From jer15@hermes.cam.ac.uk Wed Nov 13 11:03:43 2013 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1VgXIU-0029L9-Dg>; Wed, 13 Nov 2013 11:03:42 +0100 Received: from ppsw-52.csi.cam.ac.uk ([131.111.8.152]) by relay1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1VgXIU-001hu2-BD>; Wed, 13 Nov 2013 11:03:42 +0100 X-Cam-AntiVirus: no malware found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from cpc6-dals15-2-0-cust115.hari.cable.virginm.net ([82.35.196.116]:49415 helo=[192.168.1.4]) by ppsw-52.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.158]:587) with esmtpsa (PLAIN:jer15) (TLSv1:DHE-RSA-CAMELLIA256-SHA:256) id 1VgXIT-00060k-D6 (Exim 4.82_3-c0e5623) for seqan-dev@lists.fu-berlin.de (return-path ); Wed, 13 Nov 2013 10:03:41 +0000 Message-ID: <52834E7C.7020602@mail.cryst.bbk.ac.uk> Date: Wed, 13 Nov 2013 10:03:40 +0000 From: John Reid User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Thunderbird/24.1.0 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Sender: "J.E. Reid" X-Originating-IP: 131.111.8.152 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1384337022-00000A82-F75E61BE/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.481187, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-2.3 required=5.0 tests=RCVD_IN_DNSWL_MED X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Inverse of _getId for ESA vertexes? 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: Wed, 13 Nov 2013 10:03:44 -0000 I find property maps for ESAs very useful. I can index into a sparse data structure using the ID of a vertex in an ESA. However I couldn't find any way to reconstruct the vertex from the ID. Is this possible? At the moment I have to iterate over the whole ESA again looking to see if I have an entry for the ID for each vertex. It would be much more efficient for me to iterate over my sparse data structure and be able to map IDs back to vertexes/iterators. Thanks, John. From weese@campus.fu-berlin.de Wed Nov 13 18:51:36 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1VgebG-002v74-Hj>; Wed, 13 Nov 2013 18:51:34 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1VgebG-000dF9-Fw>; Wed, 13 Nov 2013 18:51:34 +0100 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1VgebG-002Q5W-5e>; Wed, 13 Nov 2013 18:51:34 +0100 Received: from EX02B.campus.fu-berlin.de ([130.133.170.133]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.03.0158.001; Wed, 13 Nov 2013 18:51:33 +0100 From: "Weese, David" To: SeqAn Development Thread-Topic: [Seqan-dev] Inverse of _getId for ESA vertexes? Thread-Index: AQHO4FfAKtjEHKeQh0yziHaioW6J9JojYIYA Message-ID: <5D0B7FB8-060C-4EA6-BD28-617678BDAAD3@fu-berlin.de> References: <52834E7C.7020602@mail.cryst.bbk.ac.uk> In-Reply-To: <52834E7C.7020602@mail.cryst.bbk.ac.uk> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: yes X-MS-TNEF-Correlator: Content-Type: multipart/signed; boundary="Apple-Mail=_95F7C34F-66C7-4431-92AD-DC1797AA8A50"; protocol="application/pkcs7-signature"; micalg=sha1 MIME-Version: 1.0 Date: Wed, 13 Nov 2013 18:51:32 +0100 X-Original-Date: Wed, 13 Nov 2013 17:51:32 +0000 X-Originating-IP: 130.133.170.201 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1384365094-00000A82-A1FBBA63/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000263, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Inverse of _getId for ESA vertexes? 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: Wed, 13 Nov 2013 17:51:36 -0000 --Apple-Mail=_95F7C34F-66C7-4431-92AD-DC1797AA8A50 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Hi John, _getId is a function from the set of nodes to the smallest possible = interval - in the ESA case to [0..2n) for the total number of text = characters n. For the ESA that function is more or less one interval = boundary of the node's SA interval, so that function is not reversible = as you cannot determine the other boundary directly. It would be = possible in O(n) time with a scan over the lcp to the left or right for = lcp values strictly less the the one at the boundary, but then = parentRight is still missing. However, instead you could store the whole VertexDescriptor in your = property map. With that VertexDescriptor you can resume at the = corresponding node with a TopDown iterator. Cheers, Dave -- David Weese, Ph.D. david.weese@fu-berlin.de Freie Universit=E4t Berlin http://www.inf.fu-berlin.de/ Institut f=FCr Informatik Phone: +49 30 838 75137 Takustra=DFe 9 Algorithmic Bioinformatics 14195 Berlin Room 020 Am 13.11.2013 um 11:03 schrieb John Reid : > I find property maps for ESAs very useful. I can index into a sparse > data structure using the ID of a vertex in an ESA. However I couldn't > find any way to reconstruct the vertex from the ID. Is this possible? = At > the moment I have to iterate over the whole ESA again looking to see = if > I have an entry for the ID for each vertex. It would be much more > efficient for me to iterate over my sparse data structure and be able = to > map IDs back to vertexes/iterators. >=20 > Thanks, > John. >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --Apple-Mail=_95F7C34F-66C7-4431-92AD-DC1797AA8A50 Content-Disposition: attachment; filename="smime.p7s" Content-Type: application/pkcs7-signature; name="smime.p7s" Content-Transfer-Encoding: base64 MIAGCSqGSIb3DQEHAqCAMIACAQExCzAJBgUrDgMCGgUAMIAGCSqGSIb3DQEHAQAAoIIPZjCCBCEw ggMJoAMCAQICAgDHMA0GCSqGSIb3DQEBBQUAMHExCzAJBgNVBAYTAkRFMRwwGgYDVQQKExNEZXV0 c2NoZSBUZWxla29tIEFHMR8wHQYDVQQLExZULVRlbGVTZWMgVHJ1c3QgQ2VudGVyMSMwIQYDVQQD ExpEZXV0c2NoZSBUZWxla29tIFJvb3QgQ0EgMjAeFw0wNjEyMTkxMDI5MDBaFw0xOTA2MzAyMzU5 MDBaMFoxCzAJBgNVBAYTAkRFMRMwEQYDVQQKEwpERk4tVmVyZWluMRAwDgYDVQQLEwdERk4tUEtJ MSQwIgYDVQQDExtERk4tVmVyZWluIFBDQSBHbG9iYWwgLSBHMDEwggEiMA0GCSqGSIb3DQEBAQUA A4IBDwAwggEKAoIBAQDpm8NnhfkNrvWNVMOWUDU9YuluTO2U1wBblSJ01CDrNI/W7MAxBAuZgeKm FNJSoCgjhIt0iQReW+DieMF4yxbLKDU5ey2QRdDtoAB6fL9KDhsAw4bpXCsxEXsM84IkQ4wcOItq aACa7txPeKvSxhObdq3u3ibo7wGvdA/BCaL2a869080UME/15eOkyGKbghoDJzANAmVgTe3RCSMq ljVYJ9N2xnG2kB3E7f81hn1vM7PbD8URwoqDoZRdQWvY0hD1TP3KUazZve+Sg7va64sWVlZDz+HV Ez2mHycwzUlU28kTNJpxdcVs6qcLmPkhnSevPqM5OUhqjK3JmfvDEvK9AgMBAAGjgdkwgdYwcAYD VR0fBGkwZzBloGOgYYZfaHR0cDovL3BraS50ZWxlc2VjLmRlL2NnaS1iaW4vc2VydmljZS9hZl9E b3dubG9hZEFSTC5jcmw/LWNybF9mb3JtYXQ9WF81MDkmLWlzc3Vlcj1EVF9ST09UX0NBXzIwHQYD VR0OBBYEFEm3xs/oPR9/6kR7Eyn38QpwPt5kMB8GA1UdIwQYMBaAFDHDeRu69VPXF+CJei0XbAqz K50zMA4GA1UdDwEB/wQEAwIBBjASBgNVHRMBAf8ECDAGAQH/AgECMA0GCSqGSIb3DQEBBQUAA4IB AQA74Vp3wEgX3KkY7IGvWonwvSiSpspZGBJw7Cjy565/lizn8l0ZMfYTK3S9vYCyufdnyTmieTvh ERHua3iRM347XyYndVNljjNj7s9zw7CSI0khUHUjoR8Y4pSFPT8z6XcgjaK95qGFKUD2P3MyWA0J a6bahWzAP7uNZmRWJE6uDT8yNQFb6YyC2XJZT7GGhfF0hVblw/hc843uR7NTBXDn5U2KaYMo4RMJ hp5eyOpYHgwf+aTUWgRo/Sg+iwK2WLX2oSw3VwBnqyNojWOl75lrXP1LVvarQIc01BGSbOyHxQoL BzNytG8MHVQs2FHHzL8w00Ny8TK/jM5JY6gA9/IcMIIFPjCCBCagAwIBAgIECc2lKDANBgkqhkiG 9w0BAQUFADBaMQswCQYDVQQGEwJERTETMBEGA1UEChMKREZOLVZlcmVpbjEQMA4GA1UECxMHREZO LVBLSTEkMCIGA1UEAxMbREZOLVZlcmVpbiBQQ0EgR2xvYmFsIC0gRzAxMB4XDTA3MDExNzEzNDE0 NloXDTE5MDExNTAwMDAwMFowgbUxCzAJBgNVBAYTAkRFMQ8wDQYDVQQIEwZCZXJsaW4xDzANBgNV BAcTBkJlcmxpbjEiMCAGA1UEChMZRnJlaWUgVW5pdmVyc2l0YWV0IEJlcmxpbjEOMAwGA1UECxMF WkVEQVQxMDAuBgNVBAMTJ0ZyZWllIFVuaXZlcnNpdGFldCBCZXJsaW4gLSBGVS1DQSAtIEcwMTEe MBwGCSqGSIb3DQEJARYPY2FARlUtQmVybGluLkRFMIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIB CgKCAQEAjYUI0048zDNevkmXipCDjSpIr+sEbhiXPzWnZnCnkmLOrEMFaNDWDX6kcVQ1VP71opEf GuR5LtW0P6N+JM8E8y5HXdap62bD4Yfg0KQEmlh9vpMQ75BckReW7wRKH/Ntcrg8gwn97d17Hs8h gRGk8cpBRAs5v5hcqRZcjR63mKCismsjld6MVdWSNYhZJhpcnb0dVzMa3A7Rf1OsXHwDXrhusCNp h1+Pazuw2XbIKWSCsFS4qlhHOj5QA375qk5IjjsUnw2FqljLiziu9xB4/jhSx1fz6+5RVnTe5Tb9 GMbk5RVR+dvPTnzF96T/yW5DqsFIL+xBYQ8juFoBQog3MwIDAQABo4IBrjCCAaowDwYDVR0TAQH/ BAUwAwEB/zALBgNVHQ8EBAMCAQYwHQYDVR0OBBYEFAbhPfRv9DC3ejtXsDEFiXsNWFpsMB8GA1Ud IwQYMBaAFEm3xs/oPR9/6kR7Eyn38QpwPt5kMBoGA1UdEQQTMBGBD2NhQEZVLUJlcmxpbi5ERTCB iAYDVR0fBIGAMH4wPaA7oDmGN2h0dHA6Ly9jZHAxLnBjYS5kZm4uZGUvZ2xvYmFsLXJvb3QtY2Ev