From djsmrhak@pusan.ac.kr Thu Nov 11 10:53:38 2010 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 <1PGTqX-0002RA-RN>; Thu, 11 Nov 2010 10:53:34 +0100 Received: from sniper1.pusan.ac.kr ([164.125.7.131] helo=sniperdata.pusan.ac.kr) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PGTqW-0001Oc-Tb>; Thu, 11 Nov 2010 10:53:33 +0100 Received: from unknown (HELO webmail.pusan.ac.kr) (164.125.9.3) by 10.10.1.11 with SMTP; 11 Nov 2010 18:44:43 +0900 X-Original-SENDERIP: 164.125.9.3 X-Original-MAILFROM: djsmrhak@pusan.ac.kr Received: from 164.125.68.153 (164.125.68.153 [164.125.68.153]) by webmail.pusan.ac.kr (DeepMTA 3.6.48) with ESMTP id <000001cb8186$484c45b0$d8e4d110$@ac.kr> for ; Thu, 11 Nov 2010 18:49:07 +0900 From: =?ks_c_5601-1987?B?sei5zMGk?= To: Date: Thu, 11 Nov 2010 18:53:24 +0900 Message-ID: <000001cb8186$484c45b0$d8e4d110$@ac.kr> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01CB81D1.B833EDB0" X-Mailer: Microsoft Office Outlook 12.0 Thread-Index: AcuBhke9HLsKrDJJTL+qopjrr5S06g== Content-Language: ko X-IP: 164.125.68.153 X-FROM-DOMAIN: pusan.ac.kr X-FROM-EMAIL: djsmrhak@pusan.ac.kr X-Originating-IP: 164.125.7.131 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1289469213-00000C0F-E860B4E7/0-0/0-0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.500002, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.-Berlin.DE X-Spam-Level: xxxx X-Spam-Status: No, score=4.1 required=5.0 tests=FU_BOGO_UNSURE,HTML_MESSAGE, HTML_WEB_BUGS,RCVD_BY_IP,RCVD_NUMERIC_HELO,SPF_HELO_PASS,SPF_PASS, TRACKER_ID X-Mailman-Approved-At: Fri, 12 Nov 2010 10:28:51 +0100 Subject: [Seqan-dev] I have a question !! :) X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 11 Nov 2010 09:53:38 -0000 This is a multi-part message in MIME format. ------=_NextPart_000_0001_01CB81D1.B833EDB0 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: quoted-printable =20 Hi, I=A1=AFm Mi jeong Kim and student from korea. I attend to class about Topics in Bioinformatics. We studied about convenience of alignment tool by using SeqAn at last w= eek and found the use of wildcard braces { }. But we couldn=A1=AFt use braces. =20 The core of this mail !! =20 We want to know the using of the braces at this situation. for example GCGTTGCGCGCGCTTTATCGTTGCGCTTATGC (GC) <- repeat =20 We tried many pattern=20 For example 1. needle =3D =A1=B0(GC){2, 4}=A1=B1 2. needle =3D =A1=B0GC{2, 4}=A1=B1 3. needle =3D =A1=B0GC{2, 4}+=A1=B1 4. needle =3D =A1=B0GC+{2, 4}=A1=B1 5. needle =3D =A1=B0(GC)+{2, 4}=A1=B1 =A1=A6=A1=A6=A1=A6 but this program didn=A1=AFt work. =20 Could you tell me how to use the braces at this situation ? =20 =20 Thank you for read my awkward mail and hope you to answer me. Have a nice day !=20 =20 =20 ------=_NextPart_000_0001_01CB81D1.B833EDB0 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: quoted-printable

Hi, I=A1=AFm Mi jeong Kim and student from korea.<= /p>

I attend to class about Topi= cs in Bioinformatics.

We studied about convenience of alignment tool by using Seq= An at last week

and found the use of wildcard braces { }.

But we couldn=A1=AFt use braces.<= o:p>

= ;

The core of t= his mail !!

We want to know the using of the braces at this situation.=

<= p class=3DMsoNormal>We tried many pattern

for example

GCGTTGCGCGCGCTTTATCGTTGCGCTTATGC

(GC) <- repeat

For example

1. = ne= edle =3D =A1=B0(GC){2, 4}=A1=B1

2. <= span lang=3DEN-US>needle =3D =A1=B0GC{2, 4}=A1=B1

3. <= /span>needle =3D =A1=B0GC{2, 4}+=A1=B1

4. &nb= sp; needle =3D =A1=B0= GC+{2, 4}=A1=B1

5. = ne= edle =3D =A1=B0(GC)+{2, 4}=A1=B1

=A1=A6=A1=A6=A1=A6<= o:p>

but this program didn=A1=AFt work.

Could you tell me how to use the braces at th= is situation ?

T= hank you for read my awkward mail and hope you to answer me.=

Have a nice day !

------=_NextPart_000_0001_01CB81D1.B833EDB0-- From matthias.dodt@mdc-berlin.de Tue Nov 16 15:41:05 2010 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 <1PIMiW-0005bU-Fd>; Tue, 16 Nov 2010 15:41:04 +0100 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PIMiW-0005hf-D1>; Tue, 16 Nov 2010 15:41:04 +0100 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id 139CF17C8D4 for ; Tue, 16 Nov 2010 15:41:04 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:subject:subject:mime-version :user-agent:from:from:date:date:message-id:received:received :received:received; s=dkim1; t=1289918458; x=1291732858; bh=nKpp JTcnApOCbQ9APceuWM4gFfzmIsWdp82rnrigOAk=; b=J65tlfgsxg1/zYEEM6zQ rIfCtmKKonu4Le2plVEC6Mf6TOc+7/mvnELN2BnxYfaJ5KnquOSSOeHABxpqiubX sqy8xijf/AhixHwdcdt4wHz/TKTOkQQ+/bya/1Ro6oNrG5aeAlkkmy82aE7cLVrY k0A3vfFTANBYzooE1tLwygE= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id e0IZ1VUsAwaJ for ; Tue, 16 Nov 2010 15:40:58 +0100 (CET) Received: from mdcmail.mdc-berlin.de (mab.citx.mdc-berlin.de [141.80.36.102]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id 8577917C89D for ; Tue, 16 Nov 2010 15:40:58 +0100 (CET) Received: from mdcexcl.mdc-berlin.net ([141.80.184.16]) by mdcmail.mdc-berlin.de with Microsoft SMTPSVC(6.0.3790.4675); Tue, 16 Nov 2010 15:42:09 +0100 Received: from cd04-macpro.local ([141.80.188.98]) by mdcexcl.mdc-berlin.net with Microsoft SMTPSVC(6.0.3790.4675); Tue, 16 Nov 2010 15:42:08 +0100 Message-ID: <4CE29840.7090204@mdc-berlin.de> Date: Tue, 16 Nov 2010 15:42:08 +0100 From: Mat User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; de; rv:1.9.2.12) Gecko/20101027 Lightning/1.0b2 Thunderbird/3.1.6 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary="------------090105060903020602000207" X-OriginalArrivalTime: 16 Nov 2010 14:42:08.0235 (UTC) FILETIME=[71E3FBB0:01CB859C] X-TM-AS-Product-Ver: SMEX-10.0.0.1412-6.500.1024-17770.002 X-TM-AS-Result: No--7.822600-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Originating-IP: 141.80.25.23 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1289918464-00000C0F-7842208D/0-0/0-0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.467329, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.-Berlin.DE X-Spam-Level: xx X-Spam-Status: No, score=2.4 required=5.0 tests=FU_BOGO_UNSURE,HTML_50_60, HTML_MESSAGE,RATWARE_GECKO_BUILD Subject: [Seqan-dev] Graph visualization X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 16 Nov 2010 14:41:05 -0000 This is a multi-part message in MIME format. --------------090105060903020602000207 Content-Type: text/plain; charset=ISO-8859-15; format=flowed Content-Transfer-Encoding: 7bit Hey Guys! I am experimenting with different Graphs in seqan. I would like to visualize the results on my graph in an easy way (like exporting the graph in a graph-file format or use some standardized way). Is there something built in with seqan? So far i only discovered "graphviz"... Thanks for any advice! Best, mat --------------090105060903020602000207 Content-Type: text/html; charset=ISO-8859-15 Content-Transfer-Encoding: 7bit Hey Guys!

