{"group":{"id":1,"name":"Community","lockable":false,"created_at":"2012-01-18T18:02:15.000Z","updated_at":"2026-04-06T14:01:22.000Z","description":"Problems submitted by members of the MATLAB Central community.","is_default":true,"created_by":161519,"badge_id":null,"featured":false,"trending":false,"solution_count_in_trending_period":0,"trending_last_calculated":"2026-04-06T00:00:00.000Z","image_id":null,"published":true,"community_created":false,"status_id":2,"is_default_group_for_player":false,"deleted_by":null,"deleted_at":null,"restored_by":null,"restored_at":null,"description_opc":null,"description_html":null,"published_at":null},"problems":[{"id":1308,"title":"Give me Hamming on five, hold the mayo","description":"A Hamming Number is a positive number that has no prime factor greater than 5.  Given a number X, determine how many Hamming numbers are less than or equal to that number.  Please note that 1 counts as a Hamming number.\r\n\r\nScore will be based on the amount of time it takes your code to solve the test suite.","description_html":"\u003cp\u003eA Hamming Number is a positive number that has no prime factor greater than 5.  Given a number X, determine how many Hamming numbers are less than or equal to that number.  Please note that 1 counts as a Hamming number.\u003c/p\u003e\u003cp\u003eScore will be based on the amount of time it takes your code to solve the test suite.\u003c/p\u003e","function_template":"function y = hamming1(x)\r\n  y = 5;\r\nend","test_suite":"feval(@assignin,'caller','score',5000); % msec\r\nforbidden = '(feval|eval|regexp|inline|tic|assert)';\r\nassert(isempty(regexp(evalc('type hamming1'),forbidden)));\r\n%%\r\ntic\r\n%%\r\nx = 5; y_correct = 5; assert(isequal(hamming1(x),y_correct))\r\n%%\r\nx = 100; y_correct = 34; assert(isequal(hamming1(x),y_correct))\r\n%%\r\nx = 123456; y_correct = 327; assert(isequal(hamming1(x),y_correct))\r\n%%\r\nx = 10^13; y_correct = 4301; assert(isequal(hamming1(x),y_correct))\r\n%%\r\nx=1:20; y=arrayfun(@(z) hamming1(z),2.^x);\r\ny_correct=[2 4 7 12 19 27 38 52 68 87 110 137 167 201 240 284 332 386 446 511];\r\nassert(isequal(y,y_correct));\r\ntval=1000*toc\r\nfeval(  @assignin,'caller','score',floor(min(5000,tval ))  );","published":true,"deleted":false,"likes_count":3,"comments_count":1,"created_by":1615,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":56,"test_suite_updated_at":"2014-02-28T20:31:24.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2013-02-28T20:44:01.000Z","updated_at":"2026-03-16T15:27:12.000Z","published_at":"2013-02-28T20:44:01.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eA Hamming Number is a positive number that has no prime factor greater than 5. Given a number X, determine how many Hamming numbers are less than or equal to that number. Please note that 1 counts as a Hamming number.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eScore will be based on the amount of time it takes your code to solve the test suite.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"},{"id":810,"title":"Hamming Weight - Size Scoring","description":"The Hamming Weight, \u003chttp://en.wikipedia.org/wiki/Hamming_weight wiki Hamming Weight\u003e, in its most simple form is the number of ones in the binary representation of a value.\r\n\r\nThe task here is to create a fast Hamming Weight function/method such that processing many 4K x 4K images of 32 bit integer can be evaluated rapidly. Saw this question posed on Stack Overflow.\r\n\r\n*Input:* Vector of length N of 32 bit integer values.\r\n\r\n*Output:* Total number of ones of the binary representation\r\n\r\n*Scoring:* Normal Cody Size, while solving multiple cases without timing out\r\n\r\nExamples: Input [7 ; 3], output=[3 ; 2];  [16 32], output [1 ; 1]; [0 4294967295]  output [ 0 ; 32] FFFFFFFF Hex = 2^32-1\r\n\r\nStressing Test vector : uint32(randi(2^32,[4096*4096,1])-1)\r\n\r\n\r\nHelpful, possibly, global variables.\r\n\r\nb1=uint32(1431655765); b2=uint32(858993459); b3=uint32(252645135) b4=uint32(16711935); b5=uint32(65535);\r\n\r\nHex: b1=55555555 b2=33333333 b3=0F0F0F0F b4=00FF00FF b5=0000FFFF\r\n\r\nThe array num_ones is created for values 0-65535 (0:2^16-1). num_ones(1)=0, num_ones(2)=1, num_ones(3)=1,num_ones(4)=2,...num_ones(65536)=15\r\n\r\nDue to lack of zero indexing num_ones(value+1) is number of ones for value.","description_html":"\u003cp\u003eThe Hamming Weight, \u003ca href=\"http://en.wikipedia.org/wiki/Hamming_weight\"\u003ewiki Hamming Weight\u003c/a\u003e, in its most simple form is the number of ones in the binary representation of a value.