int main(){
makeFileCopy("tests.log", "temp.txt");
//================================================================================
header("File Loading");
ExpHourCalc *expHourCalc = new ExpHourCalc();
GatheringLog *gatheringLog = new GatheringLog();
LogFileParser *fileNotExist = new LogFileParser("sdlfkjskldfj");
doTest("LogFileParser with invalid logfile input", fileNotExist->isOK, false);
LogFileParser *parser = new LogFileParser("temp.txt");
parser->setExpHourCalc(expHourCalc);
parser->setGatheringLog(gatheringLog);
doTest("LogFileParser with valid logfile", parser->isOK, true);
//ExpHourCalc *failtest = new ExpHourCalc("sldfkjslkdfj");
//doTest("ExpHourCalc init failtest", failtest->isOK, false);
//ExpHourCalc *expHourCalc = new ExpHourCalc("temp.txt");
//doTest("ExpHourCalc init expHourCalc", expHourCalc->isOK, true);
doTest("Level 1 exp", expHourCalc->getExpChartEntry(1), 400);
doTest("Level 65 exp", expHourCalc->getExpChartEntry(65), 584561235);
//================================================================================
header("XP / AP Gain");
expHourCalc->start(-1, -1, -1);
appendFile("temp.txt", "2013.06.27 23:35:36 : Critical Hit!You inflicted 944 damage on Wori by using Righteous Punishment I. ");
appendFile("temp.txt", "2013.06.27 23:35:36 : You have gained 1,008 Abyss Points. ");
appendFile("temp.txt", "2013.06.27 23:35:36 : You have gained 8,867 XP from Wori. ");
appendFile("temp.txt", "2013.06.27 23:35:36 : You have defeated Wori. ");
appendFile("temp.txt", "2013.06.27 23:35:36 : Invalid target. ");
parser->processLines();
cout << endl << "No level, xp, or ap input" << endl;
doTest("exp: ", expHourCalc->expGained, 8867);
//doTest("formatted exp display", expHour
cout << endl << "XP + AP gain" << endl;
doTest("XP: ", expHourCalc->expGained, 8867);
doTest("AP: ", expHourCalc->apGained, 1008);
doTest("last tick XP", expHourCalc->lastExpPacket, 8867);
doTest("last tick AP", expHourCalc->lastApPacket, 1008);
doTest("lastTickHasChanges is true", expHourCalc->lastTickHasChanges, true);
doTest("numExpPacketsOnLastChange", expHourCalc->numExpPacketsOnLastChange, 1);
doTest("numApPacketsOnLastChange", expHourCalc->numApPacketsOnLastChange, 1);
doTest("currentExp", expHourCalc->currentExp, -1);
doTest("currentAp", expHourCalc->currentExp, -1);
doTest("getLastExpPacketPercent", expHourCalc->getLastExpPacketPercent(), 0);
doTest("getLastApPacketPercent", expHourCalc->getLastApPacketPercent(), 0);
doTest("getExpChartEntry", expHourCalc->getExpChartEntry(expHourCalc->level), -1);
doTest("getNextRankAp", expHourCalc->getNextRankAp(), -1);
cout << endl << "Quest EXP with repose" << endl;
appendFile("temp.txt", "2013.06.27 22:17:33 : Roadhouse recovered 183 MP due to the effect of Strong Instant Recovery. ");
appendFile("temp.txt", "2013.06.27 22:17:34 : You have gained 20,052,999 XP from Vard (Energy of Repose 10,405). ");
appendFile("temp.txt", "2013.06.27 22:17:34 : Quest complete: Kata-where? ");
appendFile("temp.txt", "2013.06.27 22:17:34 : Quest updated: For the Dead ");
parser->processLines();
doTest("exp gained: ", expHourCalc->expGained, 20052999 + 8867);
doTest("repose consumed: ", expHourCalc->reposeExp, 10405);
doTest("currentExp", expHourCalc->currentExp, -1);
doTest("getLastExpPacketPercent", expHourCalc->getLastExpPacketPercent(), 0);
cout << endl << "Strong repose" << endl;
expHourCalc->reset();
appendFile("temp.txt", "2013.06.27 22:17:34 : You have gained 200,000 XP from Vard (Strong Energy of Repose 100,000). ");
parser->processLines();
doTest("Strong exp gained: ", expHourCalc->expGained, 200000);
doTest("Strong repose consumed: ", expHourCalc->reposeExp, 100000);
//================================================================================
header("Repose + salvation");
expHourCalc->reset();
expHourCalc->level = 20;
expHourCalc->expGained = 5000;
expHourCalc->currentExp = 12000;
appendFile("temp.txt", "2013.06.26 22:05:44 : You have gained 15,411 XP from Studio Butler (Energy of Repose 3,626, Energy of Salvation 2,719).");
parser->processLines();
doTest("current exp: ", expHourCalc->currentExp, 27411);
doTest("exp gained: ", expHourCalc->expGained, 20411);
doTest("repose consumed: ", expHourCalc->reposeExp, 3626);
doTest("salvation consumed: ", expHourCalc->salvationExp, 2719);
doTest("lastTickHasChanges is true", expHourCalc->lastTickHasChanges, true);
doTest("numExpPacketsOnLastChange", expHourCalc->numExpPacketsOnLastChange, 1);
doTest("numApPacketsOnLastChange", expHourCalc->numApPacketsOnLastChange, 0);
expHourCalc->reset();
cout << endl << "Strong Repose + salvation" << endl;
appendFile("temp.txt", "2013.06.26 22:05:44 : You have gained 23,000 XP from Studio Butler (Strong Energy of Repose 10,000, Energy of Salvation 3,000).");
parser->processLines();
doTest("exp gained: ", expHourCalc->expGained, 23000);
doTest("strong repose consumed: ", expHourCalc->reposeExp, 10000);
doTest("salvation consumed: ", expHourCalc->salvationExp, 3000);
expHourCalc->reset();
cout << endl << "Salvation only" << endl;
appendFile("temp.txt", "2013.06.26 22:05:44 : You have gained 13.000.000 XP from s u p e r c h a r g e d (Energy of Salvation 3.000.000).");
parser->processLines();
doTest("exp gained: ", expHourCalc->expGained, 13000000);
doTest("salvation consumed: ", expHourCalc->salvationExp, 3000000);
appendFile("temp.txt", "2013.06.26 22:05:44 : You have gained 6666 XP from f*****g piece of shit (Energy of Salvation 666).");
parser->processLines();
doTest("Additional salvation consumed: ", expHourCalc->salvationExp, 3000000 + 666);
//================================================================================
expHourCalc->reset();
header("With level and starting exp, gathering");
expHourCalc->level = 20;
expHourCalc->currentExp = 12000;
appendFile("temp.txt", "2013.07.29 23:55:28 : You have started gathering Ancient Aether.");
appendFile("temp.txt", "2013.07.02 01:25:12 : You have acquired [item:152000916;ver4;;;;]. ");
appendFile("temp.txt", "2013.07.02 01:25:12 : You have gained 7,580 XP. ");
appendFile("temp.txt", "2013.07.02 01:25:12 : You have gained experience from gathering. ");
appendFile("temp.txt", "2013.07.02 01:25:12 : You have started gathering Pure Ancient Aether. ");
parser->processLines();
doTest("new exp value: ", expHourCalc->currentExp, 19580);
doTest("new exp gained: ", expHourCalc->expGained, 7580);
expHourCalc->reset();
header("Level up exp rollover");
expHourCalc->level = 5;
expHourCalc->currentExp = 7000;
appendFile("temp.txt", "2013.06.27 22:17:34 : You have gained 2,000 XP from Vard.");
parser->processLines();
doTest("char exp", expHourCalc->currentExp, 7000 + 2000 - 8601);
doTest("total exp gained", expHourCalc->expGained, 2000);
doTest("char lvl", expHourCalc->level, 6);
//================================================================================
header("Pre ascension exp waste");
expHourCalc->reset();
expHourCalc->level = 9;
expHourCalc->currentExp = 10000;
appendFile("temp.txt", "2013.06.28 09:42:49 : Quest updated: Ascension ");
appendFile("temp.txt", "2013.06.28 09:42:49 : You have learned the Essencetapping skill. ");
appendFile("temp.txt", "2013.06.28 09:42:49 : You have learned the Morph Substances skill. ");
appendFile("temp.txt", "2013.06.28 09:42:49 : You have learned [recipe_ex:155005001;DeleteAfterAscen-IS]. ");
appendFile("temp.txt", "2013.06.28 09:42:49 : You have learned [recipe_ex:155005002;DeleteAfterAscen-IS]. ");
appendFile("temp.txt", "2013.06.28 09:42:49 : You have learned [recipe_ex:155005005;DeleteAfterAscen-IS]. ");
appendFile("temp.txt", "2013.06.28 09:42:49 : You have learned the Aethertapping skill. ");
appendFile("temp.txt", "2013.06.28 09:42:50 : [3.LFG] [charname:Onimushaz-SL;1.0000 0.6941 0.6941]: [cmd:rGSlNwGJGRxRQv03cJhj8zmbH1pS5sI2+Ojm4GyCo/tFUYOZnylZ5HCClET+4/tCS7qtaOGT6oZDfpuNO+D18g==]Adma Rush Need Cleric at Lannok ");
appendFile("temp.txt", "2013.06.28 09:42:57 : [3.LFG] [charname:Draizon-KR;1.0000 0.6941 0.6941]: [cmd:ZuRJ77suA3HGXknXXvlwhpPM8QnGQsOkmk/KeMfcfBdFUYOZnylZ5HCClET+4/tC4UL+Ir0PulB5jOt1gqsgzQ==]NTC need all! ");
appendFile("temp.txt", "2013.06.28 09:43:01 : [3.LFG] [charname:Demolize-TM;1.0000 0.6941 0.6941]: [cmd:P4LwuGgTZY+ycKKEACMJvuAyWLtXF0rdZGbvQ8Z9+DdFUYOZnylZ5HCClET+4/tCg5pior9yCPYe0vyEXekmgw==]?BT?NEED ALL 59+ ?? Hard Mode ");
appendFile("temp.txt", "2013.06.28 09:43:04 : You have gained 73,200 XP from Munin. ");
appendFile("temp.txt", "2013.06.28 09:43:04 : You can advance to level 10 only after you have completed the class change quest. ");
parser->processLines();
doTest("char exp", expHourCalc->currentExp, 43087);