I am experimenting with different Graphs in seqan. I would like to visualize the results on my graph in an easy way (like exporting the graph in a graph-file format or use some standardized way). Is there something built in with seqan? So far i only discovered "graphviz"...

Thanks for any advice!

Best,

mat
--------------090105060903020602000207-- From Knut.Reinert@fu-berlin.de Tue Nov 16 15:48:14 2010 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 <1PIMpR-0005qW-KI>; Tue, 16 Nov 2010 15:48:13 +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 <1PIMpR-0006qz-Hw>; Tue, 16 Nov 2010 15:48:13 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PIMpR-0002hc-Dg>; Tue, 16 Nov 2010 15:48:13 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Tue, 16 Nov 2010 15:48:13 +0100 From: "Reinert, Knut" To: SeqAn Development Date: Tue, 16 Nov 2010 15:48:11 +0100 Thread-Topic: [Seqan-dev] Graph visualization Thread-Index: AcuFnUrQkpT98LrSTMaoZ56jqD1r0g== Message-ID: In-Reply-To: <4CE29840.7090204@mdc-berlin.de> Accept-Language: en-US, de-DE Content-Language: de-DE X-MS-Has-Attach: yes X-MS-TNEF-Correlator: user-agent: Microsoft-MacOutlook/14.1.0.101012 acceptlanguage: en-US, de-DE Content-Type: multipart/signed; protocol="application/pkcs7-signature"; micalg=sha1; boundary="B_3372767291_2347911" MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1289918893-00000C0F-6F880D5B/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.007072, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED,HTML_60_70, HTML_MESSAGE Subject: Re: [Seqan-dev] Graph visualization X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 16 Nov 2010 14:48:14 -0000 --B_3372767291_2347911 Content-type: multipart/alternative; boundary="B_3372767291_2360222" --B_3372767291_2360222 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit You can output the graphs in dot format and use dotty. Knut Reinert Von: Mat Antworten an: SeqAn Development Datum: Tue, 16 Nov 2010 15:42:08 +0100 An: "seqan-dev@lists.fu-berlin.de" Betreff: [Seqan-dev] Graph visualization Hey Guys! I am experimenting with different Graphs in seqan. I would like to visualize the results on my graph in an easy way (like exporting the graph in a graph-file format or use some standardized way). Is there something built in with seqan? So far i only discovered "graphviz"... Thanks for any advice! Best, mat --B_3372767291_2360222 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable

You can output the graphs in= dot format and use dotty.

Knut Reinert

<= br>

Von: Mat <matthias.dodt@mdc-berlin.de>= ;
Antworten an: SeqAn Development = <seqan-dev@lists.fu-berlin.= de>
Datum: Tue, 16 Nov 2010= 15:42:08 +0100
An: "seqan-dev@lists.fu-berlin.de" <seqan-dev@lists.fu-berlin.de>= ;
Betreff: [Seqan-dev] Graph visua= lization

Hey Guys!

I am experimenting with different Graphs in seqan. I would like to visualize the results on my graph in an easy way (like exporting the graph in a graph-file format or use some standardized way). Is there something built in with seqan? So far i only discovered "graphviz"...

Thanks for any advice!

Best,

mat

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NSJGvJBvVSX/5j5L7RVe3ozQOrU9zzWhmgUIByi7wFEqYg5W0BEn9rYV2a82UG1waLnN+U9K sJfhoXY7jyXKxMSokoGbEScZp7k6BVGdGBDBVINRhimUa4jwq1k/nPkXigtxqWg9/nVgrTNp rpj3ydbPZA== --B_3372767291_2347911-- From Birte.Kehr@fu-berlin.de Tue Nov 16 15:48:46 2010 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 <1PIMpx-0005qx-LJ>; Tue, 16 Nov 2010 15:48:45 +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 <1PIMpx-0006yw-IZ>; Tue, 16 Nov 2010 15:48:45 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PIMpx-0002jU-EH>; Tue, 16 Nov 2010 15:48:45 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Tue, 16 Nov 2010 15:48:45 +0100 From: "Kehr, Birte" To: 'SeqAn Development' Date: Tue, 16 Nov 2010 15:48:43 +0100 Thread-Topic: [Seqan-dev] Graph visualization Thread-Index: AcuFnF79A768B+5cQu6vWNV7EglxbgAAD0ZQ Message-ID: References: <4CE29840.7090204@mdc-berlin.de> In-Reply-To: <4CE29840.7090204@mdc-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US, de-DE Content-Type: multipart/alternative; boundary="_000_DAD226CB6878494EABEFD5215AA102015570670187exchange6fube_" MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1289918925-00000C0F-332BEADB/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.004740, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE Subject: Re: [Seqan-dev] Graph visualization X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 16 Nov 2010 14:48:46 -0000 --_000_DAD226CB6878494EABEFD5215AA102015570670187exchange6fube_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Mat, you can write the graph to a dot-file and then open the file with graphviz: FILE* strmWrite =3D fopen("graph.dot", "w"); write(strmWrite, g, DotDrawing()); fclose(strmWrite); Other formats are not supported so far. Cheers, Birte From: Mat [mailto:matthias.dodt@mdc-berlin.de] Sent: Dienstag, 16. November 2010 15:42 To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] Graph visualization Hey Guys! I am experimenting with different Graphs in seqan. I would like to visualiz= e the results on my graph in an easy way (like exporting the graph in a gra= ph-file format or use some standardized way). Is there something built in w= ith seqan? So far i only discovered "graphviz"... Thanks for any advice! Best, mat --_000_DAD226CB6878494EABEFD5215AA102015570670187exchange6fube_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi Mat,

you can write the graph to a dot-file and then open the file with gra= phviz:

FILE* strmWrite = =3D fopen("graph.dot", "w");

write(strmWrite, g, DotDrawing(= ));

fclose(strmWrit= e);

&nbs= p;

Other formats a= re not supported so far.

Cheers,

Birte

= ;

From: Mat [mailto:matthias.dodt@mdc-ber= lin.de]
Sent: Dienstag, 16. November 2010 15:42
To: se= qan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Graph visualizati= on

<= /p>

Hey Guys!=

I am experimenting with different Graphs in seqan. I would like to = visualize the results on my graph in an easy way (like exporting the graph = in a graph-file format or use some standardized way). Is there something bu= ilt in with seqan? So far i only discovered "graphviz"...

= Thanks for any advice!