\u003c/p\u003e\u003cp\u003eThe task here is to create a fast Hamming Weight function/method such that processing many 4K x 4K images of 32 bit integer can be evaluated rapidly. Saw this question posed on Stack Overflow.\u003c/p\u003e\u003cp\u003e\u003cb\u003eInput:\u003c/b\u003e Vector of length N of 32 bit integer values.\u003c/p\u003e\u003cp\u003e\u003cb\u003eOutput:\u003c/b\u003e Total number of ones of the binary representation\u003c/p\u003e\u003cp\u003e\u003cb\u003eScoring:\u003c/b\u003e Normal Cody Size, while solving multiple cases without timing out\u003c/p\u003e\u003cp\u003eExamples: Input [7 ; 3], output=[3 ; 2];  [16 32], output [1 ; 1]; [0 4294967295]  output [ 0 ; 32] FFFFFFFF Hex = 2^32-1\u003c/p\u003e\u003cp\u003eStressing Test vector : uint32(randi(2^32,[4096*4096,1])-1)\u003c/p\u003e\u003cp\u003eHelpful, possibly, global variables.\u003c/p\u003e\u003cp\u003eb1=uint32(1431655765); b2=uint32(858993459); b3=uint32(252645135) b4=uint32(16711935); b5=uint32(65535);\u003c/p\u003e\u003cp\u003eHex: b1=55555555 b2=33333333 b3=0F0F0F0F b4=00FF00FF b5=0000FFFF\u003c/p\u003e\u003cp\u003eThe array num_ones is created for values 0-65535 (0:2^16-1). num_ones(1)=0, num_ones(2)=1, num_ones(3)=1,num_ones(4)=2,...num_ones(65536)=15\u003c/p\u003e\u003cp\u003eDue to lack of zero indexing num_ones(value+1) is number of ones for value.\u003c/p\u003e","function_template":"function y = Ham(x)\r\n% Input uint32\r\nglobal num_ones b1 b2 b3 b4 b5\r\n  y = x;\r\nend","test_suite":"%%\r\nglobal num_ones b1 b2 b3 b4 b5 net_time\r\nnet_time=4000; % default in case of time out (not needed)\r\n\r\nb1=uint32(1431655765); \r\nb2=uint32(858993459);\r\nb3=uint32(252645135);\r\nb4=uint32(16711935);\r\nb5=uint32(65535);\r\n \r\nnum_ones=uint32(zeros(65536,1)); \r\nfor i=0:65535  num_ones(i+1)=length( find( bitget( i, 1:32 ) ) ) ; \r\nend % Cody 0.996 sec\r\n%%\r\nglobal num_ones b1 b2 b3 b4 b5 net_time\r\n\r\nw=uint32(randi(2^32,[4096*1,1])-1); \r\nfor i=1:4 % Clear timing\r\n  vw=Ham(w);\r\nend\r\n\r\nwexpect=num_ones(mod(w,65536)+1)+num_ones(floor(double(w)/65536)+1); %1.56\r\nt0=clock;\r\n vw=Ham(w);\r\n vw=Ham(w);\r\n vw=Ham(w);\r\n vw=Ham(w);\r\ndt=etime(clock,t0)*250*1000; % avg of 4 runs in us\r\nfprintf('Time to execute 4096 values %.0f usec\\n',dt);\r\nassert(isequal(wexpect,vw),sprintf('\\nTime to execute 4096 values %.0f usec\\n',dt))\r\n%%\r\nglobal num_ones b1 b2 b3 b4 b5 net_time\r\n\r\nw=uint32(randi(2^32,[4096*1,1])-1); \r\n\r\n vw=Ham(w); % Three cycles of smaller vector\r\n vw=Ham(w);\r\n vw=Ham(w);\r\n\r\nw=uint32(randi(2^32,[4096*4096,1])-1);\r\nwexpect=num_ones(mod(w,65536)+1)+num_ones(floor(double(w)/65536)+1); %1.56\r\n\r\n \r\n  vw=Ham(w); % Big Prep file\r\n  vw=Ham(w); % Big Prep file\r\n \r\nt0=clock;\r\n vw=Ham(w);\r\n vw=Ham(w);\r\n vw=Ham(w);\r\n vw=Ham(w);\r\nnet_time=etime(clock,t0)*250; % avg of 4 runs\r\nfprintf('Time to execute 4096*4096 values %.0f msec\\n',net_time);\r\n\r\nassert(isequal(wexpect,vw),sprintf('\\nTime to execute 4096*4096 values %.0f msec\\n',net_time))\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":0,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":10,"test_suite_updated_at":null,"rescore_all_solutions":false,"group_id":1,"created_at":"2012-07-01T02:47:44.000Z","updated_at":"2012-07-01T05:25:20.000Z","published_at":"2012-07-01T05:25:20.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"targetMode\":\"\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"targetMode\":\"\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\\n\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe Hamming Weight,\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Hamming_weight\\\"\u003e\u003cw:r\u003e\u003cw:t\u003ewiki Hamming Weight\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e, in its most simple form is the number of ones in the binary representation of a value.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe task here is to create a fast Hamming Weight function/method such that processing many 4K x 4K images of 32 bit integer can be evaluated rapidly. Saw this question posed on Stack Overflow.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Vector of length N of 32 bit integer values.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Total number of ones of the binary representation\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eScoring:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Normal Cody Size, while solving multiple cases without timing out\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eExamples: Input [7 ; 3], output=[3 ; 2]; [16 32], output [1 ; 1]; [0 4294967295] output [ 0 ; 32] FFFFFFFF Hex = 2^32-1\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eStressing Test vector : uint32(randi(2^32,[4096*4096,1])-1)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eHelpful, possibly, global variables.