doTest("char level", expHourCalc->level, 9);
doTest("exp gained", expHourCalc->expGained, 33087);
expHourCalc->currentExp = 43087;
appendFile("temp.txt", "2013.06.27 22:17:34 : You have gained 2,000 XP from Vard.");
appendFile("temp.txt", "2013.06.27 09:43:04 : You can advance to level 10 only after you have completed the class change quest. ");
parser->processLines();
doTest("char exp", expHourCalc->currentExp, 43087);
doTest("char level", expHourCalc->level, 9);
cout << endl << "Ascended" << endl;
appendFile("temp.txt", "2013.06.27 22:17:34 : You have gained 2,000 XP from Vard.");
parser->processLines();
doTest("char exp", expHourCalc->currentExp, 2000);
doTest("char level", expHourCalc->level, 10);
//================================================================================
header("Fast Track Server level cap exp waste");
expHourCalc->reset();
expHourCalc->level = 55;
expHourCalc->currentExp = 103225345;
appendFile("temp.txt", "2013.09.23 22:26:04 : You have used Inggison Illusion Fortress Scroll. ");
appendFile("temp.txt", "2013.09.23 22:26:13 : aasfer-IS was affected by its own Aion's Favor I. ");
appendFile("temp.txt", "2013.09.23 22:26:15 : Quest updated: [Coin] For the Scholars ");
appendFile("temp.txt", "2013.09.23 22:26:20 : You have acquired 5 [item:186000018;ver4;;;;]s and stored them in your special cube. ");
appendFile("temp.txt", "2013.09.23 22:26:20 : You have gained 4,186,683 XP from Eduardo. ");
appendFile("temp.txt", "2013.09.23 22:26:20 : You cannot be Level 56 on the Fast-Track Server. ");
appendFile("temp.txt", "2013.09.23 22:26:20 : Quest complete: [Coin] For the Scholars ");
parser->processLines();
doTest("char exp", expHourCalc->currentExp, 104225345);
doTest("char level", expHourCalc->level, 55);
doTest("exp gained", expHourCalc->expGained, 1000000);
//================================================================================
header("Level cap exp waste");
expHourCalc->reset();
expHourCalc->level = 65;
expHourCalc->currentExp = 10000000;
appendFile("temp.txt", "2013.06.27 22:17:34 : You have gained 20,052,999 XP from Vard (Energy of Repose 10,405). ");
parser->processLines();
doTest("char exp", expHourCalc->currentExp, 30052999);
doTest("exp gained", expHourCalc->expGained, 20052999);
doTest("last exp packet", expHourCalc->lastExpPacket, 20052999);
doTest("char level", expHourCalc->level, 65);
doTest("repose consumed", expHourCalc->reposeExp, 10405);
expHourCalc->reset();
expHourCalc->level = 65;
expHourCalc->currentExp = 584561235;
appendFile("temp.txt", "2013.06.27 22:17:34 : You have gained 20,052,999 XP from Vard (Energy of Repose 10,405). ");
parser->processLines();
doTest("char exp", expHourCalc->currentExp, 584561235);
doTest("exp gained", expHourCalc->expGained, 0);
doTest("last exp packet", expHourCalc->lastExpPacket, 20052999);
doTest("char level", expHourCalc->level, 65);
doTest("repose consumed", expHourCalc->reposeExp, 10405);
//================================================================================
header("Soul Healing / EXP loss on death");
expHourCalc->reset();
//lv 13
//61581 xp
//die
//58595
//551 zeny
//gain 2171
//60766 xp
//60766
//57510
//59681
//lv 43
//21,016,061
//die
//20,648,891
//18022 zeny
//gain 244780
//20,893,671
cout << "lv 13 exp 61851" << endl;
expHourCalc->level = 13;
expHourCalc->currentExp = 61851;
appendFile("temp.txt","2013.06.27 23:03:19 : You are no longer bleeding. ");
appendFile("temp.txt","2013.06.27 23:03:19 : You have died. ");
parser->processLines();
doTest("Died to a monster, most likely XP lost, needExpUpdate is true", expHourCalc->needExpUpdate, true);
doTest("needApUpdate is false unless there was no XP loss", expHourCalc->needApUpdate, false);
appendFile("temp.txt", "2013.07.04 18:15:04 : You spent 551 Kinah.");
appendFile("temp.txt", "2013.07.04 18:15:04 : You have gained 2,171 XP. ");
appendFile("temp.txt", "2013.07.04 18:15:04 : You received Soul Healing. ");
parser->processLines();
doTest("exp change:", expHourCalc->lastExpPacket, -1085);
doTest("exp after:", expHourCalc->currentExp, 60766);
doTest("zeny spent:", expHourCalc->cashSpent, 551);
doTest("last zeny transaction:", expHourCalc->lastCashTransaction, -551);
doTest("Soul healing done, needExpUpdate is false", expHourCalc->needExpUpdate, false);
doTest("lastTickHasChanges is true", expHourCalc->lastTickHasChanges, true);
doTest("expLostToDeaths", expHourCalc->expLostToDeaths, 1085 + 2171);
expHourCalc->reset();
cout << "lv 43 exp 21016061" << endl;
expHourCalc->level = 43;
expHourCalc->currentExp = 21016061;
appendFile("temp.txt","2013.06.27 23:03:19 : You have died. ");
appendFile("temp.txt", "2013.07.04 18:40:23 : You spent 18,022 Kinah. ");
appendFile("temp.txt", "2013.07.04 18:40:23 : You have gained 244,780 XP. ");
appendFile("temp.txt", "2013.07.04 18:40:23 : You received Soul Healing.");
parser->processLines();
doTest("exp change:", expHourCalc->lastExpPacket, -122390);
doTest("exp gained so far:", expHourCalc->expGained, -122390);
doTest("exp after:", expHourCalc->currentExp, 20893671);
doTest("zeny spent:", expHourCalc->cashSpent, 18022);
doTest("last zeny transaction:", expHourCalc->lastCashTransaction, -18022);
appendFile("temp.txt","2013.06.27 23:03:19 : You have died. ");
appendFile("temp.txt", "2013.07.04 18:40:23 : You spent 18,022 Kinah. ");
appendFile("temp.txt", "2013.07.04 18:40:23 : You have gained 244,780 XP. ");
appendFile("temp.txt", "2013.07.04 18:40:23 : You received Soul Healing.");
parser->processLines();
doTest("expLostToDeaths after 2 deaths", expHourCalc->expLostToDeaths, (244780 + 122390) * 2);
doTest("exp gained so far:", expHourCalc->expGained, -244780);
doTest("currentExp:", expHourCalc->currentExp, 20893671 - 122390);
//================================================================================
header("1 zeny soul healing -> PKed");
expHourCalc->reset();
expHourCalc->level = 43;
expHourCalc->currentExp = 21016061;
appendFile("temp.txt","2013.06.27 23:03:19 : You have died. ");
appendFile("temp.txt","2013.07.05 00:54:59 : Saamn recovered 183 MP due to the effect of Strong Instant Recovery. ");
appendFile("temp.txt","2013.07.05 00:54:59 : You have resurrected. ");
appendFile("temp.txt","2013.07.05 00:55:02 : [3.LFG] [charname:ImSoBucci;1.0000 0.6941 0.6941]: [cmd:0cWaGV/kjHuy7eO6sQkkLIOFT2cFnzucw1Y29SlJmwZFUYOZnylZ5HCClET+4/tCGl2bZjvYqe8X4QPegOqKKQ==]BTHM LF DPS,TANK,HEALS ");
appendFile("temp.txt","2013.07.05 00:55:04 : Demonjon restored 1,940 HP. ");
appendFile("temp.txt","2013.07.05 00:55:04 : Demonjon restored 357 MP. ");
appendFile("temp.txt","2013.07.05 00:55:09 : You spent 1 Kinah. ");
appendFile("temp.txt","2013.07.05 00:55:09 : You received Soul Healing. ");
appendFile("temp.txt","2013.07.05 00:55:11 : The weapon has been changed. ");
parser->processLines();
doTest("PK soul healing no exp loss check:", expHourCalc->currentExp, 21016061);
//================================================================================
header("Clear needExpUpdate if no XP to recover");
expHourCalc->reset();
expHourCalc->level = 44;
expHourCalc->currentExp = 10000000;
expHourCalc->expGained = 480752;
appendFile("temp.txt","2013.07.15 18:24:31 : You can see again ");
appendFile("temp.txt","2013.07.15 18:24:31 : You have died. ");
appendFile("temp.txt","2013.07.15 16:42:31 : You have resurrected. ");
appendFile("temp.txt","2013.07.13 17:11:07 : You do not have any XP to recover. ");
doTest("needExpUpdate", expHourCalc->needExpUpdate, false);
doTest("needApUpdate", expHourCalc->needApUpdate, false);
//================================================================================
header("Manual exp update - pve death");
expHourCalc->reset();
expHourCalc->level = 44;
expHourCalc->currentExp = 10000000;
expHourCalc->expGained = 480752;
appendFile("temp.txt","2013.06.27 20:21:33 : You cannot do that while you are in combat. ");
appendFile("temp.txt","2013.06.27 20:21:33 : You have died. ");
appendFile("temp.txt","2013.06.27 20:21:49 : You have resurrected. ");
appendFile("temp.txt","2013.06.27 20:21:49 : You cannot attack the enemy faction in this region. ");
appendFile("temp.txt","2013.06.27 20:22:00 : Suder inflicted 4,192 damage on Training Dummy by using Ritual Push I. ");
parser->processLines();
expHourCalc->updateExp(10000000 - 380752);
parser->processLines();
doTest("currentExp", expHourCalc->currentExp, 10000000 - 380752);
doTest("expGained", expHourCalc->expGained, 100000);
doTest("lastExpPacket", expHourCalc->lastExpPacket, -380752);
doTest("needExpUpdate", expHourCalc->needExpUpdate, false);
doTest("expLostToDeaths", expHourCalc->expLostToDeaths, 380752);
