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/********************************************************************** |
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bitvec.cpp - Fast and efficient bitstring class. |
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|
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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|
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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|
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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|
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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|
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#include "bitvec.hpp" |
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#include "oberror.hpp" |
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|
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using namespace std; |
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|
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namespace OpenBabel |
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{ |
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|
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extern OBMessageHandler obErrorLog; |
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|
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/*! \class OBBitVec |
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\brief Fast and efficient bitstring class |
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|
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The OBBitVec class is a fast and efficient bitstring class that is |
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handy to use as a truth table. Truth tables are an easy way to store |
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whether a list of items has a particular propery. Instances of |
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OBBitVec can by dynamically resized, and have a number of overloaded |
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operators that make code simple and readable. The following examples |
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demonstrate uses of the OBBitVec class: |
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\code |
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OBBitVec bv1,bv2,bv3; |
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bv1.SetBitOn(5); |
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bv2.SetBitOff(200); |
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bv1 |= bv2; |
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bv1 = bv1 & bv2; |
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if (bv1.Empty()) //Empty() returns true if no bits are set on |
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{ |
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cout << "bv1 = " << bv1 << endl; |
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} |
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|
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int bit; |
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for (bit = bv1.NextBit(0);bit != bv1.EndBit();bit = bv1.NextBit(bit)) |
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{ |
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cout << "the next bit turned on is " << bit << endl; |
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} |
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\endcode |
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*/ |
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|
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static int bitsoff[SETWORD] = |
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{ |
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0xFFFFFFFF,0xFFFFFFFE,0xFFFFFFFC,0xFFFFFFF8,0xFFFFFFF0,0xFFFFFFE0,0xFFFFFFC0, |
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0xFFFFFF80,0xFFFFFF00,0xFFFFFE00,0xFFFFFC00,0xFFFFF800,0xFFFFF000,0xFFFFE000, |
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0xFFFFC000,0xFFFF8000,0xFFFF0000,0xFFFE0000,0xFFFC0000,0xFFF80000,0xFFF00000, |
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0xFFE00000,0xFFC00000,0xFF800000,0xFF000000,0xFE000000,0xFC000000,0xF8000000, |
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0xF0000000,0xE0000000,0xC0000000,0x80000000 |
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}; |
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|
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#ifndef LowBit |
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#define LowBit(set, bit)\ |
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{register int m;\ |
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if (set != 0)\ |
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{\ |
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bit = 31;\ |
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if (set != 0x80000000) {\ |
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if ((m = (set & 0x0000ffff))) {set = m; bit -= 16;}\ |
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if ((m = (set & 0x00ff00ff))) {set = m; bit -= 8;}\ |
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if ((m = (set & 0x0f0f0f0f))) {set = m; bit -= 4;}\ |
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if ((m = (set & 0x33333333))) {set = m; bit -= 2;}\ |
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if ((m = (set & 0x55555555))) {set = m; bit -= 1;}}}\ |
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else bit = -1;} |
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#endif |
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|
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OBBitVec::OBBitVec(const OBBitVec &bv) |
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{ |
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_size = 0; |
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(*this) = bv; |
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} |
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|
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void OBBitVec::SetBitOn(int bit) |
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{ |
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int word = bit/SETWORD; |
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bit = bit%SETWORD; |
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|
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//if (word+1 >= GetSize()) Resize((word+1)*SETWORD); |
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if (word >= _size) |
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Resize((word+1)*SETWORD); |
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_set[word] |= (1<<bit); |
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} |
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|
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void OBBitVec::SetRangeOn(int lobit, int hibit) |
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{ |
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int i; |
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|
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if (lobit > hibit) |
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return; |
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else if (lobit == hibit) |
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SetBitOn(hibit); |
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else |
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{ |
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int loword = lobit / SETWORD; |
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int hiword = hibit / SETWORD; |
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int lobitp = lobit % SETWORD; |
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int hibitp = hibit % SETWORD; |
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|
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if (hiword >= _size) |
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Resize((hiword+1) * SETWORD); |
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|
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if (loword == hiword) |