cHViL2NybC9jYWNybC5jcmwwPaA7oDmGN2h0dHA6Ly9jZHAyLnBjYS5kZm4uZGUvZ2xvYmFsLXJv b3QtY2EvcHViL2NybC9jYWNybC5jcmwwgaIGCCsGAQUFBwEBBIGVMIGSMEcGCCsGAQUFBzAChjto dHRwOi8vY2RwMS5wY2EuZGZuLmRlL2dsb2JhbC1yb290LWNhL3B1Yi9jYWNlcnQvY2FjZXJ0LmNy dDBHBggrBgEFBQcwAoY7aHR0cDovL2NkcDIucGNhLmRmbi5kZS9nbG9iYWwtcm9vdC1jYS9wdWIv Y2FjZXJ0L2NhY2VydC5jcnQwDQYJKoZIhvcNAQEFBQADggEBAEyG7FCK8+oQK8NxT7knkDmt587h p0A5N1xBtF7pwXAz3QMauXSPUp+2PikXV7BeeGxcb21TViGsdJg3nt4hLgBI+L+OKM+cs8jUDsSb WroUD5mwyIAlZENYRraiopYx4DlLaxFoor6shYCmWid7jo5/uELbJFAOpgqS6pQ2lCCAPVsSLLdU S+sZx62D/b42P57yipO+QF7p08j/J1mJIDec9QzfSzgNla1LTcxhsh3H8V+zFCo84lbonXiVNt+8 tcDXbEVSHMwyJo7vrtq+L0QstaGEcApa+sySpPdvTl6Bl+ayfRNOgeqJkbR6g0euV+7IZxCMDaWW MKkjDMXVqFEwggX7MIIE46ADAgECAgcWNEvNdomiMA0GCSqGSIb3DQEBBQUAMIG1MQswCQYDVQQG EwJERTEPMA0GA1UECBMGQmVybGluMQ8wDQYDVQQHEwZCZXJsaW4xIjAgBgNVBAoTGUZyZWllIFVu aXZlcnNpdGFldCBCZXJsaW4xDjAMBgNVBAsTBVpFREFUMTAwLgYDVQQDEydGcmVpZSBVbml2ZXJz aXRhZXQgQmVybGluIC0gRlUtQ0EgLSBHMDExHjAcBgkqhkiG9w0BCQEWD2NhQEZVLUJlcmxpbi5E RTAeFw0xMzA4MjExNDI3MTBaFw0xNjA4MjAxNDI3MTBaMIGZMQswCQYDVQQGEwJERTEPMA0GA1UE CBMGQmVybGluMQ8wDQYDVQQHEwZCZXJsaW4xIjAgBgNVBAoTGUZyZWllIFVuaXZlcnNpdGFldCBC ZXJsaW4xLjAsBgNVBAsTJUZhY2hiZXJlaWNoIE1hdGhlbWF0aWsgdW5kIEluZm9ybWF0aWsxFDAS BgNVBAMTC0RhdmlkIFdlZXNlMIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAmQBDoqxg 9VM+7+JLkO1TD+hGnlNHBPBkokZLcsnM4hw1bHKjIfojs4oT6sJwXFjFv32Ab7ZGcGs90j7gI/VR 9St7M+PPBp9ALOR56pxn9R0IMqsoCJG8xIXYZLZ8M1QAYTHmAhkL/4IAYrwfKtO758zBke9Zhcf1 GA1UZTfugJxRp+NRo01aRqIhBnFMfGc0mSYIgC2o3gCHuC0Sc+PmZcQvxW8cqi4J5LWzIXE8c9lb WKDYiNkELIEv/1Pwsk76M7Kbb2TuN74v2P6O2Xm34Q1mzuWMfmDGHSw9rbVOSWt5KNu97LbJ4xev RvqOZZZSLI1Cy2CniBUBM0SDCV32bQIDAQABo4ICKDCCAiQwLwYDVR0gBCgwJjARBg8rBgEEAYGt IYIsAQEEAwAwEQYPKwYBBAGBrSGCLAIBBAMAMAkGA1UdEwQCMAAwCwYDVR0PBAQDAgXgMB0GA1Ud JQQWMBQGCCsGAQUFBwMCBggrBgEFBQcDBDAdBgNVHQ4EFgQUwnfAMwU291B6aGcD4fmaIjBGRb0w HwYDVR0jBBgwFoAUBuE99G/0MLd6O1ewMQWJew1YWmwwcAYDVR0RBGkwZ4EZd2Vlc2VAY2FtcHVz LmZ1LWJlcmxpbi5kZYEWd2Vlc2VAaW5mLmZ1LWJlcmxpbi5kZYEYZGF2aWQud2Vlc2VAZnUtYmVy bGluLmRlgRhEYXZpZC5XZWVzZUBmdS1iZXJsaW4uZGUwdQYDVR0fBG4wbDA0oDKgMIYuaHR0cDov L2NkcDEucGNhLmRmbi5kZS9mdS1jYS9wdWIvY3JsL2NhY3JsLmNybDA0oDKgMIYuaHR0cDovL2Nk cDIucGNhLmRmbi5kZS9mdS1jYS9wdWIvY3JsL2NhY3JsLmNybDCBkAYIKwYBBQUHAQEEgYMwgYAw PgYIKwYBBQUHMAKGMmh0dHA6Ly9jZHAxLnBjYS5kZm4uZGUvZnUtY2EvcHViL2NhY2VydC9jYWNl cnQuY3J0MD4GCCsGAQUFBzAChjJodHRwOi8vY2RwMi5wY2EuZGZuLmRlL2Z1LWNhL3B1Yi9jYWNl cnQvY2FjZXJ0LmNydDANBgkqhkiG9w0BAQUFAAOCAQEASV+HktbNSFbDrXfh9+clKz4Q6AhJ+Vna vwt6xwbsoiviGt1FwsuDUu5FYFFkJhdTu19RFlnuMgS8YqgROv2FA3SeaLvcts6XdXglwmZa5yCl dM7nRdT2l4yICjrPpg085p6GCVD5GpQNxUsyOtWoaf1EllTxYT7RZ9NOToFAstTKELp4pTyRf0pR