appendFile("temp.txt","2013.06.27 20:22:02 : You spent 28,259 Kinah. ");
appendFile("temp.txt","2013.06.27 20:22:02 : You have gained 719,902 XP. ");
appendFile("temp.txt","2013.06.27 20:22:02 : You received Soul Healing. ");
parser->processLines();
doTest("soul heal after manual exp update: currentExp", expHourCalc->currentExp, 10000000 - 380752 + 719902);
doTest("needExpUpdate is false", expHourCalc->needExpUpdate, false);
doTest("needApUpdate is false", expHourCalc->needApUpdate, false);
doTest("lastCashTransaction", expHourCalc->lastCashTransaction, -28259);
doTest("cashSpent", expHourCalc->cashSpent, 28259);
doTest("expLostToDeaths", expHourCalc->expLostToDeaths, 380752);
//================================================================================
header("Abyss Rank");
expHourCalc->currentAp = 1000;
doTest("9 kyu test", expHourCalc->getAbyssRankName(), "9 kyu");
expHourCalc->currentAp = 120000;
doTest("2 kyu test", expHourCalc->getAbyssRankName(), "2 kyu");
expHourCalc->currentAp = 200000;
doTest("200000 AP test", expHourCalc->getAbyssRankName(), "???");
expHourCalc->currentAp = 2000000000;
doTest("2 billion AP test", expHourCalc->getAbyssRankName(), "???");
//================================================================================
header("AP Spending");
expHourCalc->reset();
expHourCalc->currentAp = 95000;
expHourCalc->apGained = 95000;
expHourCalc->lastApPacket = 95000;
appendFile("temp.txt","2013.07.03 18:15:39 : Your Abyss Rank has changed to Soldier, Rank 7. ");
appendFile("temp.txt","2013.07.03 18:15:39 : You used 89,775 Abyss Points. ");
appendFile("temp.txt","2013.07.03 18:15:40 : [3.LFG] [charname:Vladarina;1.0000 0.6941 0.6941]: Asmos, we expect a LOT of elyos to attack [pos:Pradeth;600060000 2676.0 2720.2 0.0 0] tonight. I need everybody (even level 50s) I can get inside of that fort EARLY, before 11 pm est vuln (5 hours). Bind ");
appendFile("temp.txt","2013.07.03 18:15:40 : You have purchased [item:140000816;ver4;;;;]. ");
parser->processLines();
doTest("AP spent ", expHourCalc->apSpent, 89775);
doTest("AP after purchase", expHourCalc->currentAp, 5225);
doTest("AP gained after purchase", expHourCalc->apGained, 5225);
doTest("last AP Packet", expHourCalc->lastApPacket, -89775);
doTest("lastTickHasChanges is true", expHourCalc->lastTickHasChanges, true);
//================================================================================
header("Got PKed, need to ask for manual AP update");
expHourCalc->reset();
expHourCalc->currentAp = 100000;
appendFile("temp.txt","2013.07.05 16:15:18 : Tip: Elyos and Asmodians cannot fight one another in a neutral zone.");
appendFile("temp.txt","2013.07.05 16:15:18 : You may be unable to use certain skills or items in this area. ");
appendFile("temp.txt","2013.07.05 16:15:18 : A survey has arrived. Click the icon to open the survey window. ");
appendFile("temp.txt","2013.07.05 16:15:20 : You have joined Standard Server. ");
appendFile("temp.txt","2013.07.07 00:56:26 : You are no longer silenced. ");
appendFile("temp.txt","2013.07.07 00:56:26 : Your movement speed is restored to normal. ");
appendFile("temp.txt","2013.07.07 00:56:26 : Your attack speed is restored to normal. ");
appendFile("temp.txt","2013.07.07 00:56:26 : You were killed by Thomasbangalter's attack. ");
appendFile("temp.txt","2013.07.07 00:56:28 : Noble Energy inflicted 684 damage on Thomasbangalter by using Noble Energy IV. ");
appendFile("temp.txt","2013.07.07 00:56:28 : Thomasbangalter inflicted 733 damage on Devios by using Illusion Storm VII. ");
parser->processLines();
doTest("I'm on Standard Server", expHourCalc->getCurrentServer(), "Standard");
doTest("Got PKed in standard server, need ap update yes", expHourCalc->needApUpdate, true);
doTest("needExpUpdate needs to be false", expHourCalc->needExpUpdate, false);
expHourCalc->updateAp(95000);
appendFile("temp.txt","2013.06.27 23:03:26 : You have resurrected. ");
appendFile("temp.txt","2013.06.27 23:03:52 : You spent 1 Kinah. ");
appendFile("temp.txt","2013.06.27 23:03:52 : You received Soul Healing. ");
parser->processLines();
doTest("already updated AP, don't apupdate again", expHourCalc->needApUpdate, false);
appendFile("temp.txt","2013.07.07 00:56:26 : You were killed by Sogyawie's attack. ");
appendFile("temp.txt","2013.06.27 23:03:26 : You have resurrected. ");
appendFile("temp.txt","2013.06.27 23:03:52 : You spent 1 Kinah. ");
appendFile("temp.txt","2013.06.27 23:03:52 : You received Soul Healing. ");
parser->processLines();
doTest("Got PKed, didn't update AP, soul healed", expHourCalc->needApUpdate, true);
header("Got killed in structured PvP, no AP loss, don't ask for update");
expHourCalc->reset();
appendFile("temp.txt","2013.06.25 14:44:14 : You have item(s) left to settle at the Broker. ");
appendFile("temp.txt","2013.06.25 14:44:16 : You have joined the group. ");
appendFile("temp.txt","2013.06.25 14:44:16 : You have joined Instance Server. ");
appendFile("temp.txt","2013.06.25 14:44:21 : You have joined the Terath Dredgion region channel. ");
appendFile("temp.txt","2013.06.25 14:44:21 : You have joined the Terath Dredgion trade channel. ");
appendFile("temp.txt","2013.06.25 14:44:21 : You have joined the LFG Channel. ");
appendFile("temp.txt","2013.06.25 14:44:23 : Nekoh-IS has joined your group. ");
appendFile("temp.txt","2013.06.25 14:44:24 : You have joined the Templar Channel. ");
appendFile("temp.txt","2013.06.27 19:04:58 : You were killed by Mrplatino's attack.");
parser->processLines();
doTest("I'm on Instance Server", expHourCalc->getCurrentServer(), "Instance");
doTest("needApUpdate should be false", expHourCalc->needApUpdate, false);
header("Got killed in by mobster in structured PvP, manual EXP enter, no EXP or AP loss, don't ask for AP update");
expHourCalc->reset();
expHourCalc->level = 60;
expHourCalc->currentExp = 1234567;
appendFile("temp.txt","2013.06.25 14:44:14 : You have item(s) left to settle at the Broker. ");
appendFile("temp.txt","2013.06.25 14:44:16 : You have joined the group. ");
appendFile("temp.txt","2013.06.25 14:44:16 : You have joined Instance Server. ");
appendFile("temp.txt","2013.06.25 14:44:21 : You have joined the Terath Dredgion region channel. ");
appendFile("temp.txt","2013.06.25 14:44:21 : You have joined the Terath Dredgion trade channel. ");
appendFile("temp.txt","2013.06.25 14:44:21 : You have joined the LFG Channel. ");
appendFile("temp.txt","2013.06.25 14:44:23 : Nekoh-IS has joined your group. ");
appendFile("temp.txt","2013.06.25 14:44:24 : You have joined the Templar Channel. ");
appendFile("temp.txt","2013.06.27 19:04:58 : You have died. ");
parser->processLines();
expHourCalc->updateExp(1234567);
parser->processLines();
doTest("needApUpdate should be false", expHourCalc->needApUpdate, false);
doTest("lastTickHasChanges is true", expHourCalc->lastTickHasChanges, true);
doTest("expLostToDeaths", expHourCalc->expLostToDeaths, 0);
doTest("apLostToPk", expHourCalc->apLostToPk, 0);
appendFile("temp.txt","2013.07.05 16:15:20 : You have joined Standard Server. ");
appendFile("temp.txt","2013.06.27 23:03:19 : You are no longer bleeding. ");
appendFile("temp.txt","2013.06.27 23:03:19 : You have died. ");
parser->processLines();
header("Back to Standard Server, attacked by enemy faction player, finished blow from monster");
doTest("Don't know whether XP was lost or not - needExpUpdate is true", expHourCalc->needExpUpdate, true);
appendFile("temp.txt","2013.06.27 23:03:19 : You do not have much flight time left. Please land on a secure place. ");
appendFile("temp.txt","2013.06.27 23:03:19 : Pashid Offense Elite Fighter is in the boost Physical Def,Magical Defense state because Pashid Offense Elite Fighter used Conqueror's Passion. ");
appendFile("temp.txt","2013.06.27 23:03:19 : Pashid Offense Elite Protector is in the boost Physical Def,Magical Defense state because Pashid Offense Elite Protector used Conqueror's Passion. ");
appendFile("temp.txt","2013.06.27 23:03:20 : Pashid Offense Elite Archer is in the boost Physical Def,Magical Defense state because Pashid Offense Elite Archer used Conqueror's Passion. ");
appendFile("temp.txt","2013.06.27 23:03:20 : Pashid Offense Elite Archer is in the boost Physical Def,Magical Defense state because Pashid Offense Elite Archer used Conqueror's Passion. ");
appendFile("temp.txt","2013.06.27 23:03:20 : Pashid Offense Elite Archer is in the boost Physical Def,Magical Defense state because Pashid Offense Elite Archer used Conqueror's Passion. ");
appendFile("temp.txt","2013.06.27 23:03:24 : [charname:Gwc;0.6118 0.9059 0.8627]: gub ");
