From bernd.jagla@pasteur.fr Mon Dec 03 14:29:13 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TfW5A-000nMh-CK>; Mon, 03 Dec 2012 14:29:12 +0100 Received: from mail-interne3.pasteur.fr ([157.99.64.82]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TfW5A-002z8t-9J>; Mon, 03 Dec 2012 14:29:12 +0100 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 75178381051 for ; Mon, 3 Dec 2012 14:29:10 +0100 (CET) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [127.0.0.1] (zillumina.pt2.pasteur.fr [157.99.241.40]) (using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by mail-interne3.pasteur.fr (Postfix) with ESMTPS id 3657D381044 for ; Mon, 3 Dec 2012 14:29:10 +0100 (CET) Message-ID: <50BCA925.5050203@pasteur.fr> Date: Mon, 03 Dec 2012 14:29:09 +0100 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:17.0) Gecko/17.0 Thunderbird/17.0 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Antivirus: avast! (VPS 120821-0, 08/21/2012), Outbound message X-Antivirus-Status: Clean X-Originating-IP: 157.99.64.82 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1354541352-00000B1F-8024B8C0/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.124466, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=0.0 required=5.0 tests=none X-Spam-Checker-Version: SpamAssassin 3.3.2 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] build system rewrite... X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 03 Dec 2012 13:29:13 -0000 Hi, I have just checked out the seqan svn to a fresh repository and see the following message: -- Configuring docs *************************************************************************** * /!\ NOTICE: YOU HAVE USED THE THE OLD SEQAN BUILD SYSTEMS FUNCTIONS /!\ * *************************************************************************** For now, we still support the old build system such that you can migrate to the new system on a slower upgrade path. However, please do so in the near future since support for the new build system will stop before the next (1.4) release in early 2013. *************************************************************************** * /!\ NOTICE: YOU HAVE USED THE THE OLD SEQAN BUILD SYSTEMS FUNCTIONS /!\* *************************************************************************** -- Configuring done Is this normal? Also, I found an e-mail that explains a bit that there is a new system with a link to a description on what the new system does... It would helpful though to have a document on how to migrate from one to the other... I guess this might be too obvious to be mentioned, but then again... Thanks a lot for the clarifications... Best, Bernd From bernd.jagla@pasteur.fr Mon Dec 03 14:52:35 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TfWRm-000p94-E8>; Mon, 03 Dec 2012 14:52:34 +0100 Received: from mail-interne3.pasteur.fr ([157.99.64.82]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TfWRm-0032ry-B9>; Mon, 03 Dec 2012 14:52:34 +0100 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id E7A79381051 for ; Mon, 3 Dec 2012 14:52:25 +0100 (CET) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [127.0.0.1] (zillumina.pt2.pasteur.fr [157.99.241.40]) (using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by mail-interne3.pasteur.fr (Postfix) with ESMTPS id C38ED381044 for ; Mon, 3 Dec 2012 14:52:25 +0100 (CET) Message-ID: <50BCAE99.8060509@pasteur.fr> Date: Mon, 03 Dec 2012 14:52:25 +0100 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:17.0) Gecko/17.0 Thunderbird/17.0 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: <50BCA925.5050203@pasteur.fr> In-Reply-To: <50BCA925.5050203@pasteur.fr> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Antivirus: avast! (VPS 120821-0, 08/21/2012), Outbound message X-Antivirus-Status: Clean X-Originating-IP: 157.99.64.82 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1354542754-00000B1F-3804B550/3724824646-0/0-1 X-Bogosity: Ham, tests=bogofilter, spamicity=0.421321, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=1.0 required=5.0 tests=FU_XPURGATE_SUSP X-Spam-Checker-Version: SpamAssassin 3.3.2 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: x Subject: Re: [Seqan-dev] build system rewrite... X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 03 Dec 2012 13:52:35 -0000 One more piece of information on this: when using clang++ ( cmake ../../seqan-trunk -DCMAKE_BUILD_TYPE=Debug \ -DCMAKE_CXX_COMPILER=/pasteur/solexa2/solexa_travail/PF2/programs/clang/build/Debug+Asserts/bin/clang++ ) I don't get this message... B On 12/3/2012 2:29 PM, Bernd Jagla wrote: > Hi, > > I have just checked out the seqan svn to a fresh repository and see > the following message: > > -- Configuring docs > *************************************************************************** > > * /!