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{ |
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for ( i = lobitp ; i <= hibitp ; i++ ) |
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_set[loword] |= (1<<i); |
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} |
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else |
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{ |
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for ( i = lobitp ; i < SETWORD ; i++ ) |
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_set[loword] |= (1<<i); |
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for ( i = loword + 1 ; i < hiword ; i++ ) |
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_set[i] = 0xFFFFFFFF; |
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for ( i = 0 ; i <= hibitp ; i++ ) |
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_set[hiword] |= (1<<i); |
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} |
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} |
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} |
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|
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void OBBitVec::SetBitOff(int bit) |
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{ |
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int word = bit/SETWORD; |
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bit = bit%SETWORD; |
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_set[word] &= (~(1 << bit)); |
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} |
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|
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void OBBitVec::SetRangeOff(int lobit, int hibit) |
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{ |
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int i; |
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|
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if (lobit > hibit) |
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return; |
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else if (lobit == hibit) |
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SetBitOff(hibit); |
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else |
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{ |
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int loword = lobit / SETWORD; |
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int hiword = hibit / SETWORD; |
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int lobitp = lobit % SETWORD; |
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int hibitp = hibit % SETWORD; |
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|
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if (hiword >= _size) |
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{ |
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hiword = _size - 1; |
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hibitp = SETWORD - 1; |
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} |
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|
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if (loword == hiword) |
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{ |
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for ( i = lobitp ; i <= hibitp ; i++ ) |
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_set[loword] &= (~(1<<i)); |
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} |
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else |
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{ |
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for ( i = lobitp ; i < SETWORD ; i++ ) |
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_set[loword] &= (~(1<<i)); |
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for ( i = loword + 1 ; i < hiword ; i++ ) |
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_set[i] = 0x00000000; |
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for ( i = 0 ; i <= hibitp ; i++ ) |
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_set[hiword] &= (~(1<<i)); |
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} |
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} |
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} |
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|
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int OBBitVec::NextBit(int last) |
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{ |
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unsigned s; |
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register int bit,wrdcnt; |
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last++; |
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|
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wrdcnt = last/SETWORD; |
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|
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if (wrdcnt >= _size) |
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return(-1); |
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|
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if (_set[wrdcnt] != 0) |
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{ |
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s = (_set[wrdcnt]) & bitsoff[last - (wrdcnt*SETWORD)]; |
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if (s) |
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{ |
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LowBit(s,bit); |
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if (bit != -1) |
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return(bit + (wrdcnt*SETWORD)); |
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} |
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} |
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wrdcnt++; |
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|
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while(wrdcnt < _size) |
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{ |
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if (this->_set[wrdcnt] != 0) |
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{ |
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s = this->_set[wrdcnt]; |
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LowBit(s, bit); |
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|
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if (bit != -1) |
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return(bit+(wrdcnt*SETWORD)); |
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} |
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wrdcnt++; |
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} |
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|
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return(-1); |
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} |
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|
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bool OBBitVec::Resize(int maxbits) |
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{ |
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if(!maxbits) |
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return(false); |
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unsigned int maxword = maxbits/SETWORD; |
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if (maxbits%SETWORD) |
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maxword++; |
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if (maxword >= _set.size()) |
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{ |
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_set.resize(maxword); |
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_size = _set.size(); |
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} |
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|
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return(true); |
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} |
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|
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OBBitVec &OBBitVec::operator= (const OBBitVec &bv) |
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{ |
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if (_size != bv._size) |
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Resize(bv._size*SETWORD); |
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|
