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Most useful restriction enzymes cut DNA at specific recognition sites, usually four to six nucleotides in length There can be multiple restriction sites for a single endonuclease within a given piece of DNA, there can be only one (a unique restriction site), or there can be none It all depends on the sequence of the specific piece of DNA in question Cutting with restriction endonucleases is very useful for moving specific pieces of DNA around from place to place It s also a useful way to name pieces of DNA For example, a piece of DNA that is cut from a bigger piece of DNA is often named by size and given a surname that corresponds to the two restriction enzymes that did the cutting the 03-kb EcoRI-BamHI fragment Restriction enzymes themselves are named for the bacterial strains from which they were initially isolated A restriction map shows the location of restriction sites in a given DNA sequence When digested with two (or more) restriction enzymes at the same time, most large pieces of DNA give a specific pattern of different-sized DNA fragments depending on the distance separating the different cleavage sites These different fragments can then be separated by size on an agarose gel By working backward (biochemists are good at this) from the sizes of the different DNA fragments, it is possible to construct a map that locates the different restriction sites along a given piece of DNA For example, if we cut the 36-kb piece of DNA in Fig 6-1 with SmaI, we would see two bands on the agarose gel 19 and 17 kb This would tell us that the SmaI site is very near the middle of the fragment We could start constructing our map by putting the 17-kb fragment on the left side or the right side it doesn t matter, and we can t know which is right (or left) In Fig 6-1, the DNA is arbitrarily put down with the smaller fragment on the right If we cut with BamHI, we get fragments that are 09 and 27 kb Again we wouldn t know whether to put the BamHI site on the right or left of the map, but here it does matter because we already have the SmaI site on the map The way to decide where to put the BamHI site is to cut with both BamHI and SmaI Let s say that you get fragments of 09, 10, and 17 kb Notice that the 17-kb fragment is the same size as in the digest with SmaI alone This tells you that the BamHI site is in the 19-kb SmaI fragment, that is, on the left side of our map By going through this kind of reasoning over and over, it is possible to construct a map of restriction sites along your piece of DNA Restriction enzymes that recognize a specific sequence of five nucleotides should cut the DNA, on average, every 45 base pairs (this is the frequency with which a given sequence of five nucleotides would occur by chance), or every 1024 base pairs As a result, the average size.

$a = 4 + 5;

Example C-16 shows the code-behind file for Exercise 4-3.

can be reduced from four opcodes to three by instead creating a parent opcode that assigns a value of 9 to the $a variable:

$a = 9;

12 03

You can see the effect of this by comparing the opcode tree for the more complex statement with the variable and constant tree you saw earlier:

DEVELOPING APPLICATIONS { 6

TYPE = leave ===> DONE FLAGS = (VOID,KIDS,PARENS) { TYPE = enter ===> 2 } { TYPE = nextstate ===> 3 FLAGS = (VOID) LINE = 1 } { TYPE = sassign ===> 6 FLAGS = (VOID,KIDS,STACKED) { TYPE = const ===> 4 FLAGS = (SCALAR) SV = IV(9) } { TYPE = null ===> (5) (was rv2sv) FLAGS = (SCALAR,KIDS,REF,MOD,SPECIAL)

04 05

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{ 4 TYPE = gvsv ===> 5 FLAGS = (SCALAR) GV = main::a } } } }

.

03 07

The next optimization process is context propagation, which is the act of defining the context to a specific opcode and its children You are used to the terms scalar context or list context when creating and using functions Internally, Perl also supports contexts for void, Boolean, and lvalue statements Context propagation works top down that is, parent opcodes are examined first, and the context requirement is then propagated down to child opcodes The final optimization stage is a process of reduction and is handled by the peephole optimizer This process effectively executes the opcode tree, but without actually doing anything The purpose is to look ahead to future opcodes in the tree and reduce them as much as possible In Perl, the lookahead is currently only two statements, which means that a maximum of three statements could be reduced to just one statement Any larger figure would slow down the optimization process to the point that any gains made in optimizing the opcode tree would be lost in the optimization process itself Remember that Perl is still essentially an interpreter, and unlike C or Java the opcode tree is regenerated each time a script is executed When you execute a Perl script, Perl doesn t simply reexecute the previously optimized opcode tree Perl assumes the source file has changed (probably a good idea) Ultimately, this makes individual executions of the same script slower than they might be if the peephole optimization were allowed to look ahead further On the other hand, it ensures that every execution of a script is optimized to a reasonable point, even if you change just one character in the original script each time Unfortunately, there is no way of controlling the peephole process You cannot specify, for example, that when creating a stand-alone executable, the peephole lookahead value be greater than two, although this would be a great idea.

Once all three stages of the optimization have taken place, it s time to execute the code The actual path of execution is not as sequential as it may have appeared earlier All opcodes are numbered, and it s the value of the op_next (from the op structure) that defines the actual execution path Since Perl supports conditional statements like if and loops like while, some opcodes may never be executed, or may be executed several

Example C-16. The code-behind file for Exercise 4-3

20:

10 09

By default, you must have only one ScriptManager but you may need to add a proxy object (ScriptManagerProxy control) to ensure that the code, perhaps inside of a set of nested master pages, has the ScriptManager object present to execute properly

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