Best,

mat

= = --_000_DAD226CB6878494EABEFD5215AA102015570670187exchange6fube_-- From matthias.dodt@mdc-berlin.de Tue Nov 16 15:52:17 2010 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 <1PIMtM-0005zj-LJ>; Tue, 16 Nov 2010 15:52:16 +0100 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PIMtM-0007wE-Ib>; Tue, 16 Nov 2010 15:52:16 +0100 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 404B2400A7 for ; Tue, 16 Nov 2010 15:52:16 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:in-reply-to:references:subject:subject :mime-version:user-agent:from:from:date:date:message-id:received :received:received:received; s=dkim1; t=1289919130; x= 1291733530; bh=pr3VWVqtNrLpKz8deT9OdhEn+XACdVL0R5KwoCV81b4=; b=Z 4e7V8x32MjnDfcRUxABv8H4VwfVXMRP/se8wcItyCCk5tuFBBaTBOjVhQ/EambFh 3slpFaIag1QmSvNhJjc85b8W/vQ7Spx60ydWRh4sufDQbVYz9hI2pTM2uoq3Dbyn YrOVMJXW0sZ1mH11blYxMZ4P8Sxqbk8GWEupEoyWk8= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id fBhCbogh4G2s for ; Tue, 16 Nov 2010 15:52:10 +0100 (CET) Received: from mdcmail.mdc-berlin.de (mab.citx.mdc-berlin.de [141.80.36.102]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 370CC40075 for ; Tue, 16 Nov 2010 15:52:10 +0100 (CET) Received: from mdcexcl.mdc-berlin.net ([141.80.184.16]) by mdcmail.mdc-berlin.de with Microsoft SMTPSVC(6.0.3790.4675); Tue, 16 Nov 2010 15:53:21 +0100 Received: from cd04-macpro.local ([141.80.188.98]) by mdcexcl.mdc-berlin.net with Microsoft SMTPSVC(6.0.3790.4675); Tue, 16 Nov 2010 15:53:19 +0100 Message-ID: <4CE29AE0.3020202@mdc-berlin.de> Date: Tue, 16 Nov 2010 15:53:20 +0100 From: Mat User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; de; rv:1.9.2.12) Gecko/20101027 Lightning/1.0b2 Thunderbird/3.1.6 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: <4CE29840.7090204@mdc-berlin.de> In-Reply-To: Content-Type: multipart/alternative; boundary="------------010300000004040207000400" X-OriginalArrivalTime: 16 Nov 2010 14:53:19.0900 (UTC) FILETIME=[023BEDC0:01CB859E] X-TM-AS-Product-Ver: SMEX-10.0.0.1412-6.500.1024-17770.002 X-TM-AS-Result: No--6.547800-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Originating-IP: 141.80.25.30 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1289919136-00000C0F-BCA6BC26/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.026109, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=HTML_MESSAGE, RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] Graph visualization X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 16 Nov 2010 14:52:17 -0000 This is a multi-part message in MIME format. --------------010300000004040207000400 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Wow, that was fast! Thanks Birte & Knut! That was exactly what i was looking for- have a nice day! best, mat Am 11/16/10 3:48 PM, schrieb Kehr, Birte: > > FILE* strmWrite = fopen(*"graph.dot"*, *"w"*); > > write(strmWrite, g, DotDrawing()); > > fclose(strmWrite); > --------------010300000004040207000400 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Wow, that was fast! Thanks Birte & Knut!

That was exactly what i was looking for-

have a nice day!

best,

mat

Am 11/16/10 3:48 PM, schrieb Kehr, Birte:

FILE* strmWrite = fopen("graph.dot", "w");

write(strmWrite, g, DotDrawing());

fclose(strmWrite);

