (c < 0)
+      {
+        if (i == off)
+        {
+          return -1;
+        }
+        return i - off;
       }
-      buf[i] = (char)c;
+      buf[i] = (char) c;
     }
     return len;
   }
+
   public void close()
-    throws IOException
+      throws IOException
   {
     r.close();
   }
 
-  public boolean markSupported() { return false; }
+  public boolean markSupported()
+  {
+    return false;
+  }
 
   /** Get the size of the working buffer.
       The current buffer may be larger if
       the pattern demands it. */
-  public int getBufferSize() {
+  public int getBufferSize()
+  {
     return nmax;
   }
+
   /** Set the size of the working buffer.
       The current buffer may be larger if
       the pattern demands it. */
-  public void setBufferSize(int n) {
+  public void setBufferSize(int n)
+  {
     nmax = n;
   }
 
   int max_lines = 2;
   /** This function no longer serves any purpose.
       @deprecated
-      */
-  public int getMaxLines() { return max_lines; }
+   */
+  public int getMaxLines()
+  {
+    return max_lines;
+  }
+
   /** This function no longer serves any purpose.
       @deprecated
-      */
-  public void setMaxLines(int ml) { max_lines = ml; }
+   */
+  public void setMaxLines(int ml)
+  {
+    max_lines = ml;
+  }
 
   char EOLchar = '\n';
   /** This function no longer serves any purpose.
       @deprecated
-      */
-  public char getEOLchar() {
+   */
+  public char getEOLchar()
+  {
     return EOLchar;
   }
+
   /** This function no longer serves any purpose.
       @deprecated
-      */
-  public void setEOLchar(char c) {
+   */
+  public void setEOLchar(char c)
+  {
     EOLchar = c;
   }
 
-  public long skip(long d) throws IOException {
+  public long skip(long d)
+      throws IOException
+  {
     // This is probably inefficient, I just did it
     // this way to avoid possible bugs.
     long n = 0;
-    while(n<d && read() != -1)
+    while (n < d && read() != -1)
+    {
       n++;
+    }
     return n;
   }
 
   /*
-  static void test(String re,String inp,int n) throws Exception {
+     static void test(String re,String inp,int n) throws Exception {
     Reader r = new StringReader(inp);
     r = new BufferedReader(r);
     Regex rex = Regex.perlCode(re);
@@ -222,8 +299,8 @@ public class RegexReader extends Reader {
       System.out.println("res2="+res2);
       System.exit(255);
     }
-  }
-  public static void main(String[] args) throws Exception {
+     }
+     public static void main(String[] args) throws Exception {
     for(int n=6;n<15;n++) {
       test("s/x/y/","-----x123456789",n);
       test("s/x/y/","x123456789",n);
@@ -243,6 +320,6 @@ public class RegexReader extends Reader {
       test("s/x/$&/","xxx",n);
     }
     System.out.println("Success!!!");
-  }
-  */
+     }
+   */
 }