Hi Henry - It's difficult to know without knowing how you made the model. The code example in BioJava in Anger http://www.biojava.org/docs/bj_in_anger/profileHMM.htm worked last time I tried. It could be that the ProfileHMM has not been properly initialized. It could also be a real bug :)
If the above example doesn't help can you send the code where you set up the HMM? - Mark > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > Sent: Friday, 11 July 2003 3:56 a.m. > To: [EMAIL PROTECTED] > Subject: [Biojava-l] Creating a dp object for a profile HMM (2) > > > Hi, > > I have narrowed down the problem in creating a dp object for > a profile HMM to a > possible bug in the code below from the DP class. I could > really use some help > here.. > > Thanks, > > Henry Romijn > > public static State[] stateList(MarkovModel mm) > throws IllegalSymbolException, IllegalTransitionException, > BioException { > > // .....code here works ok > > for (Iterator addStates = alpha.iterator(); > addStates.hasNext(); ) { > Object state = addStates.next(); > if (state instanceof MagicalState) { > emissionStates.add(0, state); > } > else if (state instanceof EmissionState) { > emissionStates.add(state); > } > else { > ListIterator checkOld = dotStates.listIterator(); > int insertPos = -1; > while (checkOld.hasNext() && insertPos == -1) { > Object oldState = checkOld.next(); > if (comp.compare(state, oldState) == comp.LESS_THAN) { > insertPos = checkOld.nextIndex() - 1; > } > } > if (insertPos >= 0) { > dotStates.add(insertPos, state); > } > else { > dotStates.add(state); > } > } > } > > //...... > } > > > Quoting [EMAIL PROTECTED]: > > > Hi, > > > > After I have successfully created and initialized a profile > HMM, I try > > to > > register the model with a new DP object as follows: > > > > DP dp = DPFactory.DEFAULT.createDP(profile); > > > > This causes the program to hang. Any ideas why this may not work? > > > > Thanks, > > > > Henry Romijn > > > > _______________________________________________ > > Biojava-l mailing list - [EMAIL PROTECTED] > > http://biojava.org/mailman/listinfo/biojava-l > > > > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