\ NOTICE: YOU HAVE USED THE THE OLD SEQAN BUILD SYSTEMS > FUNCTIONS /!\ * > *************************************************************************** > > > For now, we still support the old build system such that you can > migrate to the new system on a slower upgrade path. However, please > do so in the near future since support for the new build system will > stop before the next (1.4) release in early 2013. > > *************************************************************************** > > * /!\ NOTICE: YOU HAVE USED THE THE OLD SEQAN BUILD SYSTEMS > FUNCTIONS /!\* > *************************************************************************** > > -- Configuring done > > Is this normal? > > Also, I found an e-mail that explains a bit that there is a new system > with a link to a description on what the new system does... It would > helpful though to have a document on how to migrate from one to the > other... I guess this might be too obvious to be mentioned, but then > again... > > Thanks a lot for the clarifications... > > Best, > > Bernd > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > From manuel.holtgrewe@fu-berlin.de Tue Dec 04 13:21:58 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TfrVc-003pjx-TE>; Tue, 04 Dec 2012 13:21:57 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TfrVc-0009kR-RT>; Tue, 04 Dec 2012 13:21:56 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TfrVc-002oQn-GB>; Tue, 04 Dec 2012 13:21:56 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.02.0318.004; Tue, 4 Dec 2012 13:21:55 +0100 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] build system rewrite... Thread-Index: AQHN0Vo1Q2FsVNUG0ES+h97rueEfX5gHB2GAgAGJoDs= Message-ID: References: <50BCA925.5050203@pasteur.fr>,<50BCAE99.8060509@pasteur.fr> In-Reply-To: <50BCAE99.8060509@pasteur.fr> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 Date: Tue, 04 Dec 2012 13:21:55 +0100 X-Original-Date: Tue, 4 Dec 2012 12:21:55 +0000 X-Originating-IP: 130.133.170.203 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1354623716-00000B1F-C422E99B/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.137693, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.3.2 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] build system rewrite... X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 04 Dec 2012 12:21:58 -0000 Dear Bernd,=0A= =0A= I tried to reproduce the problem but could not.=0A= =0A= My guess is that you might have some old CMakeCache.txt lying around. Pleas= e try to create a clean checkout and try again.=0A= =0A= HTH,=0A= Manuel=0A= ________________________________________=0A= From: Bernd Jagla [bernd.jagla@pasteur.fr]=0A= Sent: Monday, December 03, 2012 2:52 PM=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: Re: [Seqan-dev] build system rewrite...=0A= =0A= One more piece of information on this:=0A= when using clang++=0A= (=0A= cmake ../../seqan-trunk -DCMAKE_BUILD_TYPE=3DDebug \=0A= -DCMAKE_CXX_COMPILER=3D/pasteur/solexa2/solexa_travail/PF2/programs/clang/b= uild/Debug+Asserts/bin/clang++=0A= )=0A= I don't get this message...=0A= =0A= B=0A= On 12/3/2012 2:29 PM, Bernd Jagla wrote:=0A= > Hi,=0A= >=0A= > I have just checked out the seqan svn to a fresh repository and see=0A= > the following message:=0A= >=0A= > -- Configuring docs=0A= > *************************************************************************= **=0A= >=0A= > * /!\ NOTICE: YOU HAVE USED THE THE OLD SEQAN BUILD SYSTEMS=0A= > FUNCTIONS /!\ *=0A= > *************************************************************************= **=0A= >=0A= >=0A= > For now, we still support the old build system such that you can=0A= > migrate to the new system on a slower upgrade path. However, please= =0A= > do so in the near future since support for the new build system will= =0A= > stop before the next (1.4) release in early 2013.