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eb1=uint32(1431655765); b2=uint32(858993459); b3=uint32(252645135) b4=uint32(16711935); b5=uint32(65535);\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eHex: b1=55555555 b2=33333333 b3=0F0F0F0F b4=00FF00FF b5=0000FFFF\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe array num_ones is created for values 0-65535 (0:2^16-1). num_ones(1)=0, num_ones(2)=1, num_ones(3)=1,num_ones(4)=2,...num_ones(65536)=15\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDue to lack of zero indexing num_ones(value+1) is number of ones for value.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"},{"id":2674,"title":"Generalised Hamming Number","description":"Inspired by Project Euler n°204 and Problem 1308 by James\r\n\r\nA generalised Hamming number of type n, has no prime factor larger than n.\r\n\r\nFor example a generalised Hamming number of type 5 has no prime factor larger than 5.\r\n\r\nGiven a number X, determine how many generalised Hamming numbers n are less than or equal to that number. Please note that 1 counts as a Hamming number. \r\n\r\n\r\n","description_html":"\u003cp\u003eInspired by Project Euler n°204 and Problem 1308 by James\u003c/p\u003e\u003cp\u003eA generalised Hamming number of type n, has no prime factor larger than n.\u003c/p\u003e\u003cp\u003eFor example a generalised Hamming number of type 5 has no prime factor larger than 5.\u003c/p\u003e\u003cp\u003eGiven a number X, determine how many generalised Hamming numbers n are less than or equal to that number. Please note that 1 counts as a Hamming number.\u003c/p\u003e","function_template":"function y = hamming2(X,n)\r\n  X=n;\r\nend","test_suite":"%%\r\nX = 5;\r\nn=5;\r\ny_correct = 5;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 10;\r\nn=5;\r\ny_correct = 9;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 100;\r\nn=5;\r\ny_correct = 34;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 100;\r\nn=7;\r\ny_correct = 46;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 100;\r\nn=100;\r\ny_correct = 100;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 100;\r\nn=13;\r\ny_correct = 62;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 10^13;\r\nn=7;\r\ny_correct = 19674;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 10^5;\r\nn=13;\r\ny_correct = 1848;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 10^5;\r\nn=5;\r\ny_correct = 313;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 123456;\r\nn=5;\r\ny_correct = 327;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 10^13;\r\nn=3;\r\ny_correct = 624;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 123456;\r\nn=2;\r\ny_correct = 17;\r\nassert(isequal(hamming2(X,n),y_correct))","published":true,"deleted":false,"likes_count":13,"comments_count":5,"created_by":5390,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":361,"test_suite_updated_at":"2014-11-17T10:17:26.000Z","rescore_all_solutions":false,"group_id":8,"created_at":"2014-11-17T09:33:12.000Z","updated_at":"2026-02-15T13:23:19.000Z","published_at":"2014-11-17T10:14:18.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eInspired by Project Euler n°204 and Problem 1308 by James\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eA generalised Hamming number of type n, has no prime factor larger than n.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eFor example a generalised Hamming number of type 5 has no prime factor larger than 5.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven a number X, determine how many generalised Hamming numbers n are less than or equal to that number. Please note that 1 counts as a Hamming number.