appendFile("temp.txt","2013.06.27 23:03:26 : You have resurrected. ");
appendFile("temp.txt","2013.06.27 23:03:50 : [charname:Mystfang;0.6118 0.9059 0.8627]: omg ");
appendFile("temp.txt","2013.06.27 23:03:52 : You spent 1 Kinah. ");
appendFile("temp.txt","2013.06.27 23:03:52 : You received Soul Healing. ");
parser->processLines();
doTest("1 zeny soul healing means u lost AP", expHourCalc->needApUpdate, true);
doTest("No EXP loss when you lost AP", expHourCalc->needExpUpdate, false);
doTest("Soul healing done, needExpUpdate is false", expHourCalc->needExpUpdate, false);
expHourCalc->currentExp = 100000;
expHourCalc->currentAp = 1000000;
header("Manual XP update, EXP unchanged (no exp loss) = possible AP loss");
appendFile("temp.txt","2013.06.27 23:03:19 : You are no longer bleeding. ");
appendFile("temp.txt","2013.06.27 23:03:19 : You have died. ");
parser->processLines();
expHourCalc->updateExp(100000);
parser->processLines();
doTest("needApUpdate", expHourCalc->needApUpdate, true);
doTest("clear needExpUpdate", expHourCalc->needExpUpdate, false);
doTest("lastTickHasChanges is true", expHourCalc->lastTickHasChanges, true);
expHourCalc->updateAp(999000);
parser->processLines();
doTest("After manual AP update, needExpUpdate false", expHourCalc->needExpUpdate, false);
doTest("After manual AP update, needApUpdate false", expHourCalc->needApUpdate, false);
doTest("current exp", expHourCalc->currentExp, 100000);
doTest("current ap", expHourCalc->currentAp, 999000);
doTest("last exp packet", expHourCalc->lastExpPacket, 0);
doTest("last ap packet", expHourCalc->lastApPacket, -1000);
doTest("expLostToDeaths", expHourCalc->expLostToDeaths, 0);
doTest("apLostToPk", expHourCalc->apLostToPk, 1000);
doTest("lastTickHasChanges is true", expHourCalc->lastTickHasChanges, true);
appendFile("temp.txt","2013.06.27 23:03:52 : You spent 1 Kinah. ");
appendFile("temp.txt","2013.06.27 23:03:52 : You received Soul Healing. ");
parser->processLines();
doTest("After manual AP update, soul healed, don't ask for AP update again", expHourCalc->needApUpdate, false);
//================================================================================
header("Promopt for AP update due to AP loss on death");
expHourCalc->reset();
expHourCalc->currentAp = 95000;
expHourCalc->apGained = 95000;
expHourCalc->lastApPacket = 1234;
appendFile("temp.txt","2013.06.27 19:04:58 : You were killed by Mrplatino's attack.");
parser->processLines();
cout << endl << "Invalid update" << endl;
expHourCalc->updateAp(95001);
parser->processLines();
doTest("currentAp after invalid update", expHourCalc->currentAp, 95000);
doTest("apGained after invalid update", expHourCalc->apGained, 95000);
doTest("lastApPacket after invalid update", expHourCalc->lastApPacket, 1234);
doTest("apLostToPk after invalid update", expHourCalc->apLostToPk, 0);
doTest("Still need ap update", expHourCalc->needApUpdate, true);
doTest("lastTickHasChanges is false", expHourCalc->lastTickHasChanges, false);
doTest("apLostToPk", expHourCalc->apLostToPk, 0);
cout << endl << "Valid update" << endl;
expHourCalc->updateAp(94500);
parser->processLines();
doTest("currentAp after getting PKed", expHourCalc->currentAp, 94500);
doTest("apGained after getting PKed", expHourCalc->apGained, 94500);
doTest("lastApPacket after getting PKed", expHourCalc->lastApPacket, -500);
doTest("apLostToPk after getting PKed", expHourCalc->apLostToPk, 500);
doTest("Still need ap update", expHourCalc->needApUpdate, false);
doTest("lastTickHasChanges is true", expHourCalc->lastTickHasChanges, true);
doTest("apLostToPk", expHourCalc->apLostToPk, 500);
header("Double deaths");
appendFile("temp.txt","2013.06.27 17:08:23 : You have gained 3,421,093 XP from Lumiden. ");
appendFile("temp.txt","2013.06.27 17:08:23 : You have gained 402 Abyss Points. ");
appendFile("temp.txt","2013.06.27 17:08:23 : You can receive the weekly quest again at 9 in the morning on Wednesday. ");
appendFile("temp.txt","2013.09.05 20:35:58 : You were killed by SteveForansi's attack.");
parser->processLines();
expHourCalc->updateAp(93602);
parser->processLines();
doTest("currentAp after getting PKed for second time", expHourCalc->currentAp, 93602);
doTest("apGained after getting PKed for second time", expHourCalc->apGained, 93602);
doTest("lastApPacket after getting PKed for second time", expHourCalc->lastApPacket, -1300);
doTest("apLostToPk", expHourCalc->apLostToPk, 1800);
doTest("Still need ap update", expHourCalc->needApUpdate, false);
doTest("lastTickHasChanges is true", expHourCalc->lastTickHasChanges, true);
cout << endl << "Reject inputs that exceed currentAP + apLostToPk" << endl;
appendFile("temp.txt","2013.09.05 20:35:58 : You were killed by V****a's attack.");
parser->processLines();
expHourCalc->updateAp(95403);
parser->processLines();
doTest("currentAp", expHourCalc->currentAp, 93602);
doTest("apGained ", expHourCalc->apGained, 93602);
doTest("lastApPacket", expHourCalc->lastApPacket, -1300);
doTest("apLostToPk", expHourCalc->apLostToPk, 1800);
doTest("Still need ap update", expHourCalc->needApUpdate, true);
doTest("lastTickHasChanges is true", expHourCalc->lastTickHasChanges, false);
expHourCalc->updateAp(95402);
parser->processLines();
cout << endl << "Allow manual updates up to currentAP + apLostToPk" << endl;
doTest("currentAp", expHourCalc->currentAp, 95402);
doTest("apGained ", expHourCalc->apGained, 95402);
doTest("lastApPacket", expHourCalc->lastApPacket, 1800);
doTest("apLostToPk", expHourCalc->apLostToPk, 0);
doTest("Still need ap update", expHourCalc->needApUpdate, false);
doTest("lastTickHasChanges is true", expHourCalc->lastTickHasChanges, true);
//================================================================================
header("AP not entered during startup");
expHourCalc->reset();
expHourCalc->level = 60;
expHourCalc->currentExp = 50000000;
expHourCalc->currentAp = -1;
expHourCalc->apGained = 95000;
expHourCalc->lastApPacket = 1234;
appendFile("temp.txt","2013.06.27 19:04:58 : You were killed by Mrplatino's attack.");
parser->processLines();
doTest("Still need ap update", expHourCalc->needApUpdate, false);
doTest("lastTickHasChanges is false", expHourCalc->lastTickHasChanges, false);
cout << endl << "Attacked by player, finishing blow by monster, soul healing" << endl;
appendFile("temp.txt","2013.06.27 23:03:19 : You have died. ");
appendFile("temp.txt","2013.06.27 23:03:52 : You spent 1 Kinah. ");
appendFile("temp.txt","2013.06.27 23:03:52 : You received Soul Healing. ");
parser->processLines();
doTest("Still need ap update", expHourCalc->needApUpdate, false);
doTest("lastTickHasChanges is false", expHourCalc->lastTickHasChanges, false);
cout << endl << "Attacked by player, finishing blow by monster, manual exp update" << endl;
appendFile("temp.txt","2013.06.27 23:03:19 : You have died. ");
parser->processLines();
expHourCalc->updateExp(50000000);
parser->processLines();
doTest("don't need exp update", expHourCalc->needExpUpdate, false);
doTest("Still need ap update", expHourCalc->needApUpdate, false);
doTest("lastTickHasChanges is false", expHourCalc->lastTickHasChanges, true);
//================================================================================
header("Blood Marks and AP Relics");
expHourCalc->reset();
expHourCalc->currentAp = 10000;
expHourCalc->apGained = 1000;
appendFile("temp.txt","2013.07.23 12:32:19 : You have acquired [item:186000066;ver4;;;;]. ");
appendFile("temp.txt","2013.07.23 12:32:19 : You have acquired 2 [item:162000120;ver4;;;;](s). ");
parser->processLines();
doTest("currentAP after lesser icon", expHourCalc->currentAp, 10000);
doTest("apGained after lesser icon", expHourCalc->apGained, 1000);
doTest("relicAp after lesser icon", expHourCalc->relicAp, 315);
appendFile("temp.txt","2013.07.22 17:19:53 : Quest updated: [Daily] Sweeping Away the Elyos ");
appendFile("temp.txt","2013.07.22 17:19:54 : You have acquired 12 [item:186000236;ver4;;;;]s and stored them in your special cube. ");
appendFile("temp.txt","2013.07.22 17:19:54 : You have gained 3,446,516 XP from Hrund. ");
appendFile("temp.txt","2013.07.22 17:19:54 : You can receive the weekly quest again at 9 in the morning on Wednesday. ");
appendFile("temp.txt","2013.07.22 17:19:54 : Quest complete: [Daily] Sweeping Away the Elyos ");
parser->processLines();
doTest("relicAp after 12 blood mark", expHourCalc->relicAp, 6413);
//================================================================================
header("NPC Sales");
//isNpcSales
appendFile("temp.txt","2013.11.07 03:15:58 : Sales complete.");
appendFile("temp.txt","2013.11.07 03:15:58 : You have earned 288 Kinah.");