=0A= >=0A= > *************************************************************************= **=0A= >=0A= > * /!\ NOTICE: YOU HAVE USED THE THE OLD SEQAN BUILD SYSTEMS=0A= > FUNCTIONS /!\*=0A= > *************************************************************************= **=0A= >=0A= > -- Configuring done=0A= >=0A= > Is this normal?=0A= >=0A= > Also, I found an e-mail that explains a bit that there is a new system=0A= > with a link to a description on what the new system does... It would=0A= > helpful though to have a document on how to migrate from one to the=0A= > other... I guess this might be too obvious to be mentioned, but then=0A= > again...=0A= >=0A= > Thanks a lot for the clarifications...=0A= >=0A= > Best,=0A= >=0A= > Bernd=0A= >=0A= > _______________________________________________=0A= > seqan-dev mailing list=0A= > seqan-dev@lists.fu-berlin.de=0A= > https://lists.fu-berlin.de/listinfo/seqan-dev=0A= >=0A= =0A= =0A= _______________________________________________=0A= seqan-dev mailing list=0A= seqan-dev@lists.fu-berlin.de=0A= https://lists.fu-berlin.de/listinfo/seqan-dev=0A= From Jochen.Singer@fu-berlin.de Mon Dec 10 17:44:46 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Ti6TF-003PDz-3u>; Mon, 10 Dec 2012 17:44:45 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Ti6TF-000RgF-2B>; Mon, 10 Dec 2012 17:44:45 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Ti6TE-0044X2-Pc>; Mon, 10 Dec 2012 17:44:45 +0100 Received: from EX01B.campus.fu-berlin.de ([130.133.170.131]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.02.0318.004; Mon, 10 Dec 2012 17:44:39 +0100 From: "Singer, Jochen" To: SeqAn Development Thread-Topic: Segment implementation changed Thread-Index: AQHN1vWlXNakxQEUfUKcDSf7dRzRMQ== Message-ID: <73449C0BDF63A24B9D899806E0BA25240B6813@ex01b.campus.fu-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_73449C0BDF63A24B9D899806E0BA25240B6813ex01bcampusfuberl_" MIME-Version: 1.0 Date: Mon, 10 Dec 2012 17:44:38 +0100 X-Original-Date: Mon, 10 Dec 2012 16:44:38 +0000 X-Originating-IP: 130.133.170.203 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1355157885-00000B1F-520E0B9A/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.058313, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.2 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Segment implementation changed X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 10 Dec 2012 16:44:46 -0000 --_000_73449C0BDF63A24B9D899806E0BA25240B6813ex01bcampusfuberl_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Hi all, we cleaned up the Segment class implementation such that our (and your) cod= e becomes more readable and less error prone. For example, the "assign" function did two different things, depending on w= hether or not the corresponding segment was already assigned to a string. F= or the following example: String text =3D "ABCDEFGH"; Segment< String, InfixSegment> inf; assign(inf, infix(text, 2, 5)); assign(inf, infix(text, 5, 8)); the first assign function would assign text to inf as the underlying string= , while the second assign would assign the values from text[5:7] to text[2:= 6]. Therefore, text was changed to "ABFGHFGH". Since this behavior is not obvious and you might not able to tell what is h= appening we removed the second alternative, such that the assign function a= lways sets the underlying string of an segment and does not change the unde= rlying string at any time. In addition, we also remove every function working on segments which change= d the underlying string, such as append, appendValue, resize, replace =85 T= he reason for this is, that you are able to use those functions directly on= the underlying string. Using the functions directly on the underlying stri= ng makes your intention obvious and the code easier to read. If you have any questions just write an email. Cheers, Jochen --_000_73449C0BDF63A24B9D899806E0BA25240B6813ex01bcampusfuberl_ Content-Type: text/html; charset="Windows-1252" Content-ID: <8D350BEC886B7A4FB6BD234DB5E32DED@campus.fu-berlin.de> Content-Transfer-Encoding: quoted-printable Hi all,