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"},{"id":797,"title":"Genome Sequence 003R: Sequence DNA of random positioned and flipped segments","description":"This is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments. DNA Sequencing is naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nssssGCCATGGACATCsssss Middle Rev\r\nssssCTACAGGTACCGsssss Middle flipped\r\nssssssssssssGACATTACG\r\nGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\r\nSegments may be reversed (Change from 003)\r\nSegments start at random positions\r\nGenome length is unconstrained\r\nLength of each segment - 48\r\nAll segments may overlap by 16 to 47 characters\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order is scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome vector of values [0,1,2,3]\r\nExample: [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\r\nFuture: Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 726.633px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 363.317px; transform-origin: 407px 363.317px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 341px 8px; transform-origin: 341px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 133.5px 8px; transform-origin: 133.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 368.5px 8px; transform-origin: 368.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 102.167px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 51.0833px; transform-origin: 404px 51.0833px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 128px 8.5px; transform-origin: 128px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssGCCATGGACATCsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 40px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 40px 8.5px; \"\u003eMiddle Rev\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 144px 8.5px; transform-origin: 144px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssCTACAGGTACCGsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 56px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 56px 8.5px; \"\u003eMiddle flipped\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 382px 8px; transform-origin: 382px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 163.467px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 81.7333px; transform-origin: 391px 81.7333px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 148.5px 8px; transform-origin: 148.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments may be reversed (Change from 003)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 111.5px 8px; transform-origin: 111.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments start at random positions\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome length is unconstrained\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 153.5px 8px; transform-origin: 153.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments may overlap by 16 to 47 characters\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 88.5px 8px; transform-origin: 88.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order is scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 128.5px 8px; transform-origin: 128.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 324.5px 8px; transform-origin: 324.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 84px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 42px; text-align: left; transform-origin: 384px 42px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 355.5px 8px; transform-origin: 355.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_003R(segs)\r\n% segs is an array of N segments of length 48\r\n% Construct the unique Gout sequence\r\n% Guaranteed 16 long blocks are unique\r\n  Gout=[];\r\nend","test_suite":"%%\r\ntic\r\nL=563*17;\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n  Gseg(j,:)=Gtruth(j:j+15);\r\n  Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n  Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n  break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=2000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n  Gseg(j,:)=Gtruth(j:j+15);\r\n  Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n  Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n  break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=4000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n  Gseg(j,:)=Gtruth(j:j+15);\r\n  Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n  Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n  break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":3,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":2,"test_suite_updated_at":"2021-07-16T14:52:10.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-06-27T17:37:02.000Z","updated_at":"2021-07-16T14:52:10.000Z","published_at":"2012-10-07T22:51:12.