From benjamin@menkuec.de Tue Jul 21 22:32:38 2015 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1ZHeDM-000zGL-Nf>; Tue, 21 Jul 2015 22:32:36 +0200 Received: from mo4-p00-ob.smtp.rzone.de ([81.169.146.219]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1ZHeDM-0015yA-M3>; Tue, 21 Jul 2015 22:32:36 +0200 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; t=1437510755; l=494; s=domk; d=menkuec.de; h=Content-Transfer-Encoding:Content-Type:Subject:To:MIME-Version:From: Date; bh=Dl9BzcXUGF0qbVcqwwljbSegV6l5PnvtEfuvylxifkw=; b=ITWd81rmXb6JeNFVbklLkIX2p8tu6dYuA5zg3Keo+VhoIq0FIaTZyZYP4SfQ6g8sDK2 u+3VpkbLL8LlkPijMvFmgBspjsxP4fMGbuT42n//xBHfzurkkNzqsbpvh1gQp3K0pZgDP mU6K6KqzNN/fdM5xk7aFbgMObYtibQWVAg0= X-RZG-AUTH: :LmkKf0GlcvE1OcMjl5gAC6YvAPkDYM7jGirUFFsff+WOX1hogpYCszNCbw== X-RZG-CLASS-ID: mo00 Received: from [192.168.1.124] (dslb-178-008-100-001.178.008.pools.vodafone-ip.de [178.8.100.1]) by smtp.strato.de (RZmta 37.8 DYNA|AUTH) with ESMTPSA id N0452er6LKWZryd (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (curve secp521r1 with 521 ECDH bits, eq. 15360 bits RSA)) (Client did not present a certificate) for ; Tue, 21 Jul 2015 22:32:35 +0200 (CEST) Message-ID: <55AEAC64.90803@menkuec.de> Date: Tue, 21 Jul 2015 22:32:36 +0200 From: Benjamin Menkuec User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20130801 Thunderbird/17.0.8 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de X-Enigmail-Version: 1.6 Content-Type: text/plain; charset=ISO-8859-15 Content-Transfer-Encoding: 7bit X-Originating-IP: 81.169.146.219 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1437510756-0005941F-15667E82/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.319470, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.0 required=5.0 tests=RCVD_IN_DNSWL_NONE, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.1 on Tokelau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] seqan 2 system_condition problems on windows X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 21 Jul 2015 20:32:38 -0000 Hi Daniel, I know your question is already 4 months old, but maybe its still useful for you. I think you forgot to add -D_WIN32_WINNT=0x0600 to the g++ command line. I can still compile with mingw_w64, even though I dont recommend it because support for it was dropped by the seqan team :) PS: this commandline works for my simple testproject g++ -I ..\..\seqan\include -DWIN32 -D_WINDOWS -D_WIN32_WINNT=0x0600 testprojekt.cpp -o testprojekt_mingw.exe Best Regards, Benjamin From cecile.moulin@u-psud.fr Thu Jul 23 11:46:18 2015 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1ZID4y-000KVf-Am>; Thu, 23 Jul 2015 11:46:16 +0200 Received: from mx2.u-psud.fr ([129.175.212.65]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1ZID4y-000oql-75>; Thu, 23 Jul 2015 11:46:16 +0200 Received: from mx2.u-psud.fr (mx2 [127.0.0.1]) by localhost (MTA) with SMTP id CD1DA303342 for ; Thu, 23 Jul 2015 11:46:14 +0200 (CEST) Received: from zstore3.di.u-psud.fr (zstore3.di.u-psud.fr [172.20.4.14]) by mx2.u-psud.fr (MTA) with ESMTP id A0C733032FC for ; Thu, 23 Jul 2015 11:46:14 +0200 (CEST) Date: Thu, 23 Jul 2015 11:46:14 +0200 (CEST) From: =?utf-8?Q?C=C3=A9cile?= Moulin To: seqan-dev@lists.fu-berlin.de Message-ID: <1450763668.1728952.1437644774265.JavaMail.zimbra@u-psud.fr> In-Reply-To: <1770992732.1727858.1437644534707.JavaMail.zimbra@u-psud.fr> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_1728951_91699681.1437644774264" X-Mailer: Zimbra 8.0.6_GA_5922 (ZimbraWebClient - FF38 (Linux)/8.0.6_GA_5922) Thread-Topic: Finite Alphabet and Multiple Alignment Thread-Index: C3ykyygD/fGEUM4vaEMdT7aIWS0T2Q== X-Originating-IP: 129.175.212.65 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1437644776-0005941F-A1B812F7/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000152, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-2.3 required=5.0 tests=HTML_MESSAGE, RCVD_IN_DNSWL_MED X-Spam-Checker-Version: SpamAssassin 3.4.1 on Palau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Finite Alphabet and Multiple Alignment X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 23 Jul 2015 09:46:18 -0000 ------=_Part_1728951_91699681.1437644774264 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi,=20 I want to align sequences with arbitrary alphabet. I think I could use Fini= te Alphabet but I don't know how and I can't see the actual documentation (= 403 Forbidden).=20 What can I do ?=20 Thanks=20 C=C3=A9cile Moulin=20 =09 ------=_Part_1728951_91699681.1437644774264 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi,

