X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fcom%2Fstevesoft%2Fpat%2FRegexReader.java;h=2e10f169bfdb921e4e763ae86140f4f2bbd79b4e;hb=8f8e6868f55cfe6ab73b3fe82cfb360f3e71a025;hp=0ff33e395245327d936be4591fb310d575ce0837;hpb=c40cf903f740a72ab63dd1abc10fa33450ce660d;p=jalview.git

diff --git a/src/com/stevesoft/pat/RegexReader.java b/src/com/stevesoft/pat/RegexReader.java
index 0ff33e3..2e10f16 100755
--- a/src/com/stevesoft/pat/RegexReader.java
+++ b/src/com/stevesoft/pat/RegexReader.java
@@ -1,248 +1,309 @@
-//
-// 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;
-
-import java.io.*;
-import com.stevesoft.pat.wrap.*;
-
-/** This class allows you to replace the text in strings
-    as you read them in.  Be careful what you do with
-    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 {
-  RBuffer rb = new RBuffer(new StringBuffer());
-  PartialBuffer wrap = new PartialBuffer(rb.sb);
-  boolean moreToRead = true;
-  Reader r;
-  Replacer rp;
-
-  // the buffer size
-  int nmax = 2*1024;
-
-  public RegexReader(Regex rex,Reader r) {
-    this.r = r;
-    rp = rex.getReplacer();
-  }
-  public RegexReader(Transformer tex,Reader r) {
-    this.r = r;
-    rp = tex.getReplacer();
-  }
-  public void reset() throws IOException {
-    r.reset();
-    rb = new RBuffer(new StringBuffer());
-    wrap = new PartialBuffer(rb.sb);
-    moreToRead = true;
-  }
-  void readData() throws IOException {
-    int c;
-    int n = 0;
-    while( (c = r.read()) != -1) {
-      rb.sb.append((char)c);
-      if(n++ > nmax)
-        break;
-    }
-    if(c == -1 && n == 0) {
-      moreToRead = false;
-      wrap.allowOverRun = false;
-    }
-  }
-  void getMoreData() throws IOException {
-    while(rb.pos >= rb.epos) {
-      wrap.overRun = false;
-      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) {
-        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;
-	    }
-            rb3.pos = npos;
-	  } else {
-	    rb3.pos = rb3.epos = npos;
-	  }
-
-        }
-      } 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) {
-      getMoreData();
-      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
-  {
-    int c = -1;
-    int end = off+len;
-    for(int i=off;i<end;i++) {
-      c = read();
-      if(c < 0) {
-	if(i == off)
-	  return -1;
-        return i-off;
-      }
-      buf[i] = (char)c;
-    }
-    return len;
-  }
-  public void close()
-    throws IOException
-  {
-    r.close();
-  }
-
-  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() {
-    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) {
-    nmax = n;
-  }
-
-  int max_lines = 2;
-  /** This function no longer serves any purpose.
-      @deprecated
-      */
-  public int getMaxLines() { return max_lines; }
-  /** This function no longer serves any purpose.
-      @deprecated
-      */
-  public void setMaxLines(int ml) { max_lines = ml; }
-
-  char EOLchar = '\n';
-  /** This function no longer serves any purpose.
-      @deprecated
-      */
-  public char getEOLchar() {
-    return EOLchar;
-  }
-  /** This function no longer serves any purpose.
-      @deprecated
-      */
-  public void setEOLchar(char c) {
-    EOLchar = c;
-  }
-
-  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)
-      n++;
-    return n;
-  }
-
-  /*
-  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);
-    String res1 = rex.replaceAll(inp);
-    int c = -1;
-    StringBuffer sb = new StringBuffer();
-    RegexReader rr = new RegexReader(rex,r);
-    rr.setBufferSize(n);
-    while( (c = rr.read()) != -1)
-      sb.append((char)c);
-    String res2 = sb.toString();
-    if(!res1.equals(res2)) {
-      System.out.println("nmax="+n);
-      System.out.println("re="+re);
-      System.out.println("inp="+inp);
-      System.out.println("res1="+res1);
-      System.out.println("res2="+res2);
-      System.exit(255);
-    }
-  }
-  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);
-      test("s/x/y/","-----x",n);
-      test("s/x.*?x/y/",".xx..x..x...x...x....x....x",n);
-      test("s/x.*x/[$&]/","--x........x--xx",n);
-      test("s/x.*x/[$&]/","--x........x------",n);
-      test("s/.$/a/m","bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbbbbbbbbbbbb",n);
-      test("s/.$/a/","123",n);
-      test("s/.$/a/","bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb",n);
-      test("s/^./a/","bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb",n);
-      test("s/$/a/","bbb",n);
-      test("s/^/a/","bbb",n);
-      test("s/^/a/","",n);
-      test("s{.*}{N}","xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx",n);