parser->processLines();
doTest("cashGained", expHourCalc->cashGained, 288);
doTest("cashSpent", expHourCalc->cashSpent, 0);
doTest("lastCashTransaction", expHourCalc->lastCashTransaction, 288);
doTest("getNetCashFlow()", expHourCalc->getNetCashFlow(), 288);
doTest("npcSales", expHourCalc->npcSales, 288);
appendFile("temp.txt", "2013.09.03 22:39:32 : You sold the item. ");
appendFile("temp.txt", "2013.09.03 22:39:32 : You have gained 376,068 Abyss Points. ");
parser->processLines();
doTest("currentAp", expHourCalc->currentAp, 10000 + 376068);
doTest("apGained", expHourCalc->apGained, 1000 + 376068);
doTest("relicAp", expHourCalc->relicAp, 6413 - 376068);
header("Not NPC Sales");
appendFile("temp.txt", "2013.11.05 13:04:54 : You have earned 11,550,000 Kinah.");
parser->processLines();
doTest("cashGained", expHourCalc->cashGained, 11550000 + 288);
doTest("cashSpent", expHourCalc->cashSpent, 0);
doTest("lastCashTransaction", expHourCalc->lastCashTransaction, 11550000);
doTest("getNetCashFlow()", expHourCalc->getNetCashFlow(), 11550288);
doTest("npcSales", expHourCalc->npcSales, 288);
appendFile("temp.txt", "2013.11.05 13:43:19 : Captain Anusa is under attack. ");
appendFile("temp.txt", "2013.11.05 13:43:20 : You have gained 5,674 Abyss Points. ");
appendFile("temp.txt", "2013.11.05 13:43:20 : Quest updated: [Service/Group] Unending Assault ");
parser->processLines();
doTest("currentAp", expHourCalc->currentAp, 10000 + 376068 + 5674);
doTest("apGained", expHourCalc->apGained, 1000 + 376068 + 5674);
doTest("relicAp", expHourCalc->relicAp, 6413 - 376068);
//================================================================================
header("Join Channel");
appendFile("temp.txt","2013.07.24 15:28:52 : You have joined the Poeta region channel. ");
appendFile("temp.txt","2013.07.24 15:28:52 : You have joined the Poeta trade channel. ");
appendFile("temp.txt","2013.07.24 15:28:52 : You have joined the LFG Channel. ");
appendFile("temp.txt","2013.07.24 15:28:55 : You have joined the Assassin Channel. ");
appendFile("temp.txt","2013.07.24 15:28:55 : You have joined the Ranger Channel. ");
appendFile("temp.txt","2013.06.25 14:44:16 : You have joined Instance Server.");
parser->processLines();
doTest("currentServer", expHourCalc->currentServer, INSTANCE_SERVER);
doTest("lastTickHasChanges is false", expHourCalc->lastTickHasChanges, false);
//================================================================================
header("Do not recognize user chat as commands");
expHourCalc->reset();
expHourCalc->level = 43;
expHourCalc->currentExp = 21016061;
expHourCalc->lastExpPacket = 10000;
expHourCalc->lastCashTransaction = 62351;
appendFile("temp.txt","2013.07.24 15:24:51 : [3.LFG] [charname:Eikwel;1.0000 0.6941 0.6941]: blah blah blah : You received Soul Healing.");
parser->processLines();
doTest("Soul healing from chat", expHourCalc->currentExp, 21016061);
doTest("Soul healing from chat", expHourCalc->lastExpPacket, 10000);
doTest("lastTickHasChanges is false", expHourCalc->lastTickHasChanges, false);
//================================================================================
printSummary();
delete(parser);
remove("temp.txt");
getchar();
return 0;
}
int main(int argc, char **argv) {
cache_built_param param;
cache_output_param output;
output.hits = 0;
output.misses = 0;
output.evicts = 0;
char *trace_file;
FILE *input_file;
char trace_op;
unsigned long long int address; // hold for 64-bytes address
int size;
char c;
while ((c = getopt(argc, argv, "s: E: b: t: hv")) != -1) {
switch(c) {
case 's':
param.s = atoi(optarg); // transfer input string argument to integer
break;
case 'E':
param.E = atoi(optarg);
break;
case 'b':
param.b = atoi(optarg);
break;
case 't':
trace_file = optarg;
break;
default:
break;
}
}
/*
* check whether the input parameters are legal and complete
*/
if (param.s == 0 || param.E == 0 || param.b == 0 || trace_file == NULL) {
printf("Miss required command line argument");
exit(1);
}
// create a cache according to the given parameters
cache new_cache = create_cache(param.s, param.E, param.b);
// open the input file to get operations
input_file = fopen(trace_file, "r");
if (input_file != NULL) {
/*
* get the trace command from each line
*/
while(fscanf(input_file, " %c %llx,%d", &trace_op, &address, &size) == 3) {
switch(trace_op) {
case 'I':
break;
case 'S':
printf("%c %llx %d\n", trace_op, address, size);
output = simulated_cache(&new_cache, param, output, address);
break;
case 'L':
printf("%c %llx %d\n", trace_op, address, size);
output = simulated_cache(&new_cache, param, output, address);
break;
case 'M':
printf("%c %llx %d\n", trace_op, address, size);
output = simulated_cache(&new_cache, param, output, address);
output = simulated_cache(&new_cache, param, output, address);
break;
default:
break;
}
}
printSummary(output.hits, output.misses, output.evicts); // print out the result
free_cache(&new_cache, param.s, param.E, param.b);
fclose(input_file);
return 0;
}
}
int main(int argc, char **argv)
{
FILE *fp, *fp2;
char testName[32] = "MPI_Rget", file1[64], file2[64];
int dblSize, proc, nprocs, npairs, partner;
unsigned int i, j, k, size, localSize, NLOOP = NLOOP_MAX;
unsigned int smin = MIN_P2P_SIZE, smed = MED_P2P_SIZE, smax = MAX_P2P_SIZE;
double tScale = USEC, bwScale = MB_8;
double tStart, timeMin, timeMinGlobal, overhead, threshold_lo, threshold_hi;
double msgBytes, sizeBytes, localMax, UsedMem;
double tElapsed[NREPS], tElapsedGlobal[NREPS];
double *A, *B;
MPI_Win win;
MPI_Status stat;
MPI_Request req;
// Initialize parallel environment
MPI_Init(&argc, &argv);
MPI_Comm_size( MPI_COMM_WORLD, &nprocs );
MPI_Comm_rank( MPI_COMM_WORLD, &proc );
// Test input parameters
if( nprocs%2 != 0 && proc == 0 )
fatalError( "P2P test requires an even number of processors" );
// Check for user defined limits
checkEnvP2P( proc, &NLOOP, &smin, &smed, &smax );
// Initialize local variables
localMax = 0.0;
npairs = nprocs/2;
if( proc < npairs ) partner = proc + npairs;
if( proc >= npairs ) partner = proc - npairs;
UsedMem = (double)smax*(double)sizeof(double)*2.0;
// Allocate and initialize arrays
srand( SEED );
A = doubleVector( smax );
B = doubleVector( smax );
// Open output file and write header
if( proc == 0 ){
// Check timer overhead in seconds
timerTest( &overhead, &threshold_lo, &threshold_hi );
// Open output files and write headers
sprintf( file1, "rget_time-np_%.4d.dat", nprocs );
sprintf( file2, "rget_bw-np_%.4d.dat", nprocs );
fp = fopen( file1, "a" );
fp2 = fopen( file2, "a" );
printHeaders( fp, fp2, testName, UsedMem, overhead, threshold_lo );
}
// Get type size
MPI_Type_size( MPI_DOUBLE, &dblSize );
// Set up a window for RMA
MPI_Win_create( A, smax*dblSize, dblSize, MPI_INFO_NULL, MPI_COMM_WORLD, &win );
MPI_Win_lock_all( 0, win );
//================================================================
// Single loop with minimum size to verify that inner loop length
// is long enough for the timings to be accurate
//================================================================
// Warmup with a medium size message
if( proc < npairs ){
MPI_Rget( B, smed, MPI_DOUBLE, partner, 0, smed, MPI_DOUBLE, win, &req );
MPI_Wait( &req, &stat );
MPI_Win_flush_all( win );
}
// Test if current NLOOP is enough to capture fastest test cases
MPI_Barrier( MPI_COMM_WORLD );
tStart = benchTimer();
if( proc < npairs ){
for(j = 0; j < NLOOP; j++){
MPI_Rget( B, smin, MPI_DOUBLE, partner, 0, smin, MPI_DOUBLE, win, &req );
MPI_Wait( &req, &stat );
MPI_Win_flush_all( win );
}
}
timeMin = benchTimer() - tStart;
MPI_Reduce( &timeMin, &timeMinGlobal, 1, MPI_DOUBLE, MPI_MIN, 0, MPI_COMM_WORLD );
if( proc == 0 ) resetInnerLoop( timeMinGlobal, threshold_lo, &NLOOP );
MPI_Bcast( &NLOOP, 1, MPI_INT, 0, MPI_COMM_WORLD );
//================================================================
// Execute test for each requested size
//================================================================
for( size = smin; size <= smax; size = size*2 ){
// Warmup with a medium size message
if( proc < npairs ){
MPI_Rget( B, smed, MPI_DOUBLE, partner, 0, smed, MPI_DOUBLE, win, &req );
MPI_Wait( &req, &stat );
MPI_Win_flush_all( win );
}
// Repeat NREPS to collect statistics
for(i = 0; i < NREPS; i++){
MPI_Barrier( MPI_COMM_WORLD );
tStart = benchTimer();
if( proc < npairs ){
for(j = 0; j < NLOOP; j++){
MPI_Rget( B, size, MPI_DOUBLE, partner, 0, size, MPI_DOUBLE, win, &req );
MPI_Wait( &req, &stat );
MPI_Win_flush_all( win );
}
}
tElapsed[i] = benchTimer() - tStart;
}
MPI_Reduce( tElapsed, tElapsedGlobal, NREPS, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD );
// Only task 0 needs to do the analysis of the collected data
if( proc == 0 ){
// sizeBytes is size to write to file
// msgBytes is actual data exchanged on the wire
msgBytes = (double)size*(double)npairs*(double)dblSize;
sizeBytes = (double)size*(double)dblSize;
post_process( fp, fp2, threshold_hi, tElapsedGlobal, tScale,
bwScale, size*dblSize, sizeBytes, msgBytes, &NLOOP,
&localMax, &localSize );
}
MPI_Bcast( &NLOOP, 1, MPI_INT, 0, MPI_COMM_WORLD );
}
MPI_Win_unlock_all( win );
MPI_Win_free( &win );
MPI_Barrier( MPI_COMM_WORLD );
free( A );
free( B );
//================================================================
// Print completion message, free memory and exit
//================================================================
if( proc == 0 ){
printSummary( fp2, testName, localMax, localSize );
fclose( fp2 );
fclose( fp );
}
MPI_Finalize();
return 0;
}
int main (int argc, char** argv) {
double snp_mutation_rate = 0.001;
double indel_mutation_rate = 0.0001;
double het_rate = 0.5;
double afs_alpha = 1;
double indel_alpha = 3;
double microsatellite_afs_alpha = 1;
double microsatellite_len_alpha = 1.7;
double microsatellite_mutation_rate = 0.0001;
double mnp_ratio = 0.01;
double tstv_ratio = 2.5;
double deamination_ratio = 1.8;
int microsatellite_min_length = 1;
int indel_max = 1000;
int ploidy = 1;
int population_size = 1;
int sample_id_max_digits = 1;
int seed = time(NULL);
string fastaFileName;
string file_prefix = "";
string sample_prefix = "";
bool dry_run = false;
int repeat_size_max = 20;
bool uniform_indel_distribution = false;
double p, lambda, shape, mu, sigma;
string command_line = argv[0];
for (int i = 1; i < argc; ++i) {
command_line += " ";
command_line += argv[i];
}
int c;
while (true) {
static struct option long_options[] =
{
/* These options set a flag. */
//{"verbose", no_argument, &verbose_flag, 1},
//{"brief", no_argument, &verbose_flag, 0},
{"help", no_argument, 0, 'h'},
{"snp-rate", required_argument, 0, 's'},
{"mnp-ratio", required_argument, 0, 'M'},
{"indel-rate", required_argument, 0, 'i'},
{"indel-alpha", required_argument, 0, 'z'},
{"indel-max", required_argument, 0, 'X'},
{"repeat-size-max", required_argument, 0, 'q'},
{"microsat-rate", required_argument, 0, 'm'},
{"microsat-afs-alpha", required_argument, 0, 't'},
{"microsat-len-alpha", required_argument, 0, 'j'},
{"microsat-min-len", required_argument, 0, 'l'},
{"afs-alpha", required_argument, 0, 'a'},
{"ploidy", required_argument, 0, 'p'},
{"population-size", required_argument, 0, 'n'},
{"file-prefix", required_argument, 0, 'P'},
{"sample-prefix", required_argument, 0, 'S'},
{"random-seed", required_argument, 0, 'g'},
{"dry-run", no_argument, 0, 'd'},
{"uniform-indels", no_argument, 0, 'U'},
{"ts-tv-ratio", required_argument, 0, 'T'},
{"deamination-ratio", required_argument, 0, 'D'},
{0, 0, 0, 0}
};
/* getopt_long stores the option index here. */
int option_index = 0;
c = getopt_long (argc, argv, "hdUa:z:s:i:q:p:n:M:X:t:m:P:S:g:l:j:T:", long_options, &option_index);
/* Detect the end of the options. */
if (c == -1)
break;
switch (c)
{
case 0:
/* If this option set a flag, do nothing else now. */
if (long_options[option_index].flag != 0)
break;
printf ("option %s", long_options[option_index].name);
if (optarg)
printf (" with arg %s", optarg);
printf ("\n");
break;
case 'd':
dry_run = true;
break;
case 'U':
uniform_indel_distribution = true;
break;
case 'q':
if (!convert(optarg, repeat_size_max)) {
cerr << "could not read -q, --repeat-size-max" << endl;
exit(1);
}
break;
case 's':
if (!convert(optarg, snp_mutation_rate)) {
cerr << "could not read -s, --snp-rate" << endl;
exit(1);
}
break;
case 'i':
if (!convert(optarg, indel_mutation_rate)) {
cerr << "could not read -i, --indel-rate" << endl;
exit(1);
}
break;
case 'a':
if (!convert(optarg, afs_alpha)) {
cerr << "could not read -a, --afs-alpha" << endl;
exit(1);
}
break;
case 'z':
if (!convert(optarg, indel_alpha)) {
cerr << "could not read -z, --indel-alpha" << endl;
exit(1);
}
break;
case 'X':
if (!convert(optarg, indel_max)) {
cerr << "could not read -M, --indel-max" << endl;
exit(1);
}
break;
case 'M':
if (!convert(optarg, mnp_ratio)) {
cerr << "could not read -m, --mnp-ratio" << endl;
exit(1);
}
break;
case 'm':
if (!convert(optarg, microsatellite_mutation_rate)) {
cerr << "could not read -m, --microsat-rate" << endl;
exit(1);
}
break;
case 'T':
if (!convert(optarg, tstv_ratio)) {
cerr << "could not read -T, --ts-tv-ratio" << endl;
exit(1);
}
break;
case 't':
if (!convert(optarg, microsatellite_afs_alpha)) {
cerr << "could not read -m, --microsatellite-afs-alpha" << endl;
exit(1);
}
break;
case 'j':
if (!convert(optarg, microsatellite_len_alpha)) {
cerr << "could not read -m, --microsatellite-len-alpha" << endl;
exit(1);
}
break;
case 'l':
if (!convert(optarg, microsatellite_min_length)) {
cerr << "could not read -l, --microsat-min-len" << endl;
exit(1);
}
break;
case 'p':
if (!convert(optarg, ploidy)) {
cerr << "could not read -p, --ploidy" << endl;
exit(1);
}
break;
case 'P':
file_prefix = optarg;
break;
case 'S':
sample_prefix = optarg;
break;
case 'n':
if (!convert(optarg, population_size)) {
cerr << "could not read -n, --population-size" << endl;
exit(1);
}
sample_id_max_digits = strlen(optarg);
break;
case 'g':
if (!convert(optarg, seed)) {
cerr << "could not read -g, --random-seed" << endl;
exit(1);
}
break;
case 'h':
printSummary();
exit(0);
break;
case '?':
/* getopt_long already printed an error message. */
printSummary();
exit(1);
break;
default:
abort ();
}
}
/* Print any remaining command line arguments (not options). */
if (optind < argc) {
//cerr << "fasta file: " << argv[optind] << endl;
fastaFileName = argv[optind];
} else {
cerr << "please specify a fasta file" << endl;
printSummary();
exit(1);
}
init_genrand(seed); // seed mt with current time
//mt19937 eng(seed);
int bpPerHaplotypeMean = 1000;
double bpPerHaplotypeSigma = 200;
normal_distribution<double> normal(mu, sigma);
//lambda = 7.0;
//poisson_distribution<int> poisson(lambda);
//poisson(eng);
string seqname;
string sequence; // holds sequence so we can process it
FastaReference fr;
fr.open(fastaFileName);
string bases = "ATGC";
vcf::VariantCallFile vcfFile;
// write the VCF header
stringstream headerss;
headerss
<< "##fileformat=VCFv4.1" << endl
<< "##fileDate=" << dateStr() << endl
<< "##source=mutatrix population genome simulator" << endl
<< "##seed=" << seed << endl
<< "##reference=" << fastaFileName << endl
<< "##phasing=true" << endl
<< "##commandline=" << command_line << endl
<< "##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Alternate allele count\">" << endl
<< "##INFO=<ID=TYPE,Number=A,Type=String,Description=\"Type of each allele (snp, ins, del, mnp, complex)\">" << endl
<< "##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of samples at the site\">" << endl
<< "##INFO=<ID=NA,Number=1,Type=Integer,Description=\"Number of alternate alleles\">" << endl
<< "##INFO=<ID=LEN,Number=A,Type=Integer,Description=\"Length of each alternate allele\">" << endl
<< "##INFO=<ID=MICROSAT,Number=0,Type=Flag,Description=\"Generated at a sequence repeat loci\">" << endl
<< "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">" << endl
<< "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT";
vector<string> samples;
for (int i = 0; i < population_size; ++i) {
stringstream sampless;
sampless << sample_prefix << setfill('0') << setw(sample_id_max_digits) << i + 1; // one-based sample names
samples.push_back(sampless.str());
headerss << "\t" << sampless.str();
}
// and set up our VCF output file
string header = headerss.str();
vcfFile.openForOutput(header);
cout << vcfFile.header << endl;
int copies = ploidy * population_size;
map<string, vector<SampleFastaFile*> > sequencesByRefseq;
if (!dry_run) {
for (FastaIndex::iterator s = fr.index->begin(); s != fr.index->end(); ++s) {
FastaIndexEntry& indexEntry = s->second;
seqname = indexEntry.name;
vector<SampleFastaFile*>& sequences = sequencesByRefseq[seqname];
for (int i = 0; i < population_size; ++i) {
stringstream sname;
sname << sample_prefix << setfill('0') << setw(sample_id_max_digits) << i + 1;
string samplename = sname.str();
for (int j = 0; j < ploidy; ++j) {
stringstream cname;
cname << j;
string chromname = cname.str();
string fullname = samplename + ":" + seqname + ":" + chromname;
string filename = file_prefix + fullname + ".fa";
//sequences.push_back(SampleFastaFile(filename, seqname));
sequences.push_back(new SampleFastaFile(filename, seqname));
}
}
}
}
for (FastaIndex::iterator s = fr.index->begin(); s != fr.index->end(); ++s) {
FastaIndexEntry& indexEntry = s->second;