I want to align sequences with arbitrary alphabet. I think I could use Fi= nite Alphabet but I don't know how and I can't see the actual documentation= (403 Forbidden).

What can I do ?

Thanks

C=C3=A9cile Moulin

 



------=_Part_1728951_91699681.1437644774264-- From NHTran@ntu.edu.sg Fri Jul 24 08:24:58 2015 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1ZIWPg-00037I-9t>; Fri, 24 Jul 2015 08:24:56 +0200 Received: from smtp3.ntu.edu.sg ([155.69.5.81]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1ZIWPf-00059M-IY>; Fri, 24 Jul 2015 08:24:56 +0200 X-AuditID: 9b450551-f79566d000000cef-74-55b1da3395c2 Received: from EXSMTP6.staff.main.ntu.edu.sg ( [155.69.5.101]) by SMTP3.ntu.edu.sg (Symantec Messaging Gateway) with SMTP id 28.D4.03311.33AD1B55; Fri, 24 Jul 2015 14:24:51 +0800 (SGT) Received: from EXCHHUB13.staff.main.ntu.edu.sg (172.21.5.78) by EXSMTP6.staff.main.ntu.edu.sg (155.69.5.101) with Microsoft SMTP Server (TLS) id 14.3.123.3; Fri, 24 Jul 2015 14:24:07 +0800 Received: from EXCHMBOX33.staff.main.ntu.edu.sg ([169.254.3.250]) by EXCHHUB13.staff.main.ntu.edu.sg ([155.69.25.16]) with mapi id 14.03.0123.003; Fri, 24 Jul 2015 14:24:50 +0800 From: "Tran Ngoc Hieu (Dr)" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: Simple radix tree for a set of strings Thread-Index: AdDF2XFkzpr0nxxaQvq1TPX9aAtMUg== Date: Fri, 24 Jul 2015 06:24:50 +0000 Message-ID: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_DA28F38A7BD3CF4799A3B54A9986CAFF0167727884EXCHMBOX33sta_" MIME-Version: 1.0 X-Brightmail-Tracker: H4sIAAAAAAAAA+NgFtrCKsWRmVeSWpSXmKPExsUy25U1Vdf41sZQg4YmFYvt71azOzB6bNqx ly2AMYrLJiU1J7MstUjfLoEr4+inTpaCG7IVbx/fYG1gnCnZxcjJISFgItE2bSkrhC0mceHe erYuRi4OIYFdjBIXji9ghHAOMEosmDEdytnGKHHz8BxGkBY2AX2Jfz/vg9kiAo4SfT1tQO0c HMJA8W+PdSHCJhJ7zs9lg7D1JL7Nus0EUsIioCrxoEEVJMwrEClx88AidhCbEeiI76fWMIHY zALiEreezGeCOE5AYsme88wQtqjEy8f/oI5WlJhz6REbRH2+xN5jfawQMwUlTs58wgJiCwnI Sdx53sQ0gVFkFpKxs5C0zELSAhHXkViw+xMbhK0tsWzha2YY+8yBx0zI4gsY2VcxCgT7hgQY 6+WVlOqlppTqFadvYoRETuAOxqt/9A4xCnAwKvHwttzYGCrEmlhWXJl7iFGSg0lJlPfuUqAQ X1J+SmVGYnFGfFFpTmrxIUYJDmYlEV6GY0A53pTEyqrUonyYlDQHi5I477MlG0KFBNITS1Kz U1MLUotgsjIcHEoSvBdA9ggWpaanVqRl5pQgpJk4OEGG8wANvwhSw1tckJhbnJkOkT/FqCgl zlsJkhAASWSU5sH1whLbK0ZxoFeEeeNBqniASRGu+xXQYCagwTx9G0AGlyQipKQaGFerR+de 4U9MOr9S5On7f6mLlsWren5Zv6bgmTXv45Zws7jgnfPvFkkebDuwZ2d4wpxIh1uF++qYFMvS T4bW5bd7bl2cVOMUeXb/wlm6PMopE9W5ZutW2P5e5HXW935z0AOupatSH5dZnGDnKIlc1L9Q ZJHmlJDJZ55+063/f6/l6Z7HO9jvb1diKc5INNRiLipOBAAlGua8RwMAAA== X-Originating-IP: 155.69.5.81 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1437719096-0005941F-91E57B5C/0/0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.504718, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.5 required=5.0 tests=FU_BOGO_UNSURE, HTML_IMAGE_ONLY_24,HTML_MESSAGE,RCVD_IN_DNSWL_MED,T_REMOTE_IMAGE X-Spam-Checker-Version: SpamAssassin 3.4.1 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Simple radix tree for a set of strings X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 24 Jul 2015 06:24:58 -0000 --_000_DA28F38A7BD3CF4799A3B54A9986CAFF0167727884EXCHMBOX33sta_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear All, Could you please advise if there is any built-in way to construct a simple = radix tree of a given set of strings? I don't need random access to prefixe= s or suffixes of individual strings. I only need a DFS iterator to traverse= from the first to the last character of each string. A simple example: if my set is {"to", "tea", "ten"}, then I need to process= in this order: "t", "te", "tea", "ten", "to". I know that some built-in SeqAn indices, e.g. IndexSa, can do what I want, = and even offer more support but they also require more memory space. So is = there any simple way to do that? Thanks a lot! Regards, Hieu [SG50] ________________________________ CONFIDENTIALITY: This email is intended solely for the person(s) named and = may be confidential and/or privileged. If you are not the intended recipien= t, please delete it, notify us and do not copy, use, or disclose its conten= ts. Towards a sustainable earth: Print only when necessary. Thank you. --_000_DA28F38A7BD3CF4799A3B54A9986CAFF0167727884EXCHMBOX33sta_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear All,