--------------010300000004040207000400-- From f.buske@uq.edu.au Tue Nov 23 04:43:14 2010 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 <1PKjmi-0002uO-T1>; Tue, 23 Nov 2010 04:43:13 +0100 Received: from mailhub4.uq.edu.au ([130.102.149.131]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PKjmi-0000I1-31>; Tue, 23 Nov 2010 04:43:12 +0100 Received: from smtp4.uq.edu.au (smtp4.uq.edu.au [130.102.128.19]) by mailhub4.uq.edu.au (8.13.8/8.13.8) with ESMTP id oAN3h7GL002990 for ; Tue, 23 Nov 2010 13:43:07 +1000 Received: from imb10-008701.imb.uq.edu.au (imb10-008701.imb.uq.edu.au [130.102.118.152]) (authenticated bits=0) by smtp4.uq.edu.au (8.13.8/8.13.8) with ESMTP id oAN3h5XG000855 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Tue, 23 Nov 2010 13:43:07 +1000 Message-ID: <4CEB3848.5020304@uq.edu.au> Date: Tue, 23 Nov 2010 13:43:04 +1000 From: Fabian Buske User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.12) Gecko/20101027 Thunderbird/3.1.6 MIME-Version: 1.0 To: SeqAn Development Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-UQ-FilterTime: 1290483788 X-Scanned-By: MIMEDefang 2.58 on UQ Mailhub on 130.102.149.131 X-Originating-IP: 130.102.149.131 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1290483792-00000C0F-B93D0D18/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.064436, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=RATWARE_GECKO_BUILD Subject: [Seqan-dev] Skiplist does not find existing key X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 23 Nov 2010 03:43:14 -0000 Hi, I observed a rather peculiar phenomenon for the Skiplist map specialisation, a data type I use quite extensively. Using a custom key class and comparator the skiplist sometimes does not find a key that has been inserted into the map. Since the skiplist is a randomised data structure this behaviour occurs by chance. When using the iterator to go through the Skiplist the element will actually be output. I observed that the order of the objects (keys) in the output is not the ordered lists of keys according to the comparator (which I was expecting) but to the order in which the keys where inserted into the map. I'm not sure if this is intended. I created a ticket for this phenomenon, which has an extended test_map class attached demonstrating this behaviour: http://trac.mi.fu-berlin.de/seqan/ticket/589 This phenomenon may have serious consequences on any application relying on Skiplists. Best, Fabian -- Fabian Buske Institute for Molecular Bioscience The University of Queensland Brisbane, Qld. 4072 Australia Phone: (61)-(7)-334-62608 From Knut.Reinert@fu-berlin.de Tue Nov 23 08:46:45 2010 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 <1PKnaO-00028T-Hq>; Tue, 23 Nov 2010 08:46:44 +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 <1PKnaO-0008Ga-Fp>; Tue, 23 Nov 2010 08:46:44 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PKnaO-000454-AI>; Tue, 23 Nov 2010 08:46:44 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Tue, 23 Nov 2010 08:46:43 +0100 From: "Reinert, Knut" To: SeqAn Development Date: Tue, 23 Nov 2010 08:46:40 +0100 Thread-Topic: [Seqan-dev] Skiplist does not find existing key Thread-Index: AcuK4pH0yv6d6RDqQyCzAERC/WIpvA== Message-ID: In-Reply-To: <4CEB3848.5020304@uq.edu.au> Accept-Language: en-US, de-DE Content-Language: de-DE X-MS-Has-Attach: yes X-MS-TNEF-Correlator: user-agent: Microsoft-MacOutlook/14.1.0.101012 acceptlanguage: en-US, de-DE Content-Type: multipart/signed; protocol="application/pkcs7-signature"; micalg=sha1; boundary="B_3373346800_2648072" MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1290498404-00000C0F-96595850/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.004752, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] Skiplist does not find existing key X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 23 Nov 2010 07:46:45 -0000 --B_3373346800_2648072 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Hm So beim direkten compilieren gibt es Fehler (s.u.) Compiliert das test file mit dem SVN head bei Dir? Building CXX object tests/CMakeFiles/test_map.dir/Users/reinert/seqan/projects/tests/map/test_m ap.cpp.o /Users/reinert/seqan/projects/tests/map/test_map_extended.h: In function =8Cvoid Test_Map_Complex_Key() [with TMap =3D seqan::Map, seqan::VectorSet > >]=B9: /Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: instantiated from here /Users/reinert/seqan/projects/tests/map/test_map_extended.h:470: error: =8Cstruct=20 seqan::Proxy, seqan::VectorSet > >, seqan::VectorSetIterator> > >=B9 has no member named =8Cvalue3=B9 /Users/reinert/seqan/projects/tests/map/test_map_extended.h:470: error: =8Cstruct=20 seqan::Proxy, seqan::VectorSet > >, seqan::VectorSetIterator> > >=B9 has no member named =8Cvalue2=B9 /Users/reinert/seqan/projects/tests/map/test_map_extended.h:470: error: =8Cstruct=20 seqan::Proxy, seqan::VectorSet > >, seqan::VectorSetIterator> > >=B9 has no member named =8Cvalue1=B9 /Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: instantiated from here /Users/reinert/seqan/projects/tests/map/test_map_extended.h:471: error: =8Cstruct=20 seqan::Proxy, seqan::VectorSet > >, seqan::VectorSetIterator> > >=B9 has no member named =8Cvalue3=B9 /Users/reinert/seqan/projects/tests/map/test_map_extended.h:471: error: =8Cstruct=20 seqan::Proxy, seqan::VectorSet > >, seqan::VectorSetIterator> > >=B9 has no member named =8Cvalue2=B9 /Users/reinert/seqan/projects/tests/map/test_map_extended.h:471: error: =8Cstruct=20 seqan::Proxy, seqan::VectorSet > >, seqan::VectorSetIterator> > >=B9 has no member named =8Cvalue1=B9 /Users/reinert/seqan/projects/tests/map/test_map_extended.h:472: error: =8Cstruct=20 seqan::Proxy, seqan::VectorSet > >, seqan::VectorSetIterator> > >=B9 has no member named =8Cvalue3=B9 /Users/reinert/seqan/projects/tests/map/test_map_extended.h:472: error: =8Cstruct=20 seqan::Proxy, seqan::VectorSet > >, seqan::VectorSetIterator> > >=B9 has no member named =8Cvalue2=B9 /Users/reinert/seqan/projects/tests/map/test_map_extended.h:472: error: =8Cstruct=20 seqan::Proxy, seqan::VectorSet > >, seqan::VectorSetIterator> > >=B9 has no member named =8Cvalue1=B9 /Users/reinert/seqan/projects/library/seqan/basic/basic_alphabet_interface. h: At global scope: /Users/reinert/seqan/projects/library/seqan/basic/basic_alphabet_interface. h: In instantiation of =8Cseqan::ValueSize >=B9: /Users/reinert/seqan/projects/library/seqan/map/map_vector.h:103: instantiated from =8Cseqan::Map >::Map() [with TValue =3D TestKey, TSpec =3D seqan::Alloc]=B9 /Users/reinert/seqan/projects/tests/map/test_map_extended.h:452: instantiated from =8Cvoid Test_Map_Complex_Key() [with TMap =3D seqan::Map, seqan::VectorSet > >]=B9 /Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: instantiated from here /Users/reinert/seqan/projects/library/seqan/basic/basic_alphabet_interface. h:963: warning: left shift count >=3D width of type /Users/reinert/seqan/projects/library/seqan/sequence/lexical.h: In function =8Cunsigned int seqan::ordValue(const TValue&) [with TValue =3D TestKey]=B9: /Users/reinert/seqan/projects/library/seqan/map/map_vector.h:328: instantiated from =8Ctypename seqan::Iterator >, typename seqan::DefaultIteratorSpec > >::Type>::Type seqan::find(seqan::Map >&, >const TKey&) [with TKey =3D TestKey, TKey2 =3D TestKeylong int>, TSpec =3D seqan::Alloc]=B9 /Users/reinert/seqan/projects/tests/map/test_map_extended.h:464: instantiated from =8Cvoid Test_Map_Complex_Key() [with TMap =3D seqan::Map, seqan::VectorSet > >]=B9 /Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: instantiated from here /Users/reinert/seqan/projects/library/seqan/sequence/lexical.h:787: error: cannot convert =8Cconst TestKey=B9 to =8Cunsigned int=B9 in return make[3]: ***=20 [tests/CMakeFiles/test_map.dir/Users/reinert/seqan/projects/tests/map/test_ map.cpp.o] Error 1 make[2]: *** [tests/CMakeFiles/test_map.dir/all] Error 2 make[1]: *** [tests/CMakeFiles/test_map.dir/rule] Error 2 Am 11/23/10 4:43 AM schrieb "Fabian Buske" unter : >Hi, > >I observed a rather peculiar