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nssssGCCATGGACATCsssss Middle Rev\\nssssCTACAGGTACCGsssss Middle flipped\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments may be reversed (Change from 003)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments start at random positions\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome length is unconstrained\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments may overlap by 16 to 47 characters\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order is scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"}],"problem_search":{"errors":[],"problems":[{"id":1308,"title":"Give me Hamming on five, hold the mayo","description":"A Hamming Number is a positive number that has no prime factor greater than 5.  Given a number X, determine how many Hamming numbers are less than or equal to that number.  Please note that 1 counts as a Hamming number.\r\n\r\nScore will be based on the amount of time it takes your code to solve the test suite.","description_html":"\u003cp\u003eA Hamming Number is a positive number that has no prime factor greater than 5.  Given a number X, determine how many Hamming numbers are less than or equal to that number.  Please note that 1 counts as a Hamming number.\u003c/p\u003e\u003cp\u003eScore will be based on the amount of time it takes your code to solve the test suite.\u003c/p\u003e","function_template":"function y = hamming1(x)\r\n  y = 5;\r\nend","test_suite":"feval(@assignin,'caller','score',5000); % msec\r\nforbidden = '(feval|eval|regexp|inline|tic|assert)';\r\nassert(isempty(regexp(evalc('type hamming1'),forbidden)));\r\n%%\r\ntic\r\n%%\r\nx = 5; y_correct = 5; assert(isequal(hamming1(x),y_correct))\r\n%%\r\nx = 100; y_correct = 34; assert(isequal(hamming1(x),y_correct))\r\n%%\r\nx = 123456; y_correct = 327; assert(isequal(hamming1(x),y_correct))\r\n%%\r\nx = 10^13; y_correct = 4301; assert(isequal(hamming1(x),y_correct))\r\n%%\r\nx=1:20; y=arrayfun(@(z) hamming1(z),2.^x);\r\ny_correct=[2 4 7 12 19 27 38 52 68 87 110 137 167 201 240 284 332 386 446 511];\r\nassert(isequal(y,y_correct));\r\ntval=1000*toc\r\nfeval(  @assignin,'caller','score',floor(min(5000,tval ))  );","published":true,"deleted":false,"likes_count":3,"comments_count":1,"created_by":1615,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":56,"test_suite_updated_at":"2014-02-28T20:31:24.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2013-02-28T20:44:01.000Z","updated_at":"2026-03-16T15:27:12.000Z","published_at":"2013-02-28T20:44:01.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eA Hamming Number is a positive number that has no prime factor greater than 5. Given a number X, determine how many Hamming numbers are less than or equal to that number. Please note that 1 counts as a Hamming number.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eScore will be based on the amount of time it takes your code to solve the test suite.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"},{"id":810,"title":"Hamming Weight - Size Scoring","description":"The Hamming Weight, \u003chttp://en.wikipedia.org/wiki/Hamming_weight wiki Hamming Weight\u003e, in its most simple form is the number of ones in the binary representation of a value.\r\n\r\nThe task here is to create a fast Hamming Weight function/method such that processing many 4K x 4K images of 32 bit integer can be evaluated rapidly. Saw this question posed on Stack Overflow.\r\n\r\n*Input:* Vector of length N of 32 bit integer values.\r\n\r\n*Output:* Total number of ones of the binary representation\r\n\r\n*Scoring:* Normal Cody Size, while solving multiple cases without timing out\r\n\r\nExamples: Input [7 ; 3], output=[3 ; 2];  [16 32], output [1 ; 1]; [0 4294967295]  output [ 0 ; 32] FFFFFFFF Hex = 2^32-1\r\n\r\nStressing Test vector : uint32(randi(2^32,[4096*4096,1])-1)\r\n\r\n\r\nHelpful, possibly, global variables.\r\n\r\nb1=uint32(1431655765); b2=uint32(858993459); b3=uint32(252645135) b4=uint32(16711935); b5=uint32(65535);\r\n\r\nHex: b1=55555555 b2=33333333 b3=0F0F0F0F b4=00FF00FF b5=0000FFFF\r\n\r\nThe array num_ones is created for values 0-65535 (0:2^16-1). num_ones(1)=0, num_ones(2)=1, num_ones(3)=1,num_ones(4)=2,...num_ones(65536)=15\r\n\r\nDue to lack of zero indexing num_ones(value+1) is number of ones for value.","description_html":"\u003cp\u003eThe Hamming Weight, \u003ca href=\"http://en.wikipedia.org/wiki/Hamming_weight\"\u003ewiki Hamming Weight\u003c/a\u003e, in its most simple form is the number of ones in the binary representation of a value.\u003c/p\u003e\u003cp\u003eThe task here is to create a fast Hamming Weight function/method such that processing many 4K x 4K images of 32 bit integer can be evaluated rapidly. Saw this question posed on Stack Overflow.\u003c/p\u003e\u003cp\u003e\u003cb\u003eInput:\u003c/b\u003e Vector of length N of 32 bit integer values.