Trojans,viruses etc

[#1]

Assume you transferred a program from a cd on to your hard drive but when you come to run the program your virus scanner detects a virus, trojan etc and you then transfer it to quarantine  or delete it, can you still run the program or is the virus/trojan still there ?
Equally are you already in trouble simply by transferring the program or can it only affect you once you attempt to open/run the program ?

[#2]

the answer to all those question, unfortunately is "how long is a piece of string"
some Virus Trojan install themselves without you knowing it, just opening a web site does it
A good antivirus program can "heal" the problem and the infected program can then be run again
dont try and do anything with items in your virus vault, wait a while to make sure it is not wanted and them empty the vault

[#3]

The virus is in the program (or the virus is the program)... it is the program that has the virus in it that has been transferred to the virus vault, not the virus itself.
The program should not be run or your system will become infected. If you want to run it, you will have to source another uninfected version.

[#4]

Most viruses masquerade as legitimate programs so the virus is the program.  A very small minority of viruses mange to append themselves onto legitimate programs so that running the legitimate program also runs the virus.  A virus scanner may be able to heal such programs by removing the virus component.
You could copy your program executable file to your hard drive, scan it with your virus scanner and then see if it is still there but reduced in size (as would be the case for a 'healed' file) or removed completely.  Personally, I would not take the risk unless I had no other option.