seqname = indexEntry.name;
sequence = fr.getSequence(s->first);
vector<SampleFastaFile*>& sequences = sequencesByRefseq[seqname];
//sequences.resize(copies);
long int pos = 0;
long int microsatellite_end_pos = 0;
while (pos < sequence.size()) {
//cout << pos + 1 << " microsat end pos " << microsatellite_end_pos << endl;
string ref = sequence.substr(pos, 1); // by default, ref is just the current base
// skip non-DNA sequence information
if (!(ref == "A" || ref == "T" || ref == "C" || ref == "G")) {
pos += ref.size();
for (vector<SampleFastaFile*>::iterator s = sequences.begin(); s != sequences.end(); ++s) {
(*s)->write(ref);
}
continue;
}
vector<Allele> alleles;
// establish if we are in a repeat
// and what motif is being repeated, how many times
int len = 1;
// get reference repeats
// if we have a repeat, adjust the mutation rate
// using length and direction-dependent
// formula from "Likelihood-Based Estimation of Microsatellite Mutation Rates"
// http://www.genetics.org/cgi/content/full/164/2/781#T1
if (pos > microsatellite_end_pos) {
map<string, int> repeats = repeatCounts(pos + 1, (const string&) sequence, repeat_size_max);
string seq;
int repeat_count = 0;
// get the "biggest" repeat, the most likely ms allele at this site
for (map<string, int>::iterator r = repeats.begin(); r != repeats.end(); ++r) {
if (repeat_count < r->second) {
repeat_count = r->second;
seq = r->first;
}
}
//cout << pos + 1 << " " << sequence.substr(pos + 1, seq.size() * repeat_count) << " ?= " << seq * repeat_count << endl;
// guard ensures that we are in a pure repeat situoation, tandem-tandem repeats are not handled presently
if (repeats.size() > 0 && sequence.substr(pos + 1, seq.size() * repeat_count) == seq * repeat_count) {
int microsatellite_length = repeat_count * seq.size();
// record end of microsatellite so we don't generate more mutations until we pass it
microsatellite_end_pos = pos + microsatellite_length - 1;
if (microsatellite_length > microsatellite_min_length
//&& genrand_real1() / copies
// < microsatellite_mutation_rate * repeat_count) {
&& genrand_real1() > pow(1 - (microsatellite_mutation_rate * repeat_count), log(copies) * 2)) {
// establish the relative rate of ins and del events
/*
long double repeatMutationDelProbability = microsatelliteDelProb(repeat_count);
long double repeatMutationInsProbability = microsatelliteInsProb(repeat_count);
long double indel_balance = 1;
if (repeatMutationInsProbability > repeatMutationDelProbability) {
indel_balance = repeatMutationInsProbability / repeatMutationDelProbability;
} else {
indel_balance = 1 - (repeatMutationInsProbability / repeatMutationDelProbability);
}
*/
double indel_balance = 0.5;
// how many alleles at the site?
//int numalleles = min((int) floor(zetarandom(microsatellite_afs_alpha)), (int) ((double) repeat_count * indel_balance));
int numalleles = random_allele_frequency(repeat_count, microsatellite_afs_alpha);
//cout << "repeat_count: " << repeat_count << " numalleles: " << numalleles << endl;
map<int, bool> allele_lengths;
// lengths of the alleles
while (allele_lengths.size() < numalleles) {
int allele_length;
// TODO adjust length so that shorter events are more likely...
if (genrand_real1() > indel_balance) {
allele_length = -1 * min((int) floor(zetarandom(microsatellite_len_alpha)), repeat_count);
} else {
allele_length = min((int) floor(zetarandom(microsatellite_len_alpha)), repeat_count);
}
//cout << allele_length << endl;
map<int, bool>::iterator f = allele_lengths.find(allele_length);
if (f == allele_lengths.end()) {
allele_lengths[allele_length] = true;
}
}
// generate alleles
for (map<int, bool>::iterator f = allele_lengths.begin();
f != allele_lengths.end(); ++f) {
int allele_length = f->first;
int c = abs(f->first);
string alt = seq;
for (int i = 1; i < c; ++i)
alt += seq;
if (allele_length > 0) {
alleles.push_back(Allele(ref, ref + alt, "MICROSAT"));
} else {
alleles.push_back(Allele(ref + alt, ref, "MICROSAT"));
}
//cout << pos + 1 << " " << microsatellite_length << " " << alleles.back() << endl;
}
//cout << "alleles.size() == " << alleles.size() << endl;
}
}
}
// snp case
if (genrand_real1() > pow(1 - snp_mutation_rate, log(max(copies, 2)) * 2)) {
// make an alternate allele
/*
string alt = ref;
while (alt == ref) {
alt = string(1, bases.at(genrand_int32() % 4));
}
*/
string alt = ref;
if (genrand_real1() > 1 / (1 + tstv_ratio)) {
if (ref == "A") {
alt = "G";
} else if (ref == "G") {
alt = "A";
} else if (ref == "C") {
alt = "T";
} else if (ref == "T") {
alt = "C";
}
} else {
while (alt == ref || isTransition(ref, alt)) {
alt = string(1, bases.at(genrand_int32() % 4));
}
}
if (genrand_real1() < mnp_ratio) {
int i = 1;
do {
ref += sequence.substr(pos + i, 1);
alt += sequence.substr(pos + i, 1);
++i;
while (alt.at(alt.size() - 1) == ref.at(ref.size() - 1)) {
alt.at(alt.size() - 1) = bases.at(genrand_int32() % 4);
}
} while (genrand_real1() < mnp_ratio);
len = alt.size();
}
alleles.push_back(Allele(ref, alt));
}
// indel case
if (genrand_real1() > pow(1 - indel_mutation_rate, log(max(copies, 2)) * 2)) {
// how many bp?
if (uniform_indel_distribution) {
len = (int) floor(genrand_real1() * indel_max);
} else {
len = (int) floor(zetarandom(indel_alpha));
}
// guard against out-of-sequence indels
if (pos + len < sequence.size() && len <= indel_max) {
if (genrand_int32() % 2 == 0) {
// deletion
alleles.push_back(Allele(sequence.substr(pos, 1 + len), sequence.substr(pos, 1)));
} else {
string alt = ref;
// insertion?
// insert some random de novo bases
while (alt.length() < len + 1) {
alt += string(1, bases.at(genrand_int32() % 4));
}
alleles.push_back(Allele(ref, alt));
}
} else {
// fall through
}
}
// no mutation generated
if (alleles.empty()) {
for (int i = 0; i < copies; ++i) {
if (!dry_run) {
sequences.at(i)->write(ref);
}
}
pos += ref.size();
} else {
// TODO randomly distribute all the alleles throughout the population
// generate allele frequencies for each
// fun times...
string genotype;
vector<bool> alts;
random_shuffle(alleles.begin(), alleles.end());
vector<Allele*> population_alleles;
list<Allele> present_alleles; // filtered for AFS > 0 in the sample
// AFS simulation
int remaining_copies = copies;
while (remaining_copies > 0 && !alleles.empty()) {
Allele allele = alleles.back();
alleles.pop_back();
int allele_freq = random_allele_frequency(remaining_copies, afs_alpha);
if (allele_freq > 0) {
present_alleles.push_back(allele);
Allele* allelePtr = &present_alleles.back();
for (int i = 0; i < allele_freq; ++i) {
population_alleles.push_back(allelePtr);
}
remaining_copies -= allele_freq;
}
}
if (present_alleles.empty()) {
for (int i = 0; i < copies; ++i) {
if (!dry_run) {
sequences.at(i)->write(ref);
}
}
pos += ref.size();
continue;
}
reverse(present_alleles.begin(), present_alleles.end());
// establish the correct reference sequence and alternate allele set
for (list<Allele>::iterator a = present_alleles.begin(); a != present_alleles.end(); ++a) {
Allele& allele = *a;
//cout << allele << endl;
if (allele.ref.size() > ref.size()) {
ref = allele.ref;
}
}
// reference alleles take up the rest
Allele reference_allele = Allele(ref, ref);
for (int i = 0; i < remaining_copies; ++i) {
population_alleles.push_back(&reference_allele);
}
vector<string> altstrs;
// now the reference allele is the largest possible, adjust the alt allele strings to reflect this
// if we have indels, add the base before, set the position back one
for (list<Allele>::iterator a = present_alleles.begin(); a != present_alleles.end(); ++a) {
Allele& allele = *a;
string alleleStr = ref;
if (allele.ref.size() == allele.alt.size()) {
alleleStr.replace(0, allele.alt.size(), allele.alt);
} else {
alleleStr.replace(0, allele.ref.size(), allele.alt);
}
allele.ref = ref;
allele.alt = alleleStr;
altstrs.push_back(alleleStr);
}
assert(population_alleles.size() == copies);
// shuffle the alleles around the population
random_shuffle(population_alleles.begin(), population_alleles.end());
vcf::Variant var(vcfFile);
var.sequenceName = seqname;
var.position = pos + 1;
var.quality = 99;
var.id = ".";
var.filter = ".";
var.info["NS"].push_back(convert(population_size));
var.info["NA"].push_back(convert(present_alleles.size()));
var.format.push_back("GT");
var.ref = ref;
var.alt = altstrs;
// debugging, uncomment to see sequence context
//cout << sequence.substr(pos - 10, 10) << "*" << ref << "*" << sequence.substr(pos + 1, 9) << endl;
map<string, int> alleleIndexes;
alleleIndexes[convert(reference_allele)] = 0; // XXX should we handle this differently, by adding the reference allele to present_alleles?