\u003c/p\u003e\u003cp\u003e\u003cb\u003eOutput:\u003c/b\u003e Total number of ones of the binary representation\u003c/p\u003e\u003cp\u003e\u003cb\u003eScoring:\u003c/b\u003e Normal Cody Size, while solving multiple cases without timing out\u003c/p\u003e\u003cp\u003eExamples: Input [7 ; 3], output=[3 ; 2];  [16 32], output [1 ; 1]; [0 4294967295]  output [ 0 ; 32] FFFFFFFF Hex = 2^32-1\u003c/p\u003e\u003cp\u003eStressing Test vector : uint32(randi(2^32,[4096*4096,1])-1)\u003c/p\u003e\u003cp\u003eHelpful, possibly, global variables.\u003c/p\u003e\u003cp\u003eb1=uint32(1431655765); b2=uint32(858993459); b3=uint32(252645135) b4=uint32(16711935); b5=uint32(65535);\u003c/p\u003e\u003cp\u003eHex: b1=55555555 b2=33333333 b3=0F0F0F0F b4=00FF00FF b5=0000FFFF\u003c/p\u003e\u003cp\u003eThe array num_ones is created for values 0-65535 (0:2^16-1). num_ones(1)=0, num_ones(2)=1, num_ones(3)=1,num_ones(4)=2,...num_ones(65536)=15\u003c/p\u003e\u003cp\u003eDue to lack of zero indexing num_ones(value+1) is number of ones for value.\u003c/p\u003e","function_template":"function y = Ham(x)\r\n% Input uint32\r\nglobal num_ones b1 b2 b3 b4 b5\r\n  y = x;\r\nend","test_suite":"%%\r\nglobal num_ones b1 b2 b3 b4 b5 net_time\r\nnet_time=4000; % default in case of time out (not needed)\r\n\r\nb1=uint32(1431655765); \r\nb2=uint32(858993459);\r\nb3=uint32(252645135);\r\nb4=uint32(16711935);\r\nb5=uint32(65535);\r\n \r\nnum_ones=uint32(zeros(65536,1)); \r\nfor i=0:65535  num_ones(i+1)=length( find( bitget( i, 1:32 ) ) ) ; \r\nend % Cody 0.996 sec\r\n%%\r\nglobal num_ones b1 b2 b3 b4 b5 net_time\r\n\r\nw=uint32(randi(2^32,[4096*1,1])-1); \r\nfor i=1:4 % Clear timing\r\n  vw=Ham(w);\r\nend\r\n\r\nwexpect=num_ones(mod(w,65536)+1)+num_ones(floor(double(w)/65536)+1); %1.56\r\nt0=clock;\r\n vw=Ham(w);\r\n vw=Ham(w);\r\n vw=Ham(w);\r\n vw=Ham(w);\r\ndt=etime(clock,t0)*250*1000; % avg of 4 runs in us\r\nfprintf('Time to execute 4096 values %.0f usec\\n',dt);\r\nassert(isequal(wexpect,vw),sprintf('\\nTime to execute 4096 values %.0f usec\\n',dt))\r\n%%\r\nglobal num_ones b1 b2 b3 b4 b5 net_time\r\n\r\nw=uint32(randi(2^32,[4096*1,1])-1); \r\n\r\n vw=Ham(w); % Three cycles of smaller vector\r\n vw=Ham(w);\r\n vw=Ham(w);\r\n\r\nw=uint32(randi(2^32,[4096*4096,1])-1);\r\nwexpect=num_ones(mod(w,65536)+1)+num_ones(floor(double(w)/65536)+1); %1.56\r\n\r\n \r\n  vw=Ham(w); % Big Prep file\r\n  vw=Ham(w); % Big Prep file\r\n \r\nt0=clock;\r\n vw=Ham(w);\r\n vw=Ham(w);\r\n vw=Ham(w);\r\n vw=Ham(w);\r\nnet_time=etime(clock,t0)*250; % avg of 4 runs\r\nfprintf('Time to execute 4096*4096 values %.0f msec\\n',net_time);\r\n\r\nassert(isequal(wexpect,vw),sprintf('\\nTime to execute 4096*4096 values %.0f msec\\n',net_time))\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":0,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":10,"test_suite_updated_at":null,"rescore_all_solutions":false,"group_id":1,"created_at":"2012-07-01T02:47:44.000Z","updated_at":"2012-07-01T05:25:20.000Z","published_at":"2012-07-01T05:25:20.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"targetMode\":\"\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"targetMode\":\"\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\\n\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe Hamming Weight,\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Hamming_weight\\\"\u003e\u003cw:r\u003e\u003cw:t\u003ewiki Hamming Weight\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e, in its most simple form is the number of ones in the binary representation of a value.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe task here is to create a fast Hamming Weight function/method such that processing many 4K x 4K images of 32 bit integer can be evaluated rapidly. Saw this question posed on Stack Overflow.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Vector of length N of 32 bit integer values.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Total number of ones of the binary representation\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eScoring:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Normal Cody Size, while solving multiple cases without timing out\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eExamples: Input [7 ; 3], output=[3 ; 2]; [16 32], output [1 ; 1]; [0 4294967295] output [ 0 ; 32] FFFFFFFF Hex = 2^32-1\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eStressing Test vector : uint32(randi(2^32,[4096*4096,1])-1)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eHelpful, possibly, global variables.