Removed

git-svn-id: svn+ssh://idea.nguyen.vg/svn/sxsi/trunk/TextCollection@334 3cdefd35-fc62-479d-8e8d-bae585ffb9ca

diff --git a/GapEncode.cpp b/GapEncode.cpp
deleted file mode 100644 (file)
index 32102ac..0000000
--- a/GapEncode.cpp
+++ /dev/null
@@ -1,151 +0,0 @@
-/**
- * Gap encoding scheme
- * Niko Välimäki
- *
- */
-
-#include "GapEncode.h"
-#include <stdexcept>
-using namespace std;
-
-
-GapEncode::GapEncode(ulong *B, ulong u, bool freeB = false)
-{
-    ulong i, lastIndex, *bitRun, *runLength;
-    this->u = u;
-    this->numberOfRuns = 0;
-    bitRun = new ulong[u/W + 1];
-    for (i = 0; i < u/W + 1; i ++)
-        bitRun[i]  = 0;
-
-    // Collect the runs of 1- or 0-bits
-    totalLength = 0;
-    uchar curBit = 0xFF;
-    lastIndex = 0;
-    for (i = 0; i < u; i ++)
-        if (Tools::GetField(B, 1, i) != curBit)
-        {
-            if (curBit == 1)
-                totalLength += i - lastIndex;
-            else if (Tools::GetField(B, 1, i))
-                Tools::SetField(bitRun, 1, i, 1);
-
-            lastIndex = i;
-            curBit = Tools::GetField(B, 1, i);
-        }
-    // Handle the last run
-    if (curBit == 1)
-        totalLength += i - lastIndex;
-    
-    runLength = new ulong[totalLength/W + 1];
-    for (i = 0; i < totalLength/W + 1; i ++)
-        runLength[i] = 0;
-    
-    // Calculate run lengths
-    totalLength = 0;
-    curBit = 0xFF;
-    lastIndex = 0;
-    for (i = 0; i < u; i ++)
-        if (Tools::GetField(B, 1, i) != curBit)
-        {
-            if (curBit == 1)
-            {
-                totalLength += i - lastIndex;
-                Tools::SetField(runLength, 1, totalLength - 1, 1);
-            }
-            lastIndex = i;
-            curBit = Tools::GetField(B, 1, i);
-        }
-    // Handle the last run
-    if (curBit == 1)
-    {
-        totalLength += i - lastIndex;
-        Tools::SetField(runLength, 1, totalLength - 1, 1);
-    }
-    
-    // Construct BSGAP structures
-    this->bitRun = new BSGAP(bitRun, u, true, 0);
-    numberOfRuns = this->bitRun->rank(u-1);
-    this->runLength = new BSGAP(runLength, totalLength, true, 0);
-    
-    if (freeB)
-        delete [] B;
-}
-
-GapEncode::~GapEncode()
-{
-    // Free BSGAP structures
-    delete bitRun;
-    delete runLength;
-}
-
-ulong GapEncode::rank(ulong i)
-{
-    ulong pred, r = bitRun->rank(i);
-    if (r == 0)
-        return 0;
-    pred = bitRun->select(r);
-    
-    ulong bitsBeforeRun = 0;
-    if (r > 1)
-        bitsBeforeRun = runLength->select(r - 1) + 1;
-    
-    ulong bitsInRun = runLength->select(r) + 1 - bitsBeforeRun;
-    if (i - pred >= bitsInRun)
-        return bitsBeforeRun + bitsInRun;
-    
-    return bitsBeforeRun + i - pred + 1;
-}
-
-ulong GapEncode::rank0(ulong i)
-{
-    return i - rank(i) + 1;
-}
-
-ulong GapEncode::select(ulong i)
-{
-    throw logic_error("GapEncode::select() is not implemented");
-    return 0;
-}
-
-ulong GapEncode::select0(ulong i)
-{
-    throw logic_error("GapEncode::select0() is not implemented");
-    return 0; // To be implemented...
-}
-
-/**
- * Saving data fields:
-    ulong u;                // Universe size, number of bits in B
-    ulong numberOfRuns;     // Number of 1-bit runs
-    BSGAP *bitRun,          // Contains 1-bit at the start of each 1-bit-run
-          *runLength;       // Contains run lengths for each 1-bit-run
-    ulong totalLength;      // Total length of runs
-*/
-void GapEncode::Save(FILE *file) const
-{
-    if (std::fwrite(&(this->u), sizeof(ulong), 1, file) != 1)
-        throw std::runtime_error("GapEncode::Save(): file write error (u).");
-    if (std::fwrite(&(this->numberOfRuns), sizeof(ulong), 1, file) != 1)
-        throw std::runtime_error("GapEncode::Save(): file write error (numberOfRuns).");
-
-    bitRun->Save(file);
-    runLength->Save(file);
-
-    if (std::fwrite(&(this->totalLength), sizeof(ulong), 1, file) != 1)
-        throw std::runtime_error("GapEncode::Save(): file write error (totalLength).");
-}
-
-GapEncode::GapEncode(FILE *file)
-{
-    if (std::fread(&(this->u), sizeof(ulong), 1, file) != 1)
-        throw std::runtime_error("GapEncode::Load(): file read error (u).");
-    if (std::fread(&(this->numberOfRuns), sizeof(ulong), 1, file) != 1)
-        throw std::runtime_error("GapEncode::Load(): file read error (numberOfRuns).");
-
-    bitRun = new BSGAP(file);
-    runLength = new BSGAP(file);
-
-    if (std::fread(&(this->totalLength), sizeof(ulong), 1, file) != 1)
-        throw std::runtime_error("GapEncode::Load(): file read error (totalLength).");
-}