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int i; |
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for ( i = 0 ; i < bv._size ; i++ ) |
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_set[i] = bv._set[i]; |
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for ( ; i < _size ; i++ ) |
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_set[i] = 0; |
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|
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return(*this); |
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} |
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|
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OBBitVec &OBBitVec::operator&= ( OBBitVec &bv) |
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{ |
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int i; |
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int min = (bv._size < _size) ? bv._size : _size; |
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|
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for (i = 0;i < min;i++) |
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_set[i] &= bv._set[i]; |
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for (;i < _size;i++) |
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_set[i] = 0; |
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|
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return(*this); |
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} |
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|
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OBBitVec &OBBitVec::operator|= (OBBitVec &bv) |
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{ |
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if (_size != bv._size) |
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{ |
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if (_size < bv._size) |
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Resize(bv._size*SETWORD); |
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else |
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bv.Resize(_size*SETWORD); |
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} |
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for (int i = 0;i < _size;i++) |
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_set[i] |= bv._set[i]; |
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|
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return(*this); |
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} |
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|
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OBBitVec &OBBitVec::operator^= (OBBitVec &bv) |
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{ |
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int i; |
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if (_size != bv._size) |
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{ |
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if (_size < bv._size) |
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Resize(bv._size*SETWORD); |
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else |
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bv.Resize(_size*SETWORD); |
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} |
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for (i = 0;i < _size;i++) |
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_set[i] ^= bv._set[i]; |
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|
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return(*this); |
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} |
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|
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OBBitVec &OBBitVec::operator-= (OBBitVec &bv) |
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{ |
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if (GetSize() != bv._size) |
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obErrorLog.ThrowError(__func__, "Subtracting sets of != size", obDebug); |
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else |
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{ |
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OBBitVec tmp; |
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tmp = *this ^ bv; |
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*this &= tmp; |
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} |
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return(*this); |
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} |
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|
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OBBitVec &OBBitVec::operator+= (OBBitVec &bv) |
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{ |
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int old_size = _size; |
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Resize(_size*SETWORD+bv._size*SETWORD); |
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for (int i = 0;i < bv._size;i++) |
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_set[i+old_size] = bv._set[i]; |
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return(*this); |
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} |
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|
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OBBitVec operator| (OBBitVec &bv1,OBBitVec &bv2) |
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{ |
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OBBitVec bv; |
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bv = bv1; |
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bv |= bv2; |
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|
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return(bv); |
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} |
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|
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OBBitVec operator& (OBBitVec &bv1, OBBitVec &bv2) |
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{ |
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OBBitVec bv; |
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bv = bv1; |
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bv &= bv2; |
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|
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return(bv); |
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} |
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|
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OBBitVec operator^ (OBBitVec &bv1, OBBitVec &bv2) |
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{ |
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OBBitVec bv; |
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bv = bv1; |
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bv ^= bv2; |
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return(bv); |
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} |
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|
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bool operator== (const OBBitVec &bv1,const OBBitVec &bv2) |
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{ |
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if (bv1._size != bv2._size) |
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return(false); |
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|
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int i; |
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for (i = 0;i < bv1._size;i++) |
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if (bv1._set[i] != bv2._set[i]) |
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return(false); |
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|
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return(true); |
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} |
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|
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OBBitVec operator- (OBBitVec &bv1,OBBitVec &bv2) |
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{ |
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OBBitVec bv; |
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bv = bv1 ^ bv2; |
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bv &= bv1; |
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return(bv); |