 

Could you please advise if there is any built-in way= to construct a simple radix tree of a given set of strings? I don’t = need random access to prefixes or suffixes of individual strings. I only ne= ed a DFS iterator to traverse from the first to the last character of each string.

 

A simple example: if my set is {“to”, &#= 8220;tea”, “ten”}, then I need to process in this order: = “t”, “te”, “tea”, “ten”, &#= 8220;to”.

 

I know that some built-in SeqAn indices, e.g. IndexS= a, can do what I want, and even offer more support but they also require mo= re memory space. So is there any simple way to do that?

 

Thanks a lot!

 

Regards,

Hieu

 

3D"SG50"
CONFIDENTIALITY: This email = is intended solely for the person(s) named and may be confidential and/or p= rivileged. If you are not the intended recipient, please delete it, notify = us and do not copy, use, or disclose its contents.
Towards a sustainable earth: Print only when necessary. Thank you. --_000_DA28F38A7BD3CF4799A3B54A9986CAFF0167727884EXCHMBOX33sta_-- From rene.maerker@fu-berlin.de Fri Jul 24 11:31:00 2015 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1ZIZJh-000ICO-U7>; Fri, 24 Jul 2015 11:30:58 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1ZIZJh-002ErQ-Ss>; Fri, 24 Jul 2015 11:30:57 +0200 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1ZIZJh-002p6Q-FL>; Fri, 24 Jul 2015 11:30:57 +0200 Received: from EX03A.campus.fu-berlin.de ([130.133.170.134]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0248.002; Fri, 24 Jul 2015 11:30:56 +0200 From: =?utf-8?B?UmFobiwgUmVuw6k=?= To: SeqAn Development Thread-Topic: [Seqan-dev] Finite Alphabet and Multiple Alignment Thread-Index: C3ykyygD/fGEUM4vaEMdT7aIWS0T2ahCLwgA Message-ID: References: <1450763668.1728952.1437644774265.JavaMail.zimbra@u-psud.fr> In-Reply-To: <1450763668.1728952.1437644774265.JavaMail.zimbra@u-psud.fr> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_E435F0FCA73D4804977D2C39AC769948zedatfuberlinde_" MIME-Version: 1.0 Date: Fri, 24 Jul 2015 11:30:55 +0200 X-Original-Date: Fri, 24 Jul 2015 09:30:55 +0000 X-Originating-IP: 130.133.170.202 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1437730257-0005941F-BA334309/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.4.1 on Vanuatu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: 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