we cleaned up the Segment class implementation such that our (and your= ) code becomes more readable and less error prone.

For example, the "assign" function did two different things,= depending on whether or not the corresponding segment was already assigned= to a string. For the following example:

String<char> text =3D "ABCDEFGH";
Segment< String<char>, InfixSegment> inf;
assign(inf, infix(text, 2, 5)); 
assign(inf, infix(text, 5, 8)); 

the first assign function would assign text to inf as the underlying string, while the second assign would assign the values from text[5:7] to text[2:6]= . Therefore, text was changed to "ABFGHFGH". 

Since this behavior is not obvious and you might not able to tell what= is happening we removed the second alternative, such that the assign funct= ion always sets the underlying string of an segment and does not change the= underlying string at any time. 

In addition, we also remove every function working on segments which c= hanged the underlying string, such as append, appendValue, resize, replace = =85 The reason for this is, that you are able to use those functions direct= ly on the underlying string. Using the functions directly on the underlying string makes your intention obvio= us and the code easier to read.

If you have any questions just write an email. 

Cheers,
Jochen
--_000_73449C0BDF63A24B9D899806E0BA25240B6813ex01bcampusfuberl_-- From rene.maerker@fu-berlin.de Fri Dec 21 22:07:16 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Tm9oI-000iq9-Rh>; Fri, 21 Dec 2012 22:07:14 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Tm9oI-003j8e-Po>; Fri, 21 Dec 2012 22:07:14 +0100 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Tm9oI-003aw4-EY>; Fri, 21 Dec 2012 22:07:14 +0100 Received: from EX03B.campus.fu-berlin.de ([130.133.170.135]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.02.0328.009; Fri, 21 Dec 2012 22:07:13 +0100 From: =?iso-8859-1?Q?Rahn=2C_Ren=E9?= To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: Replacing the alignment algorithms. Thread-Index: AQHN35AURM38hJxriUuqc0Mc71tEQZgju/Z4 Message-ID: <1E17D2681681D24D9E09E2B9A726C6D43F504C8B@ex03b.campus.fu-berlin.de> References: <1E17D2681681D24D9E09E2B9A726C6D43F500B95@ex03b.campus.fu-berlin.de> In-Reply-To: <1E17D2681681D24D9E09E2B9A726C6D43F500B95@ex03b.campus.fu-berlin.de> Accept-Language: de-DE, en-US Content-Language: de-DE X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_1E17D2681681D24D9E09E2B9A726C6D43F504C8Bex03bcampusfube_" MIME-Version: 1.0 Date: Fri, 21 Dec 2012 22:07:12 +0100 X-Original-Date: Fri, 21 Dec 2012 21:07:12 +0000 X-Originating-IP: 130.133.170.201 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1356124034-00000B1F-5CE3C979/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000009, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.2 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Replacing the alignment algorithms. X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 21 Dec 2012 21:07:16 -0000 --_000_1E17D2681681D24D9E09E2B9A726C6D43F504C8Bex03bcampusfube_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, we have made substantial modifications to the alignment algorithms. The ent= ire alignment module was refactored concerning the algorithms so with the c= urrent trunk version you will use the new implementation which facilitates = a unification of all standard dp algorithms. For a detailed list of changes you can review the white paper on http://tra= c.seqan.de/wiki/WhitePapers/AlignmentAlgorithmsStructure. There you find a description of the general concept of the new alignment al= gorithms and where you can find the source code regarding the new implement= ation. The global alignment interfaces haven't changed, so that most of you should= have no problems using the new core. We also still support the old algorit= hms but they are not included in the align.h header file anymore. You have = to include them explicitly in order to get access to the old implementation= s. Note that in the early year of 2013 we will remove them completely from = our trunk. The Waterman-Eggert implementation is yet not affected by the ch= ange but the migration of this algorithm will come soon. Note that for the specialized alignment algorithms Meyers-Bitvector, Hirsch= berg and Meyers-Hirschberg, will be not affected by the remodelling. There are some changes that might affect your algorithms: 1. Now all dp algorithms use the same traceback function: All InDels are = left-aligned. And a gap in the horizontal sequence is preferred over a gap = in the vertical sequence if multiple alignments are possible. This is diffe= rent to the behavior of the old Needleman-Wunsch and the Smith-Waterman alg= orithm but the same as with the Gotoh implementation. 2. The global score interfaces have been modified. Please, review the wh= ite paper http://trac.seqan.de/wiki/WhitePapers/AlignmentAlgorithmsStructur= e to get more details. (information regarding the score will be updated soo= n) 3. Now we also support Fragments for the local alignment. 4. You can determine the gap cost function by specifying the costs for ga= p open and gap extend of the Score object. 5. We do not support all bands anymore. That is for the standard global a= lignment the band has to cover both the sink and the origin of the alignmen= t matrix. If this is not given no alignment will be computed and minus infi= nity (MinValue::VALUE, where TScoreValue is the value type for= the Score object), will be reported. In order to compute bands where both,= the lower and the upper diagonal of the band, cross the same row, and acco= rdingly column, the respective initial- or/and end-gaps have to be free. We support most of the old behavior hoping this makes the migration less la= borious. Nonetheless, don't hesitate to contact me if something is broken i= n your implementation so we can figure out what happened and how to fix it. I wish you all a merry Christmas and a happy New Year!!! Kind regards, Ren=E9 Rahn --- Ren=E9 Rahn Ph.D. Student ------------------------------------------------ rene.rahn@fu-berlin.de +49 (0)30 838 75 277 ------------------------------------------------ Algorithmic Bioinformatics (ABI) Department of Informatics Room 018 ------------------------------------------------ Freie Universit=E4t Berlin Takustra=DFe 9 14195 Berlin ------------------------------------------------ --_000_1E17D2681681D24D9E09E2B9A726C6D43F504C8Bex03bcampusfube_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all, 
http://trac.seqan.de/wiki/WhitePapers/AlignmentAlgori= thmsStructure.
There you find a description of the general concept of the new alignme= nt algorithms and where you can find the source code regarding the new impl= ementation.