phenomenon for the Skiplist map >specialisation, a data type I use quite extensively. > >Using a custom key class and comparator the skiplist sometimes does not >find a key that has been inserted into the map. Since the skiplist is a >randomised data structure this behaviour occurs by chance. > >When using the iterator to go through the Skiplist the element will >actually be output. I observed that the order of the objects (keys) in >the output is not the ordered lists of keys according to the comparator >(which I was expecting) but to the order in which the keys where >inserted into the map. I'm not sure if this is intended. > >I created a ticket for this phenomenon, which has an extended test_map >class attached demonstrating this behaviour: >http://trac.mi.fu-berlin.de/seqan/ticket/589 > >This phenomenon may have serious consequences on any application relying >on Skiplists. > >Best, >Fabian > >--=20 > >Fabian Buske >Institute for Molecular Bioscience >The University of Queensland >Brisbane, Qld. 4072 Australia >Phone: (61)-(7)-334-62608 > > >_______________________________________________ >seqan-dev mailing list >seqan-dev@lists.fu-berlin.de >https://lists.fu-berlin.de/listinfo/seqan-dev --B_3373346800_2648072 Content-Type: application/pkcs7-signature; name="smime.p7s" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="smime.p7s" MIINuQYJKoZIhvcNAQcCoIINqjCCDaYCAQExCzAJBgUrDgMCGgUAMAsGCSqGSIb3DQEHAaCC CzwwggX2MIIE3qADAgECAgQOPlW+MA0GCSqGSIb3DQEBBQUAMIG1MQswCQYDVQQGEwJERTEP MA0GA1UECBMGQmVybGluMQ8wDQYDVQQHEwZCZXJsaW4xIjAgBgNVBAoTGUZyZWllIFVuaXZl 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<1PKopq-0004of-0f>; Tue, 23 Nov 2010 10:06:46 +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 <1PKopp-0002a0-Uh>; Tue, 23 Nov 2010 10:06:46 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PKopp-0002FA-Oy>; Tue, 23 Nov 2010 10:06:45 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Tue, 23 Nov 2010 10:06:45 +0100 From: "Reinert, Knut" To: SeqAn Development Date: Tue, 23 Nov 2010 10:06:42 +0100 Thread-Topic: [Seqan-dev] Skiplist does not find existing key Thread-Index: AcuK7cAofcgXVy7HSuu7877hc2jPMg== Message-ID: In-Reply-To: Accept-Language: en-US, de-DE Content-Language: de-DE X-MS-Has-Attach: yes X-MS-TNEF-Correlator: user-agent: Microsoft-MacOutlook/14.1.0.101012 acceptlanguage: en-US, de-DE Content-Type: multipart/signed; protocol="application/pkcs7-signature"; micalg=sha1; boundary="B_3373351602_2818314" MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1290503206-00000C0F-1D801BDA/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.001958, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] Skiplist does not find existing key X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 23 Nov 2010 09:06:47 -0000 --B_3373351602_2818314 Content-type: text/plain; charset="UTF-8" Content-transfer-encoding: quoted-printable Dear Fabian, The skip lists are OK. Your operator< is wrong. For (4,3,2) < (2,4,4) it yields true, which is not what you intend. Here is the fixed version with which your test works. template bool TestKey::operator<(const TestKey & b) const { if (value1 < b.value1) return true; if (value1 > b.value1) return false; if (value2 < b.value2) return true; if (value2 > b.value2) return false;=20 if (value3 < b.value3) return true; if (value3 > b.value3) return false;=20 return false; } Cheers, Knut Am 11/23/10 8:46 AM schrieb "Reinert, Knut" unter : >Hm >So beim direkten compilieren gibt es Fehler (s.u.) > >Compiliert das test file mit dem SVN head bei Dir? > > > >Building CXX object >tests/CMakeFiles/test_map.dir/Users/reinert/seqan/projects/tests/map/test_ >m >ap.cpp.o >/Users/reinert/seqan/projects/tests/map/test_map_extended.h: In function >=C5=92void Test_Map_Complex_Key() [with TMap =3D seqan::Mapint>, seqan::VectorSet > >]=C2=B9: >/Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: >instantiated from here >/Users/reinert/seqan/projects/tests/map/test_map_extended.h:470: error: >=C5=92struct=20 >seqan::Proxyint>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>=C2=B9 has no member named =C5=92value3=C2=B9 >/Users/reinert/seqan/projects/tests/map/test_map_extended.h:470: error: >=C5=92struct=20 >seqan::Proxyint>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>=C2=B9 has no member named =C5=92value2=C2=B9 >/Users/reinert/seqan/projects/tests/map/test_map_extended.h:470: error: >=C5=92struct=20 >seqan::Proxyint>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>=C2=B9 has no member named =C5=92value1=C2=B9 >/Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: >instantiated from here >/Users/reinert/seqan/projects/tests/map/test_map_extended.h:471: error: >=C5=92struct=20 >seqan::Proxyint>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>=C2=B9 has no member named =C5=92value3=C2=B9 >/Users/reinert/seqan/projects/tests/map/test_map_extended.h:471: error: >=C5=92struct=20 >seqan::Proxyint>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>=C2=B9 has no member named =C5=92value2=C2=B9 >/Users/reinert/seqan/projects/tests/map/test_map_extended.h:471: error: >=C5=92struct=20 >seqan::Proxyint>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>=C2=B9 has no member named =C5=92value1=C2=B9 >/Users/reinert/seqan/projects/tests/map/test_map_extended.h:472: error: >=C5=92struct=20 >seqan::Proxyint>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>=C2=B9 has no member named =C5=92value3=C2=B9 >/Users/reinert/seqan/projects/tests/map/test_map_extended.h:472: error: >=C5=92struct=20 >seqan::Proxyint>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>=C2=B9 has no member named =C5=92value2=C2=B9 >/Users/reinert/seqan/projects/tests/map/test_map_extended.h:472: error: >=C5=92struct=20 >seqan::Proxyint>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>=C2=B9 has no member named =C5=92value1=C2=B9 >/Users/reinert/seqan/projects/library/seqan/basic/basic_alphabet_interface >. >h: At global scope: >/Users/reinert/seqan/projects/library/seqan/basic/basic_alphabet_interface >. >h: In instantiation of =C5=92seqan::ValueSize >=C2=B9: >/Users/reinert/seqan/projects/library/seqan/map/map_vector.h:103: >instantiated from =C5=92seqan::Map >::Map() >[with TValue =3D TestKey, TSpec =3D seqan::Alloc]=C2=B9 >/Users/reinert/seqan/projects/tests/map/test_map_extended.h:452: >instantiated from =C5=92void Test_Map_Complex_Key() [with TMap =3D >seqan::Map, seqan::VectorSet > >>]=C2=B9 >/Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: >instantiated from here >/Users/reinert/seqan/projects/library/seqan/basic/basic_alphabet_interface >. >h:963: warning: left shift count >=3D width of type >/Users/reinert/seqan/projects/library/seqan/sequence/lexical.h: In >function =C5=92unsigned int seqan::ordValue(const TValue&) [with TValue =3D >TestKey]=C2=B9: >/Users/reinert/seqan/projects/library/seqan/map/map_vector.h:328: >instantiated from =C5=92typename seqan::Iteratorseqan::VectorSet >, typename >seqan::DefaultIteratorSpec > >>::Type>::Type seqan::find(seqan::Map >&, >>const TKey&) [with TKey =3D TestKey, TKey2 =3D TestKey>long int>, TSpec =3D seqan::Alloc]=C2=B9 >/Users/reinert/seqan/projects/tests/map/test_map_extended.h:464: >instantiated from =C5=92void Test_Map_Complex_Key() [with TMap =3D >seqan::Map, seqan::VectorSet > >>]=C2=B9 >/Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: >instantiated from here >/Users/reinert/seqan/projects/library/seqan/sequence/lexical.h:787: error: >cannot convert =C5=92const TestKey=C2=B9 to =C5=92unsigned int=C2=B9 in ret= urn >make[3]: ***=20 >[tests/CMakeFiles/test_map.dir/Users/reinert/seqan/projects/tests/map/test >_ >map.cpp.o] Error 1 >make[2]: *** [tests/CMakeFiles/test_map.dir/all] Error 2 >make[1]: *** [tests/CMakeFiles/test_map.dir/rule] Error 2 > > > >Am 11/23/10 4:43 AM schrieb "Fabian Buske" unter : > >>Hi, >> >>I observed a rather peculiar phenomenon for the Skiplist map >>specialisation, a data type I use quite extensively. >> >>Using a custom key class and comparator the skiplist sometimes does not >>find a key that