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} |
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|
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istream& operator>> ( istream &is, OBBitVec &bv ) |
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{ |
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size_t startpos = 0, endpos = 0; |
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vector<string> tokens; |
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string line; |
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|
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getline(is,line); |
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|
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for (;;) |
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{ |
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startpos = line.find_first_not_of(" \t\n",startpos); |
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endpos = line.find_first_of(" \t\n",startpos); |
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|
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if (endpos < line.size() && startpos <= line.size()) |
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tokens.push_back(line.substr(startpos,endpos-startpos)); |
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else |
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break; |
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|
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startpos = endpos + 1; |
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} |
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|
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for (unsigned int i = 0 ; i < tokens.size() ; i++ ) |
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{ |
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if ( tokens[i] == "[" ) |
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continue; |
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else if ( tokens[i] == "]" ) |
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break; |
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|
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int bit = atoi(tokens[i].c_str()); |
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|
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if (bit >= 0) |
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bv.SetBitOn(bit); |
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else |
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{ |
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#ifdef HAVE_SSTREAM |
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stringstream errorMsg; |
| 397 |
#else |
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strstream errorMsg; |
| 399 |
#endif |
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errorMsg << "Negative Bit: " << bit << endl; |
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obErrorLog.ThrowError(__func__, errorMsg.str(), obDebug); |
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} |
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} |
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|
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return is; |
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} |
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|
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ostream& operator<< ( ostream &os, const OBBitVec& bv) |
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{ |
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os << "[ " << flush; |
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|
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int i,j; |
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for (i = 0;i < bv._size;i++) |
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for (j = 0;j < SETWORD;j++) |
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if (bv._set[i]>>(j%SETWORD)&1) |
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os << (j+(i*SETWORD)) << ' ' << flush; |
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|
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os << "]" << flush; |
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return(os); |
| 420 |
} |
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|
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void OBBitVec::Fold(int nbits) |
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{ |
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int nwords = nbits/SETWORD; |
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|
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if (_size < nwords) |
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{ |
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_set.resize(nwords); |
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_size = nwords; |
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return; |
| 431 |
} |
| 432 |
|
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int i,idx = nwords; |
| 434 |
for (i = 0,idx=nwords;idx < _size;idx++) |
| 435 |
{ |
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_set[i] |= _set[idx]; |
| 437 |
if (i+1 < nwords) |
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i++; |
| 439 |
else |
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i = 0; |
| 441 |
} |
| 442 |
_set.resize(nwords); |
| 443 |
_size = nwords; |
| 444 |
} |
| 445 |
|
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void OBBitVec::FromVecInt(vector<int> &v) |
| 447 |
{ |
| 448 |
vector<int>::iterator i; |
| 449 |
int max = 0; |
| 450 |
|
| 451 |
for (i = v.begin();i != v.end();i++) |
| 452 |
if (*i > max) |
| 453 |
max = *i; |
| 454 |
|
| 455 |
Resize(max/SETWORD); |
| 456 |
for (i = v.begin();i != v.end();i++) |
| 457 |
SetBitOn(*i); |
| 458 |
} |
| 459 |
|
| 460 |
void OBBitVec::FromString(string &line, int bits) |
| 461 |
{ |
| 462 |
size_t startpos = 0, endpos = 0; |
| 463 |
vector<string> tokens; |
| 464 |
|
| 465 |
Resize(bits); |
| 466 |
Clear(); |
| 467 |
|
| 468 |
for (;;) |
| 469 |
{ |
| 470 |
startpos = line.find_first_not_of(" \t\n",startpos); |
| 471 |
endpos = line.find_first_of(" \t\n",startpos); |
| 472 |
|
| 473 |
if (endpos < line.size() && startpos <= line.size()) |
| 474 |
tokens.push_back(line.substr(startpos,endpos-startpos)); |
| 475 |
else |
| 476 |
break; |
| 477 |
|
| 478 |
startpos = endpos + 1; |
| 479 |
} |
| 480 |
|
| 481 |
for (unsigned int i = 0 ; i < tokens.size() ; i++ ) |
| 482 |
{ |
| 483 |
if ( tokens[i] == "[" ) |
| 484 |
continue; |
| 485 |
else if ( tokens[i] == "]" ) |
| 486 |
break; |
| 487 |
|
| 488 |
int bit = atoi(tokens[i].c_str()); |
| 489 |
|
| 490 |
if (bit >= 0) |
| 491 |
SetBitOn(bit); |
| 492 |
else |
| 493 |
{ |
| 494 |
#ifdef HAVE_SSTREAM |
| 495 |
stringstream errorMsg; |
| 496 |
#else |
| 497 |
strstream errorMsg; |
| 498 |
#endif |
| 499 |
errorMsg << "Negative Bit: " << bit << endl; |
| 500 |
obErrorLog.ThrowError(__func__, errorMsg.str(), obDebug); |
| 501 |
} |
| 502 |
} |
| 503 |
} |
| 504 |
|
| 505 |
void OBBitVec::ToVecInt(vector<int> &v) |
| 506 |
{ |
| 507 |
v.clear(); |
| 508 |
v.reserve(CountBits()); |
| 509 |
for (int i = NextBit(-1);i != -1;i = NextBit(i)) |
| 510 |
v.push_back(i); |
| 511 |
} |
| 512 |
|
| 513 |
void OBBitVec::Clear() |
| 514 |
{ |
| 515 |
vector<int>::iterator i; |
| 516 |
for (i = _set.begin();i != _set.end();i++) |
| 517 |
*i = 0; |
| 518 |
} |
| 519 |
|
| 520 |
int OBBitVec::CountBits() |
| 521 |
{ |
| 522 |
int i,count=0; |
| 523 |
for (i = NextBit(-1);i != -1;i = NextBit(i)) |
| 524 |
count++; |
| 525 |
|
| 526 |
return(count); |
| 527 |
} |
| 528 |
|
| 529 |
bool OBBitVec::IsEmpty() |
| 530 |
{ |
| 531 |
vector<int>::iterator i; |
| 532 |
for (i = _set.begin();i != _set.end();i++) |
| 533 |
if (*i) |
| 534 |
return(false); |
| 535 |
|
| 536 |
return(true); |
| 537 |
} |
| 538 |
|
| 539 |
double Tanimoto(OBBitVec &bv1,OBBitVec &bv2) |
| 540 |
{ |
| 541 |
OBBitVec bvtmp; |
| 542 |
double andbits,orbits; |
| 543 |
|
| 544 |
bvtmp = bv1 & bv2; |
| 545 |
andbits = (double)bvtmp.CountBits(); |
| 546 |
bvtmp = bv1 | bv2; |
| 547 |
orbits = (double)bvtmp.CountBits(); |
| 548 |
|
| 549 |
return(andbits/orbits); |
| 550 |
} |
| 551 |
|
| 552 |
} // end namespace OpenBabel |
| 553 |
|
| 554 |
//! \file bitvec.cpp |
| 555 |
//! \brief Fast and efficient bitstring class |
| 556 |
|
