Yesterday’s disclosure that as part of the Boston peace treaty Apple Computer Inc and Microsoft Corp will be aligning their future Java technologies – including Java Virtual Machine implementations – looks on paper to be bad news for Sun Microsystems Inc, which believes the kind of Windows-specific Java technologies Microsoft is creating for developers is poisoning Java. Even though Apple said the Java component of its deal won’t force its customers to use Microsoft’s proprietary extensions to Java, it’s not clear how it will be able to avoid being tainted by Redmond’s work. Does Apple think Microsoft is poisoning Java? We don’t know is what Apple executives told us on Wednesday, but maintained that its work with Sun on Java Foundation Classes will continue. Apple CFO Fred Anderson said both Apple and Microsoft would bring value-add to the collaboration. Apple executives called Sun’s JavaSoft unit yesterday to try and calm the waters, saying their relationship on Java would be unaffected. Following Apple’s call Sun said that still didn’t know what the implications would be.