#60 Errors when compiling all Java classes in version 39.03

[Pierre Gruet]

Hello,

I found some errors in the code of version 39.03, it is not possible to build all Java classes. Indeed, attempting to build all of them gives:

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current/jgi/CrisprFinder3.java:478: error: no suitable method found for load(String,int,int,int,boolean)
refMap=SeqMap.load(ref, kRef, maskMiddleRef, minRefCount, true);
^
method SeqMap.load(String,int,int,int,boolean,CellNet) is not applicable
(actual and formal argument lists differ in length)
method SeqMap.load(ArrayList<read>,int,int,int,boolean,CellNet) is not applicable
(actual and formal argument lists differ in length)
current/jgi/CrisprFinder2.java:471: error: no suitable method found for load(String,int,int,int,boolean)
refMap=SeqMap.load(ref, kRef, maskMiddleRef, minRefCount, true);
^
method SeqMap.load(String,int,int,int,boolean,CellNet) is not applicable
(actual and formal argument lists differ in length)
method SeqMap.load(ArrayList<read>,int,int,int,boolean,CellNet) is not applicable
(actual and formal argument lists differ in length)
current/jgi/RepeatFinder.java:512: error: cannot find symbol
return maskRepeat(((Read)r.o).bases, r.a, r.b);
^
symbol: variable o
location: variable r of type CRange
current/jgi/CrisprFinder4.java:478: error: no suitable method found for load(String,int,int,int,boolean)
refMap=SeqMap.load(ref, kRef, maskMiddleRef, minRefCount, true);
^
method SeqMap.load(String,int,int,int,boolean,CellNet) is not applicable
(actual and formal argument lists differ in length)
method SeqMap.load(ArrayList<read>,int,int,int,boolean,CellNet) is not applicable
(actual and formal argument lists differ in length)</read></read></read>

----------------------------------8<----------------------------------------

While the attached patch allows one to compile with no error, I trust the classes (or at least some of their methods) are not useful as you did not catch these errors using your custom build. Maybe the useless portions of code could be removed.

Best,
Pierre

[Brian Bushnell]

Hi Pierre,

Sorry about that, those two and a couple other versions of CrisprFinder made it into the release accidentally. Only CrisprFinder.java should be there. I'll delete them for the next release. Thanks for notifying me!

-Brian