has been inserted into the map. Since the skiplist is a >>randomised data structure this behaviour occurs by chance. >> >>When using the iterator to go through the Skiplist the element will >>actually be output. I observed that the order of the objects (keys) in >>the output is not the ordered lists of keys according to the comparator >>(which I was expecting) but to the order in which the keys where >>inserted into the map. I'm not sure if this is intended. >> >>I created a ticket for this phenomenon, which has an extended test_map >>class attached demonstrating this behaviour: >>http://trac.mi.fu-berlin.de/seqan/ticket/589 >> >>This phenomenon may have serious consequences on any application relying >>on Skiplists. >> >>Best, >>Fabian >> >>--=20 >> >>Fabian Buske >>Institute for Molecular Bioscience >>The University of Queensland >>Brisbane, Qld. 4072 Australia >>Phone: (61)-(7)-334-62608 >> >> >>_______________________________________________ >>seqan-dev mailing list >>seqan-dev@lists.fu-berlin.de >>https://lists.fu-berlin.de/listinfo/seqan-dev --B_3373351602_2818314 Content-Type: application/pkcs7-signature; name="smime.p7s" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="smime.p7s" MIINuQYJKoZIhvcNAQcCoIINqjCCDaYCAQExCzAJBgUrDgMCGgUAMAsGCSqGSIb3DQEHAaCC CzwwggX2MIIE3qADAgECAgQOPlW+MA0GCSqGSIb3DQEBBQUAMIG1MQswCQYDVQQGEwJERTEP 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seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PL0iA-0006vh-IR>; Tue, 23 Nov 2010 22:47:38 +0100 Received: from mailhub4.uq.edu.au ([130.102.149.131]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PL0i9-0008Fp-D6>; Tue, 23 Nov 2010 22:47:38 +0100 Received: from smtp3.uq.edu.au (smtp3.uq.edu.au [130.102.128.18]) by mailhub4.uq.edu.au (8.13.8/8.13.8) with ESMTP id oANLlXg2000938 for ; Wed, 24 Nov 2010 07:47:33 +1000 Received: from imb10-008701.imb.uq.edu.au (imb10-008701.imb.uq.edu.au [130.102.118.152]) (authenticated bits=0) by smtp3.uq.edu.au (8.13.8/8.13.8) with ESMTP id oANLlVOr004733 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NOT) for ; Wed, 24 Nov 2010 07:47:33 +1000 Message-ID: <4CEC3673.3030604@uq.edu.au> Date: Wed, 24 Nov 2010 07:47:31 +1000 From: Fabian Buske User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.12) Gecko/20101027 Thunderbird/3.1.6 MIME-Version: 1.0 To: SeqAn Development References: In-Reply-To: Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit X-UQ-FilterTime: 1290548853 X-Scanned-By: MIMEDefang 2.58 on UQ Mailhub on 130.102.149.131 X-Originating-IP: 130.102.149.131 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1290548858-00000C0F-5AE8295F/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000069, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] Skiplist does not find existing key X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 23 Nov 2010 21:47:40 -0000 Doh! Thanks for the heads up, Knut. The VectorSet version still won't compile though even when the output via the iterator is removed from the test. Would be nice to get that one working just as well. Best, Fabian On 23/11/10 7:06 PM, Reinert, Knut wrote: > Dear Fabian, > > The skip lists are OK. > Your operator< is wrong. For (4,3,2)< (2,4,4) it yields true, which is > not what you intend. > > Here is the fixed version with which your test works. > > > template > bool TestKey::operator<(const TestKey & b) const { > if (value1< b.value1) return true; > if (value1> b.value1) return false; > if (value2< b.value2) return true; > if (value2> b.value2) return false; > if (value3< b.value3) return true; > if (value3> b.value3) return false; > return false; > } > > > Cheers, > > Knut > > > > > Am 11/23/10 8:46 AM schrieb "Reinert, Knut" unter > : > >> Hm >> So beim direkten compilieren gibt es Fehler (s.u.) >> >> Compiliert das test file mit dem SVN head bei Dir? >> >> >> >> Building CXX object >> tests/CMakeFiles/test_map.dir/Users/reinert/seqan/projects/tests/map/test_ >> m >> ap.cpp.o >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h: In function >> Œvoid Test_Map_Complex_Key() [with TMap = seqan::Map> int>, seqan::VectorSet > >]¹: >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: >> instantiated from here >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:470: error: >> Œstruct >> seqan::Proxy> int>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>> ¹ has no member named Œvalue3¹ >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:470: error: >> Œstruct >> seqan::Proxy> int>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>> ¹ has no member named Œvalue2¹ >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:470: error: >> Œstruct >> seqan::Proxy> int>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>> ¹ has no member named Œvalue1¹ >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: >> instantiated from here >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:471: error: >> Œstruct >> seqan::Proxy> int>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>> ¹ has no member named Œvalue3¹ >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:471: error: >> Œstruct >> seqan::Proxy> int>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>> ¹ has no member named Œvalue2¹ >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:471: error: >> Œstruct >> seqan::Proxy> int>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>> ¹ has no member named Œvalue1¹ >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:472: error: >> Œstruct >> seqan::Proxy> int>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>> ¹ has no member named Œvalue3¹ >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:472: error: >> Œstruct >> seqan::Proxy> int>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>> ¹ has no member named Œvalue2¹ >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:472: error: >> Œstruct >> seqan::Proxy> int>, seqan::VectorSet > >, seqan::VectorSetIterator> > >>> ¹ has no member named Œvalue1¹ >> /Users/reinert/seqan/projects/library/seqan/basic/basic_alphabet_interface >> . >> h: At global scope: >> /Users/reinert/seqan/projects/library/seqan/basic/basic_alphabet_interface >> . >> h: In instantiation of Œseqan::ValueSize >¹: >> /Users/reinert/seqan/projects/library/seqan/map/map_vector.h:103: >> instantiated from Œseqan::Map >::Map() >> [with TValue = TestKey, TSpec = seqan::Alloc]¹ >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:452: >> instantiated from Œvoid Test_Map_Complex_Key() [with TMap = >> seqan::Map, seqan::VectorSet > >>> ]¹ >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: >> instantiated from here >> /Users/reinert/seqan/projects/library/seqan/basic/basic_alphabet_interface >> . >> h:963: warning: left shift count>= width of type >> /Users/reinert/seqan/projects/library/seqan/sequence/lexical.h: In >> function Œunsigned int seqan::ordValue(const TValue&) [with TValue = >> TestKey]¹: >> /Users/reinert/seqan/projects/library/seqan/map/map_vector.h:328: >> instantiated from Œtypename seqan::Iterator> seqan::VectorSet >, typename >> seqan::DefaultIteratorSpec > >>> ::Type>::Type seqan::find(seqan::Map >&, >>> const TKey&) [with TKey = TestKey, TKey2 = TestKey>> long int>, TSpec = seqan::Alloc]¹ >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:464: >> instantiated from Œvoid Test_Map_Complex_Key() [with TMap = >> seqan::Map, seqan::VectorSet > >>> ]¹ >> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: >> instantiated from here >> /Users/reinert/seqan/projects/library/seqan/sequence/lexical.h:787: error: >> cannot convert Œconst TestKey¹ to Œunsigned int¹ in return >> make[3]: *** >> [tests/CMakeFiles/test_map.dir/Users/reinert/seqan/projects/tests/map/test >> _ >> map.cpp.o] Error 1 >> make[2]: *** [tests/CMakeFiles/test_map.dir/all] Error 2 >> make[1]: *** [tests/CMakeFiles/test_map.dir/rule] Error 2 >> >> >> >> Am 11/23/10 4:43 AM schrieb "Fabian Buske" unter: >> >>> Hi, >>> >>> I observed a rather peculiar phenomenon for the Skiplist map >>> specialisation, a data type I use quite extensively. >>> >>> Using a custom key