GFOZiFC/ftgJeXORFpZjj0pATnAdjH/eui/9PUnIX+EJ3H9KndRdDR3g2zFUNu6ryOTkPb/leFbC 472BgZ8tm5bdHVMraz9KSfr3sdi28wBKFMuQ/sHBM5q48vz86lpOemoQ/hOnTZT+qQF3tPmlTJbf FPevdzGCA/YwggPyAgEBMIHBMIG1MQswCQYDVQQGEwJERTEPMA0GA1UECBMGQmVybGluMQ8wDQYD VQQHEwZCZXJsaW4xIjAgBgNVBAoTGUZyZWllIFVuaXZlcnNpdGFldCBCZXJsaW4xDjAMBgNVBAsT BVpFREFUMTAwLgYDVQQDEydGcmVpZSBVbml2ZXJzaXRhZXQgQmVybGluIC0gRlUtQ0EgLSBHMDEx HjAcBgkqhkiG9w0BCQEWD2NhQEZVLUJlcmxpbi5ERQIHFjRLzXaJojAJBgUrDgMCGgUAoIICCTAY BgkqhkiG9w0BCQMxCwYJKoZIhvcNAQcBMBwGCSqGSIb3DQEJBTEPFw0xMzExMTMxNzUxMzNaMCMG CSqGSIb3DQEJBDEWBBRreamT5US9jE14az7qMQ5ubVSCojCB0gYJKwYBBAGCNxAEMYHEMIHBMIG1 MQswCQYDVQQGEwJERTEPMA0GA1UECBMGQmVybGluMQ8wDQYDVQQHEwZCZXJsaW4xIjAgBgNVBAoT GUZyZWllIFVuaXZlcnNpdGFldCBCZXJsaW4xDjAMBgNVBAsTBVpFREFUMTAwLgYDVQQDEydGcmVp ZSBVbml2ZXJzaXRhZXQgQmVybGluIC0gRlUtQ0EgLSBHMDExHjAcBgkqhkiG9w0BCQEWD2NhQEZV LUJlcmxpbi5ERQIHFjRLzXaJojCB1AYLKoZIhvcNAQkQAgsxgcSggcEwgbUxCzAJBgNVBAYTAkRF MQ8wDQYDVQQIEwZCZXJsaW4xDzANBgNVBAcTBkJlcmxpbjEiMCAGA1UEChMZRnJlaWUgVW5pdmVy c2l0YWV0IEJlcmxpbjEOMAwGA1UECxMFWkVEQVQxMDAuBgNVBAMTJ0ZyZWllIFVuaXZlcnNpdGFl dCBCZXJsaW4gLSBGVS1DQSAtIEcwMTEeMBwGCSqGSIb3DQEJARYPY2FARlUtQmVybGluLkRFAgcW NEvNdomiMA0GCSqGSIb3DQEBAQUABIIBACVw8j5iHsW13/O86npw11hRe9NAinHSeC1AhPu4gxbd hXC+hSWdsnmRLtisLz5VKZL6MFiZ9x5EGX31hAiZqOORFg+q0scG20Wpgj+WoRSaP1HDn/8sflW2 uE8kQYNkrEWJSxtw1k4P8xJPxKl2lMSkeeR2d8cJdDJ12Qz+PXxXZsVqMsImm3Pcb9+FBEB/Odlm CqnuRXc9yPLZvY5BYTwMi0ga895+xzonIZBNr3f1LUg/pRvHZ2qj0bqH69xAx4usWOjmmYQCwaLc ra9mF0GaU5qjcsykMUmpqdoBUAGXYLVK6ueT2JRbj+FgzGpRqpbXSkAA6wL3PQGZrYlevuEAAAAA AAA= --Apple-Mail=_95F7C34F-66C7-4431-92AD-DC1797AA8A50-- From manuel.holtgrewe@fu-berlin.de Wed Nov 20 12:04:31 2013 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Vj5aA-00250Z-2H>; Wed, 20 Nov 2013 12:04:30 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Vj5aA-001e1j-0X>; Wed, 20 Nov 2013 12:04:30 +0100 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.80.1) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Vj5a9-0034Kz-Md>; Wed, 20 Nov 2013 12:04:29 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0158.001; Wed, 20 Nov 2013 12:04:28 +0100 From: "Holtgrewe, Manuel" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: SeqAn's repository is migrating to GitHub Thread-Index: AQHO5d8XUvxJvB192kyNddpO1bc9yw== Message-ID: 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: Wed, 20 Nov 2013 12:04:27 +0100 X-Original-Date: Wed, 20 Nov 2013 11:04:27 +0000 X-Originating-IP: 130.133.170.202 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1384945470-00000A82-B7C6CC66/0-12433892719/0-2 X-Bogosity: Ham, tests=bogofilter, spamicity=0.007711, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-49.0 required=5.0 tests=ALL_TRUSTED, FU_XPURGATE_SUSP X-Spam-Checker-Version: SpamAssassin 3.3.3-zedat0a54d5a on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] SeqAn's repository is migrating to GitHub 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: Wed, 20 Nov 2013 11:04:31 -0000 Dear all,=0A= =0A= the SeqAn team is migrating SeqAn's repository to GitHub [1]. For the last = months, we have already mirrored the Subversion trunk to the master branch = at GitHub and worked on some larger changes there on the branch "develop". = Git allowed us to maintain multiple branches much easier than Subversion.= =0A= =0A= We have now decided that it is easier to continue development on GitHub. Th= us, instead of copying over the changes from our Subversion trunk to GitHub= , we will now copy over the changes in the GitHub master to the Subversion = trunk.=0A= =0A= One more thing: Everything else remains the same, i.e. http://packages.seqa= n.de still hosts our packages, http://trac.seqan.de remains our wiki, http:= //trac.seqan.de/wiki/Tutorial contains the Tutorial, http://docs.seqan.de i= s still there for our documentation.=0A= =0A= =0A= What does this mean for you?=0A= =0A= =0A= SEQAN SVN USERS=0A= =0A= You just use SeqAn in your projects and get the latest version from SeqAn's= trunk? No problem, we will continue pushing the changes from the stable Gi= t master to SeqAn's trunk. The SeqAn SVN URL stays the same. You even have = the added benefit that the new trunk will be more stable since the developm= ent will happen in different branches on GitHub. Yay!=0A= =0A= Did you know that you can also checkout GitHub repositories via Subversion?= Thus, you could also use the develop branch at Github to get the lastest (= albeit less stable) SeqAn version:=0A= =0A= svn co https://github.com/seqan/seqan/branches/develop seqan-trunk=0A= =0A= =0A= SEQAN TARBALL USERS=0A= =0A= You use the SeqAn library from a downloaded tarball or one of our applicati= ons? Nothing changes for you.=0A= =0A= =0A= SEQAN CONTRIBUTORS=0A= =0A= You are contributing to SeqAn or you want to? It's now much less hassle to = do so! GitHub allows you to easily submit patches through pull requests whi= ch we can then review and merge.=0A= =0A= More information on how we use Git and links to tutorials online can be fou= nd at [2].=0A= =0A= =0A= tl;dr We are moving to Git. Don't worry if you are using tarball downloads = or just read from our Subversion repository -- nothing changes for you.=0A= =0A= [1] https://github.com/seqan/seqan=0A= [2] http://trac.seqan.de/wiki/HowTo/UseGit=