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eb1=uint32(1431655765); b2=uint32(858993459); b3=uint32(252645135) b4=uint32(16711935); b5=uint32(65535);\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eHex: b1=55555555 b2=33333333 b3=0F0F0F0F b4=00FF00FF b5=0000FFFF\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe array num_ones is created for values 0-65535 (0:2^16-1). num_ones(1)=0, num_ones(2)=1, num_ones(3)=1,num_ones(4)=2,...num_ones(65536)=15\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDue to lack of zero indexing num_ones(value+1) is number of ones for value.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"},{"id":2674,"title":"Generalised Hamming Number","description":"Inspired by Project Euler n°204 and Problem 1308 by James\r\n\r\nA generalised Hamming number of type n, has no prime factor larger than n.\r\n\r\nFor example a generalised Hamming number of type 5 has no prime factor larger than 5.\r\n\r\nGiven a number X, determine how many generalised Hamming numbers n are less than or equal to that number. Please note that 1 counts as a Hamming number. \r\n\r\n\r\n","description_html":"\u003cp\u003eInspired by Project Euler n°204 and Problem 1308 by James\u003c/p\u003e\u003cp\u003eA generalised Hamming number of type n, has no prime factor larger than n.\u003c/p\u003e\u003cp\u003eFor example a generalised Hamming number of type 5 has no prime factor larger than 5.\u003c/p\u003e\u003cp\u003eGiven a number X, determine how many generalised Hamming numbers n are less than or equal to that number. Please note that 1 counts as a Hamming number.\u003c/p\u003e","function_template":"function y = hamming2(X,n)\r\n  X=n;\r\nend","test_suite":"%%\r\nX = 5;\r\nn=5;\r\ny_correct = 5;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 10;\r\nn=5;\r\ny_correct = 9;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 100;\r\nn=5;\r\ny_correct = 34;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 100;\r\nn=7;\r\ny_correct = 46;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 100;\r\nn=100;\r\ny_correct = 100;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 100;\r\nn=13;\r\ny_correct = 62;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 10^13;\r\nn=7;\r\ny_correct = 19674;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 10^5;\r\nn=13;\r\ny_correct = 1848;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 10^5;\r\nn=5;\r\ny_correct = 313;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 123456;\r\nn=5;\r\ny_correct = 327;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 10^13;\r\nn=3;\r\ny_correct = 624;\r\nassert(isequal(hamming2(X,n),y_correct))\r\n%%\r\nX = 123456;\r\nn=2;\r\ny_correct = 17;\r\nassert(isequal(hamming2(X,n),y_correct))","published":true,"deleted":false,"likes_count":13,"comments_count":5,"created_by":5390,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":361,"test_suite_updated_at":"2014-11-17T10:17:26.000Z","rescore_all_solutions":false,"group_id":8,"created_at":"2014-11-17T09:33:12.000Z","updated_at":"2026-02-15T13:23:19.000Z","published_at":"2014-11-17T10:14:18.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eInspired by Project Euler n°204 and Problem 1308 by James\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eA generalised Hamming number of type n, has no prime factor larger than n.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eFor example a generalised Hamming number of type 5 has no prime factor larger than 5.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven a number X, determine how many generalised Hamming numbers n are less than or equal to that number. Please note that 1 counts as a Hamming number.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"},{"id":797,"title":"Genome Sequence 003R: Sequence DNA of random positioned and flipped segments","description":"This is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments. DNA Sequencing is naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nssssGCCATGGACATCsssss Middle Rev\r\nssssCTACAGGTACCGsssss Middle flipped\r\nssssssssssssGACATTACG\r\nGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\r\nSegments may be reversed (Change from 003)\r\nSegments start at random positions\r\nGenome length is unconstrained\r\nLength of each segment - 48\r\nAll segments may overlap by 16 to 47 characters\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order is scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome vector of values [0,1,2,3]\r\nExample: [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\r\nFuture: Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 726.633px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 363.317px; transform-origin: 407px 363.317px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 341px 8px; transform-origin: 341px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 133.5px 8px; transform-origin: 133.