class and comparator the skiplist sometimes does not >>> find a key that has been inserted into the map. Since the skiplist is a >>> randomised data structure this behaviour occurs by chance. >>> >>> When using the iterator to go through the Skiplist the element will >>> actually be output. I observed that the order of the objects (keys) in >>> the output is not the ordered lists of keys according to the comparator >>> (which I was expecting) but to the order in which the keys where >>> inserted into the map. I'm not sure if this is intended. >>> >>> I created a ticket for this phenomenon, which has an extended test_map >>> class attached demonstrating this behaviour: >>> http://trac.mi.fu-berlin.de/seqan/ticket/589 >>> >>> This phenomenon may have serious consequences on any application relying >>> on Skiplists. >>> >>> Best, >>> Fabian >>> >>> -- >>> >>> Fabian Buske >>> Institute for Molecular Bioscience >>> The University of Queensland >>> Brisbane, Qld. 4072 Australia >>> Phone: (61)-(7)-334-62608 >>> >>> >>> _______________________________________________ >>> seqan-dev mailing list >>> seqan-dev@lists.fu-berlin.de >>> https://lists.fu-berlin.de/listinfo/seqan-dev -- Fabian Buske Institute for Molecular Bioscience The University of Queensland Brisbane, Qld. 4072 Australia Phone: (61)-(7)-334-62608 From weese@campus.fu-berlin.de Thu Nov 25 13:26:34 2010 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 <1PLauH-0001YP-8h>; Thu, 25 Nov 2010 13:26:33 +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 <1PLauH-0002lw-6r>; Thu, 25 Nov 2010 13:26:33 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PLauH-00012D-3V>; Thu, 25 Nov 2010 13:26:33 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Thu, 25 Nov 2010 13:26:32 +0100 From: "Weese, David" To: SeqAn Development Date: Thu, 25 Nov 2010 13:26:32 +0100 Thread-Topic: [Seqan-dev] Skiplist does not find existing key Thread-Index: AcuMm/5qiFtt9t/STrS+rZpuhfTDpg== Message-ID: <49DF9FF8-A4A6-4E9F-9D06-12D11AE55268@fu-berlin.de> References: <4CEC3673.3030604@uq.edu.au> In-Reply-To: <4CEC3673.3030604@uq.edu.au> Accept-Language: de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: de-DE Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1290687993-00000C0F-7CA4128A/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.012170, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] Skiplist does not find existing key X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 25 Nov 2010 12:26:34 -0000 Hi Fabian, VectorSets need a mapping from keys to ordinal numbers (function ordValue) = to work. They are designed for small or medium size alphabets and an effici= ent alternative to binary search based sets. They are not going to work on = your key set. ANFSCD, can you test cmake again on your machine. I hope I fixed the CUDA i= ssue. Cheers, David -- David Weese weese@inf.fu-berlin.de Freie Universit=E4t Berlin http://www.inf.fu-berlin.de/ Institut f=FCr Informatik Phone: +49 30 838 75246 Takustra=DFe 9 Algorithmic Bioinformatics 14195 Berlin Room 021=20 Am 23.11.2010 um 22:47 schrieb Fabian Buske: > Doh! Thanks for the heads up, Knut. >=20 > The VectorSet version still won't compile though even when the output=20 > via the iterator is removed from the test. Would be nice to get that one= =20 > working just as well. >=20 > Best, > Fabian >=20 >=20 > On 23/11/10 7:06 PM, Reinert, Knut wrote: >> Dear Fabian, >>=20 >> The skip lists are OK. >> Your operator< is wrong. For (4,3,2)< (2,4,4) it yields true, which is >> not what you intend. >>=20 >> Here is the fixed version with which your test works. >>=20 >>=20 >> template >> bool TestKey::operator<(const TestKey & b) const { >> if (value1< b.value1) return true; >> if (value1> b.value1) return false; >> if (value2< b.value2) return true; >> if (value2> b.value2) return false; >> if (value3< b.value3) return true; >> if (value3> b.value3) return false; >> return false; >> } >>=20 >>=20 >> Cheers, >>=20 >> Knut >>=20 >>=20 >>=20 >>=20 >> Am 11/23/10 8:46 AM schrieb "Reinert, Knut" unter >> : >>=20 >>> Hm >>> So beim direkten compilieren gibt es Fehler (s.u.) >>>=20 >>> Compiliert das test file mit dem SVN head bei Dir? >>>=20 >>>=20 >>>=20 >>> Building CXX object >>> tests/CMakeFiles/test_map.dir/Users/reinert/seqan/projects/tests/map/te= st_ >>> m >>> ap.cpp.o >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h: In functio= n >>> =8Cvoid Test_Map_Complex_Key() [with TMap =3D seqan::Map>> int>, seqan::VectorSet > >]=B9: >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: >>> instantiated from here >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:470: error: >>> =8Cstruct >>> seqan::Proxy>> int>, seqan::VectorSet > >, seqan::VectorSetIterat= or> > >>>> =B9 has no member named =8Cvalue3=B9 >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:470: error: >>> =8Cstruct >>> seqan::Proxy>> int>, seqan::VectorSet > >, seqan::VectorSetIterat= or> > >>>> =B9 has no member named =8Cvalue2=B9 >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:470: error: >>> =8Cstruct >>> seqan::Proxy>> int>, seqan::VectorSet > >, seqan::VectorSetIterat= or> > >>>> =B9 has no member named =8Cvalue1=B9 >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: >>> instantiated from here >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:471: error: >>> =8Cstruct >>> seqan::Proxy>> int>, seqan::VectorSet > >, seqan::VectorSetIterat= or> > >>>> =B9 has no member named =8Cvalue3=B9 >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:471: error: >>> =8Cstruct >>> seqan::Proxy>> int>, seqan::VectorSet > >, seqan::VectorSetIterat= or> > >>>> =B9 has no member named =8Cvalue2=B9 >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:471: error: >>> =8Cstruct >>> seqan::Proxy>> int>, seqan::VectorSet > >, seqan::VectorSetIterat= or> > >>>> =B9 has no member named =8Cvalue1=B9 >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:472: error: >>> =8Cstruct >>> seqan::Proxy>> int>, seqan::VectorSet > >, seqan::VectorSetIterat= or> > >>>> =B9 has no member named =8Cvalue3=B9 >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:472: error: >>> =8Cstruct >>> seqan::Proxy>> int>, seqan::VectorSet > >, seqan::VectorSetIterat= or> > >>>> =B9 has no member named =8Cvalue2=B9 >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:472: error: >>> =8Cstruct >>> seqan::Proxy>> int>, seqan::VectorSet > >, seqan::VectorSetIterat= or> > >>>> =B9 has no member named =8Cvalue1=B9 >>> /Users/reinert/seqan/projects/library/seqan/basic/basic_alphabet_interf= ace >>> . >>> h: At global scope: >>> /Users/reinert/seqan/projects/library/seqan/basic/basic_alphabet_interf= ace >>> . >>> h: In instantiation of =8Cseqan::ValueSize >=B9= : >>> /Users/reinert/seqan/projects/library/seqan/map/map_vector.h:103: >>> instantiated from =8Cseqan::Map >::M= ap() >>> [with TValue =3D TestKey, TSpec =3D seqan::Alloc]= =B9 >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:452: >>> instantiated from =8Cvoid Test_Map_Complex_Key() [with TMap =3D >>> seqan::Map, seqan::VectorSet = > >>>> ]=B9 >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: >>> instantiated from here >>> /Users/reinert/seqan/projects/library/seqan/basic/basic_alphabet_interf= ace >>> . >>> h:963: warning: left shift count>=3D width of type >>> /Users/reinert/seqan/projects/library/seqan/sequence/lexical.h: In >>> function =8Cunsigned int seqan::ordValue(const TValue&) [with TValue = =3D >>> TestKey]=B9: >>> /Users/reinert/seqan/projects/library/seqan/map/map_vector.h:328: >>> instantiated from =8Ctypename seqan::Iterator>> seqan::VectorSet >, typename >>> seqan::DefaultIteratorSpec > >>>> ::Type>::Type seqan::find(seqan::Map >= &, >>>> const TKey&) [with TKey =3D TestKey, TKey2 =3D TestKey<= long >>>> long int>, TSpec =3D seqan::Alloc]=B9 >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:464: >>> instantiated from =8Cvoid Test_Map_Complex_Key() [with TMap =3D >>> seqan::Map, seqan::VectorSet = > >>>> ]=B9 >>> /Users/reinert/seqan/projects/tests/map/test_map_extended.h:502: >>> instantiated