-      test("s/.{0,7}/y/","AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",n);
-      test("s/x/$&/","xxx",n);
-    }
-    System.out.println("Success!!!");
-  }
-  */
-}
+//
+// 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;
+
+import java.io.*;
+
+import com.stevesoft.pat.wrap.*;
+
+/**
+ * This class allows you to replace the text in strings as you read them in. Be
+ * careful what you do with 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
+{
+  RBuffer rb = new RBuffer(new StringBuffer());
+
+  PartialBuffer wrap = new PartialBuffer(rb.sb);
+
+  boolean moreToRead = true;
+
+  Reader r;
+
+  Replacer rp;
+
+  // the buffer size
+  int nmax = 2 * 1024;
+
+  public RegexReader(Regex rex, Reader r)
+  {
+    this.r = r;
+    rp = rex.getReplacer();
+  }
+
+  public RegexReader(Transformer tex, Reader r)
+  {
+    this.r = r;
+    rp = tex.getReplacer();
+  }
+
+  public void reset() throws IOException
+  {
+    r.reset();
+    rb = new RBuffer(new StringBuffer());
+    wrap = new PartialBuffer(rb.sb);
+    moreToRead = true;
+  }
+
+  void readData() throws IOException
+  {
+    int c;
+    int n = 0;
+    while ((c = r.read()) != -1)
+    {
+      rb.sb.append((char) c);
+      if (n++ > nmax)
+      {
+        break;
+      }
+    }
+    if (c == -1 && n == 0)
+    {
+      moreToRead = false;
+      wrap.allowOverRun = false;
+    }
+  }
+
+  void getMoreData() throws IOException
+  {
+    while (rb.pos >= rb.epos)
+    {
+      wrap.overRun = false;
+      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)
+      {
+        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;
+            }
+            rb3.pos = npos;
+          }
+          else
+          {
+            rb3.pos = rb3.epos = npos;
+          }
+
+        }
+      }
+      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)
+    {
+      getMoreData();
+      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
+  {
+    int c = -1;
+    int end = off + len;
+    for (int i = off; i < end; i++)
+    {
+      c = read();
+      if (c < 0)
+      {
+        if (i == off)
+        {
+          return -1;
+        }
+        return i - off;
+      }
+      buf[i] = (char) c;
+    }
+    return len;
+  }
+
+  public void close() throws IOException
+  {
+    r.close();
+  }
+
+  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()
+  {
+    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)
+  {
+    nmax = n;
+  }
+
+  int max_lines = 2;
+
+  /**
+   * This function no longer serves any purpose.
+   * 
+   * @deprecated
+   */
+  public int getMaxLines()
+  {
+    return max_lines;
+  }
+
+  /**
+   * This function no longer serves any purpose.
+   * 
+   * @deprecated
+   */
+  public void setMaxLines(int ml)
+  {
+    max_lines = ml;
+  }
+
+  char EOLchar = '\n';
+
+  /**
+   * This function no longer serves any purpose.
+   * 
+   * @deprecated
+   */
+  public char getEOLchar()
+  {
+    return EOLchar;
+  }
+
+  /**
+   * This function no longer serves any purpose.
+   * 
+   * @deprecated
+   */
+  public void setEOLchar(char c)
+  {
+    EOLchar = c;
+  }
+
+  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)
+    {
+      n++;
+    }
+    return n;
+  }
+
+  /*
+   * 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); String res1 = rex.replaceAll(inp); int c = -1;
+   * StringBuffer sb = new StringBuffer(); RegexReader rr = new
+   * RegexReader(rex,r); rr.setBufferSize(n); while( (c = rr.read()) != -1)
+   * sb.append((char)c); String res2 = sb.toString(); if(!res1.equals(res2)) {
+   * System.out.println("nmax="+n); System.out.println("re="+re);
+   * System.out.println("inp="+inp); System.out.println("res1="+res1);
+   * System.out.println("res2="+res2); System.exit(255); } } 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);
+   * test("s/x/y/","-----x",n);
+   * test("s/x.*?x/y/",".xx..x..x...x...x....x....x",n);
+   * test("s/x.*x/[$&]/","--x........x--xx",n);
+   * test("s/x.*x/[$&]/","--x........x------",n);
+   * test("s/.$/a/m","bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbbbbbbbbbbbb",n);
+   * test("s/.$/a/","123",n);
+   * test("s/.$/a/","bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb",n);
+   * test("s/^./a/","bb\nbbb\nbbbb\nbbbbb\nbbbbbb\nbb",n);
+   * test("s/$/a/","bbb",n); test("s/^/a/","bbb",n); test("s/^/a/","",n);
+   * test("s{.*}{N}","xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx",n);
+   * test("s/.{0,7}/y/","AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",n);
+   * test("s/x/$&/","xxx",n); } System.out.println("Success!!!"); }
+   */
+}