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 368.5px 8px; transform-origin: 368.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 102.167px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 51.0833px; transform-origin: 404px 51.0833px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 128px 8.5px; transform-origin: 128px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssGCCATGGACATCsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 40px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 40px 8.5px; \"\u003eMiddle Rev\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 144px 8.5px; transform-origin: 144px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssCTACAGGTACCGsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 56px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 56px 8.5px; \"\u003eMiddle flipped\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 382px 8px; transform-origin: 382px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 163.467px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 81.7333px; transform-origin: 391px 81.7333px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 148.5px 8px; transform-origin: 148.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments may be reversed (Change from 003)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 111.5px 8px; transform-origin: 111.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments start at random positions\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome length is unconstrained\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 153.5px 8px; transform-origin: 153.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments may overlap by 16 to 47 characters\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 88.5px 8px; transform-origin: 88.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order is scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 128.5px 8px; transform-origin: 128.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 324.5px 8px; transform-origin: 324.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 84px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 42px; text-align: left; transform-origin: 384px 42px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 355.5px 8px; transform-origin: 355.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_003R(segs)\r\n% segs is an array of N segments of length 48\r\n% Construct the unique Gout sequence\r\n% Guaranteed 16 long blocks are unique\r\n  Gout=[];\r\nend","test_suite":"%%\r\ntic\r\nL=563*17;\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n  Gseg(j,:)=Gtruth(j:j+15);\r\n  Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n  Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n  break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=2000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n  Gseg(j,:)=Gtruth(j:j+15);\r\n  Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n  Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n  break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=4000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n  Gseg(j,:)=Gtruth(j:j+15);\r\n  Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n  Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n  break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":3,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":2,"test_suite_updated_at":"2021-07-16T14:52:10.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-06-27T17:37:02.000Z","updated_at":"2021-07-16T14:52:10.000Z","published_at":"2012-10-07T22:51:12.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nssssGCCATGGACATCsssss Middle Rev\\nssssCTACAGGTACCGsssss Middle flipped\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments may be reversed (Change from 003)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments start at random positions\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome length is unconstrained\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments may overlap by 16 to 47 characters\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order is scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 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