The global alignment interfaces haven't changed, so that most of you should= have no problems using the new core. We also still support the old algorit= hms but they are not included in the align.h header file anymore. You have = to include them explicitly in order to get access to the old implementations. Note that in the early year of 2= 013 we will remove them completely from our trunk. The Waterman-Eggert impl= ementation is yet not affected by the change but the migration of this algo= rithm will come soon.
Note that for the specialized alignment algorithms Meyers-Bitvector, Hirsch= berg and Meyers-Hirschberg, will be not affected by the remodelling.

There are some changes that might affect your algorithms:
  1. Now all dp algorithms use the same traceback function: All I= nDels are left-aligned. And a gap in the horizontal sequence is preferred o= ver a gap in the vertical sequence if multiple alignments are possible. Thi= s is different to the behavior of the old Needleman-Wunsch and the Smith-Waterman algorithm but the same as with= the Gotoh implementation.
  2. The global score interfaces  have been modified. Please= , review the white paper http://trac.seqan.de/wi= ki/WhitePapers/AlignmentAlgorithmsStructure to get more details. (information regarding the score will be updated soon)
  3. Now we also support Fragments for the local alignment. =
  4. You can determine the gap cost function by specifying the co= sts for gap open and gap extend of the Score object.
  5. We do not support all bands anymore. That is for the standar= d global alignment the band has to cover both the sink and the origin of th= e alignment matrix. If this is not given no alignment will be computed and = minus infinity (MinValue<TScoreValue>::VALUE, where TScoreValue is the value type for the Score object), will be reporte= d. In order to compute bands where both, the lower and the upper diagonal o= f the band, cross the same row, and accordingly column, the respective init= ial- or/and end-gaps have to be free. 

We support most of the old behavior hoping this makes the migration le= ss laborious. Nonetheless, don't hesitate to contact me if something i= s broken in your implementation so we can figure out what happened and how = to fix it.

I wish you all a merry Christmas and a happy New Year!!!


Kind regards,

Ren=E9 Rahn
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Ren=E9 Rahn <= /span>
Ph.D. Student
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+49 (0)30 838 75 277
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Algorithmic Bioinformatics (ABI)
Department of Informatics 
Room  018
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Freie Universit=E4t Berlin
Takustra=DFe 9 
14195 Berlin
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