int i = 1;
for (list<Allele>::iterator a = present_alleles.begin(); a != present_alleles.end(); ++a, ++i) {
Allele& allele = *a;
//cout << allele << " " << i << endl;
alleleIndexes[convert(allele)] = i;
//cout << allele << " " << i << endl;
}
//for (map<string, int>::iterator a = alleleIndexes.begin(); a != alleleIndexes.end(); ++a) {
// cout << a->first << " = " << a->second << endl;
//}
int j = 0;
for (vector<string>::iterator s = samples.begin(); s != samples.end(); ++s, ++j) {
string& sample = *s;
vector<string> genotype;
// XXX hack, maybe this should get stored in another map for easier access?
for (int i = 0; i < ploidy; ++i) {
int l = (j * ploidy) + i;
//cout << l << " " << population_alleles.at(l) << " " << alleleIndexes[convert(population_alleles.at(l))] << endl;
genotype.push_back(convert(alleleIndexes[convert(*population_alleles.at(l))]));
}
var.samples[sample]["GT"].push_back(join(genotype, "|"));
//cout << var.samples[sample]["GT"].front() << endl;
}
// XXX THIS IS BROKEN BECAUSE YOUR REFERENCE ALLELE CHANGES
// LENGTH WITH DELETIONS.
//
// IT'S POSSIBLE TO GET COMPLEX ALLELES AT THE INTERSECTIONS
// BETWEEN ONE ALLELIC VARIANT AND ANOTHER. THIS IS BROKEN!
//
// TO FIX--- BUILD HAPLOTYPES, THEN DISTRIBUTE THEM WITHIN THE POPULATION
//
// now write out our sequence data (FASTA files)
for (int j = 0; j < population_size; ++j) {
for (int i = 0; i < ploidy; ++i) {
int l = (j * ploidy) + i;
Allele* allele = population_alleles.at(l);
if (!dry_run) {
sequences.at(l)->write(allele->alt);
}
}
}
// tabulate allele frequency, and write some details to the VCF
for (list<Allele>::iterator a = present_alleles.begin(); a != present_alleles.end(); ++a) {
Allele& allele = *a;
Allele* allelePtr = &*a;
vector<string> genotypes;
genotypes.resize(population_size);
int allele_freq = 0;
// obtain allele frequencies and output FASTA sequence data
// for each simulated sample
for (int j = 0; j < population_size; ++j) {
for (int i = 0; i < ploidy; ++i) {
int l = (j * ploidy) + i;
if (population_alleles.at(l) == allelePtr) {
++allele_freq;
}
}
}
// set up the allele-specific INFO fields in the VCF record
var.info["AC"].push_back(convert(allele_freq));
int delta = allele.alt.size() - allele.ref.size();
if (delta == 0) {
if (allele.ref.size() == 1) {
var.info["TYPE"].push_back("snp");
var.info["LEN"].push_back(convert(allele.ref.size()));
} else {
var.info["TYPE"].push_back("mnp");;
var.info["LEN"].push_back(convert(allele.ref.size()));
}
} else if (delta > 0) {
var.info["TYPE"].push_back("ins");;
var.info["LEN"].push_back(convert(abs(delta)));
} else {
var.info["TYPE"].push_back("del");;
var.info["LEN"].push_back(convert(abs(delta)));
}
if (!allele.type.empty()) {
var.infoFlags[allele.type] = true;
}
}
// write the VCF record to stdout
cout << var << endl;
int largest_ref = 1; // enforce one pos
for (list<Allele>::iterator a = present_alleles.begin(); a != present_alleles.end(); ++a) {
if (a->ref.size() > largest_ref) {
largest_ref = a->ref.size();
}
}
pos += largest_ref; // step by the size of the last event
}
}
}
// close, clean up files
for (map<string, vector<SampleFastaFile*> >::iterator s = sequencesByRefseq.begin(); s != sequencesByRefseq.end(); ++s) {
vector<SampleFastaFile*>& files = s->second;
for (vector<SampleFastaFile*>::iterator f = files.begin(); f != files.end(); ++f) {
delete *f;
}
files.clear();
}
return 0;
}
int main (int argc, char** argv) {
string command;
string fastaFileName;
string seqname;
string longseqname;
long long start;
long long length;
bool buildIndex = false; // flag to force index building
bool printEntropy = false; // entropy printing
bool readRegionsFromStdin = false;
//bool printLength = false;
string region;
int c;
while (true) {
static struct option long_options[] =
{
/* These options set a flag. */
//{"verbose", no_argument, &verbose_flag, 1},
//{"brief", no_argument, &verbose_flag, 0},
{"help", no_argument, 0, 'h'},
{"index", no_argument, 0, 'i'},
//{"length", no_argument, &printLength, true},
{"entropy", no_argument, 0, 'e'},
{"region", required_argument, 0, 'r'},
{"stdin", no_argument, 0, 'c'},
{0, 0, 0, 0}
};
/* getopt_long stores the option index here. */
int option_index = 0;
c = getopt_long (argc, argv, "hcier:",
long_options, &option_index);
/* Detect the end of the options. */
if (c == -1)
break;
switch (c)
{
case 0:
/* If this option set a flag, do nothing else now. */
if (long_options[option_index].flag != 0)
break;
printf ("option %s", long_options[option_index].name);
if (optarg)
printf (" with arg %s", optarg);
printf ("\n");
break;
case 'e':
printEntropy = true;
break;
case 'c':
readRegionsFromStdin = true;
break;
case 'i':
buildIndex = true;
break;
case 'r':
region = optarg;
break;
case 'h':
printSummary();
exit(0);
break;
case '?':
/* getopt_long already printed an error message. */
printSummary();
exit(1);
break;
default:
abort ();
}
}
/* Print any remaining command line arguments (not options). */
if (optind < argc) {
//cerr << "fasta file: " << argv[optind] << endl;
fastaFileName = argv[optind];
} else {
cerr << "please specify a fasta file" << endl;
printSummary();
exit(1);
}
if (buildIndex) {
FastaIndex* fai = new FastaIndex();
//cerr << "generating fasta index file for " << fastaFileName << endl;
fai->indexReference(fastaFileName);
fai->writeIndexFile((string) fastaFileName + fai->indexFileExtension());
}
string sequence; // holds sequence so we can optionally process it
FastaReference fr;
fr.open(fastaFileName);
if (region != "") {
FastaRegion target(region);
if (target.startPos == -1) {
sequence = fr.getSequence(target.startSeq);
} else {
sequence = fr.getSubSequence(target.startSeq, target.startPos - 1, target.length());
}
}
if (readRegionsFromStdin) {
string regionstr;
while (getline(cin, regionstr)) {
FastaRegion target(regionstr);
if (target.startPos == -1) {
cout << fr.getSequence(target.startSeq) << endl;
} else {
cout << fr.getSubSequence(target.startSeq, target.startPos - 1, target.length()) << endl;
}
}
} else {
if (sequence != "") {
if (printEntropy) {
if (sequence.size() > 0) {
cout << shannon_H((char*) sequence.c_str(), sequence.size()) << endl;
} else {
cerr << "please specify a region or sequence for which to calculate the shannon entropy" << endl;
}
} else { // if no statistical processing is requested, just print the sequence
cout << sequence << endl;
}
}
}
return 0;
}
/*Main function to run the cache simulator
*@return 0 if success, 1 if fail
*/
int main(int argc, char** argv)
{
int verbose = 0; // verbose flag
int s; // Number of set index bits
int E; // Number of lines per set
int b; // Number of block bits
char* trace; //the trace file name
cache* Cache;
char c;
while ((c = getopt(argc, argv, "s:E:b:t:vh")) != -1){
switch(c){
case 's':
s = atoi(optarg);
break;
case 'E':
E = atoi(optarg);
break;
case 'b':
b = atoi(optarg);
break;
case 't':
trace = optarg;
break;
case 'v':
verbose = 1;
break;
case 'h':
printUsage();
exit(0);
default:
printUsage();
exit(1);
}
}
if (s == 0 || E == 0 || b == 0 || trace == NULL){
puts("Missing arguments");
printUsage();
return 1;
}
//Create the cache
Cache = buildCache(s, E, b);
//Read from the trace
memAddr address;
char act;
int byteSize;
FILE * traceFile = fopen(trace, "r");
//initilize cache tracker
cacheParam param;
param.s = s;
param.b= b;
param.E = E;
param.S = 1 << s;
param.B = 1 << b;
param.hit =0;
param.miss = 0;
param.evict = 0;
//Usage
int state, state1, state2;
if (traceFile != NULL) {
while (fscanf(traceFile, " %c %llx,%d", &act, &address, &byteSize) == 3){
switch(act){
case 'I':
break;
case 'L':
param = rSim(Cache, param, address, &state);
if (verbose == 1) {
printf("%c %llx,%d", act, address, byteSize);
printState(state);
printf("\n");
}
break;
case 'S':
param = rSim(Cache, param, address, &state);
if (verbose == 1) {
printf("%c %llx,%d", act, address, byteSize);
printState(state);
printf("\n");
}
break;
case 'M':
param = rSim(Cache, param, address, &state1);
param = rSim(Cache, param, address, &state2);
if (verbose == 1) {
printf("%c %llx,%d", act, address, byteSize);
printState(state1);
printState(state2);
printf("\n");
}
break;
default:
break;
}
}
}
printSummary(param.hit, param.miss, param.evict);
return 0;
}