from here >>> /Users/reinert/seqan/projects/library/seqan/sequence/lexical.h:787: err= or: >>> cannot convert =8Cconst TestKey=B9 to =8Cunsigned int=B9= in return >>> make[3]: *** >>> [tests/CMakeFiles/test_map.dir/Users/reinert/seqan/projects/tests/map/t= est >>> _ >>> map.cpp.o] Error 1 >>> make[2]: *** [tests/CMakeFiles/test_map.dir/all] Error 2 >>> make[1]: *** [tests/CMakeFiles/test_map.dir/rule] Error 2 >>>=20 >>>=20 >>>=20 >>> Am 11/23/10 4:43 AM schrieb "Fabian Buske" unter: >>>=20 >>>> Hi, >>>>=20 >>>> I observed a rather peculiar phenomenon for the Skiplist map >>>> specialisation, a data type I use quite extensively. >>>>=20 >>>> Using a custom key class and comparator the skiplist sometimes does no= t >>>> find a key that has been inserted into the map. Since the skiplist is = a >>>> randomised data structure this behaviour occurs by chance. >>>>=20 >>>> When using the iterator to go through the Skiplist the element will >>>> actually be output. I observed that the order of the objects (keys) in >>>> the output is not the ordered lists of keys according to the comparato= r >>>> (which I was expecting) but to the order in which the keys where >>>> inserted into the map. I'm not sure if this is intended. >>>>=20 >>>> I created a ticket for this phenomenon, which has an extended test_map >>>> class attached demonstrating this behaviour: >>>> http://trac.mi.fu-berlin.de/seqan/ticket/589 >>>>=20 >>>> This phenomenon may have serious consequences on any application relyi= ng >>>> on Skiplists. >>>>=20 >>>> Best, >>>> Fabian >>>>=20 >>>> --=20 >>>>=20 >>>> Fabian Buske >>>> Institute for Molecular Bioscience >>>> The University of Queensland >>>> Brisbane, Qld. 4072 Australia >>>> Phone: (61)-(7)-334-62608 >>>>=20 >>>>=20 >>>> _______________________________________________ >>>> seqan-dev mailing list >>>> seqan-dev@lists.fu-berlin.de >>>> https://lists.fu-berlin.de/listinfo/seqan-dev >=20 >=20 > --=20 > Fabian Buske > Institute for Molecular Bioscience > The University of Queensland > Brisbane, Qld. 4072 Australia > Phone: (61)-(7)-334-62608 >=20 >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From weese@campus.fu-berlin.de Thu Nov 25 13:38:43 2010 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 <1PLb61-0001xh-I2>; Thu, 25 Nov 2010 13:38:41 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1PLb61-0005fY-Ep>; Thu, 25 Nov 2010 13:38:41 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1PLb61-0001yk-83>; Thu, 25 Nov 2010 13:38:41 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Thu, 25 Nov 2010 13:38:40 +0100 From: "Weese, David" To: SeqAn Development Date: Thu, 25 Nov 2010 13:38:39 +0100 Thread-Topic: [Seqan-dev] I have a question !! :) Thread-Index: AcuMnbBE43Tjv4hNSlK3HPSEfxwE4A== Message-ID: <0D7C2B29-3043-4D41-BEB0-4C4721E68062@fu-berlin.de> References: <000001cb8186$484c45b0$d8e4d110$@ac.kr> In-Reply-To: <000001cb8186$484c45b0$d8e4d110$@ac.kr> Accept-Language: de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: de-DE Content-Type: multipart/alternative; boundary="_000_0D7C2B2930434D41BEB04C4721E68062fuberlinde_" MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1290688721-00000C0F-4A8C0FFD/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.049380, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.6 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE, HTML_TAG_EXIST_TBODY,HTML_WEB_BUGS Subject: Re: [Seqan-dev] I have a question !! :) X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 25 Nov 2010 12:38:43 -0000 --_000_0D7C2B2930434D41BEB04C4721E68062fuberlinde_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 SGksDQoNCkknbSBub3QgdGhlIGF1dGhvciBvZiB0aGlzIEZpbmRlciwgYnV0IHRoZSBzb3VyY2Ug Y29kZSBzZWVtcyB0byBhbGxvdyBvbmx5IHJlcGVhdHMgb2YgY2hhcmFjdGVyIGNsYXNzZXMuIFlv dSBuZWVkIHJlcGVhdGVkIHNlcXVlbmNlcy4NClBsZWFzZSBoYXZlIGEgbG9vayBhdCB0aGUgb3Jp Z2luYWwgcHVibGljYXRpb24gb2YgdGhlIHdpbGRjYXJkIHNoaWZ0LWFuZCBhbGdvcml0aG0gaW46 DQpOYXZhcnJvLCBSYWZmaW5vdCwgIkZsZXhpYmxlIFBhdHRlcm4gTWF0Y2hpbmcgaW4gU3RyaW5n cyIgKDIwMDIpLCBzZWN0aW9uIDQuMy4xDQoNClJlZ2FyZHMsDQpEYXZpZA0KDQoNCi0tDQpEYXZp ZCBXZWVzZSB3ZWVzZUBpbmYuZnUtYmVybGluLmRlPG1haWx0bzp3ZWVzZUBpbmYuZnUtYmVybGlu LmRlPg0KRnJlaWUgVW5pdmVyc2l0w6R0IEJlcmxpbiBodHRwOi8vd3d3LmluZi5mdS1iZXJsaW4u ZGUvDQpJbnN0aXR1dCBmw7xyIEluZm9ybWF0aWsgUGhvbmU6ICs0OSAzMCA4MzggNzUyNDYNClRh 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(mab.citx.mdc-berlin.de [141.80.36.102]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Fri, 26 Nov 2010 13:51:02 +0100 (CET) Received: from mdcexcl.mdc-berlin.net ([141.80.184.16]) by mdcmail.mdc-berlin.de with Microsoft SMTPSVC(6.0.3790.4675); Fri, 26 Nov 2010 13:52:09 +0100 Received: from cd04-macpro.local ([141.80.188.98]) by mdcexcl.mdc-berlin.net with Microsoft SMTPSVC(6.0.3790.4675); Fri, 26 Nov 2010 13:52:08 +0100 Message-ID: <4CEFAD8A.6090006@mdc-berlin.de> Date: Fri, 26 Nov 2010 13:52:26 +0100 From: Mat User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; de; rv:1.9.2.12) Gecko/20101027 Lightning/1.0b2 Thunderbird/3.1.6 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary="------------030606010308030003090100" X-OriginalArrivalTime: 26 Nov 2010 12:52:08.0400 (UTC) FILETIME=[BC369500:01CB8D68] X-TM-AS-Product-Ver: SMEX-10.0.0.1412-6.500.1024-17790.003 X-TM-AS-Result: No--10.251200-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Originating-IP: 141.80.25.23 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1290775869-00000C0F-64EE9474/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.335515, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.9 required=5.0 tests=HTML_40_50,HTML_MESSAGE, RATWARE_GECKO_BUILD Subject: [Seqan-dev] problem with interval tree - assertion failed X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 26 Nov 2010 12:51:10 -0000 This is a multi-part message in MIME format. --------------030606010308030003090100 Content-Type: text/plain; charset=ISO-8859-15; format=flowed Content-Transfer-Encoding: 7bit Hey guys! I got a problem with the interval tree. I want to load contigs and create intervals of the contigs sizes: //Interval tree construction typedef int TValue; //position type typedef gip::MappedFragment TCargo; // interval id type typedef IntervalAndCargo TInterval;// interval type typedef IntervalTree TIntervalTree;// interval tree type std::cout << "Loading contigs file..." << std::endl; if(!loadContigs(fragStore,genomeFileName)){ std::cerr << "Error opening genome file!" << std::endl; return -1; } unsigned int numberOfContigs = length(fragStore.contigNameStore); std::cout << "Found " << numberOfContigs << " contigs in genome file." << std::endl; std::map contigMap; for(unsigned int n=0;n(pos) < static_cast(length(me)) was: 0 >= 0 (Trying to access an element behind the last one!) if i remove the "addInterval" statement i get the output for each contig... thanks! best, mat --------------030606010308030003090100 Content-Type: text/html; charset=ISO-8859-15 Content-Transfer-Encoding: 8bit Hey guys!

I got a problem with the interval tree. I want to load contigs and create intervals of the contigs sizes:

�� //Interval tree construction
�� typedef int TValue; //position type
�� typedef gip::MappedFragment TCargo; // interval id type
�� typedef IntervalAndCargo<TValue, TCargo*> TInterval;// interval type
�� typedef IntervalTree<TValue, TCargo*> TIntervalTree;// interval tree type

�� std::cout << "Loading contigs file..." << std::endl;
�� if(!loadContigs(fragStore,genomeFileName)){
�� std::cerr << "Error opening genome file!" << std::endl;
�� return -1;
�� }

�� unsigned int numberOfContigs = length(fragStore.contigNameStore);
�� std::cout << "Found " << numberOfContigs << " contigs in genome file." << std::endl;

�� std::map<CharString, TIntervalTree*> contigMap;

�� for(unsigned int n=0;n<numberOfContigs;++n){
�� std::cout << "NAME: " << fragStore.contigNameStore[n] << std::endl;
�� std::cout << "LENGTH: " << length(fragStore.contigStore[n].seq) << std::endl;
�� TIntervalTree *tree = new TIntervalTree;
�� TInterval in;
�� in.i1 = 0;
�� in.i2 = length(fragStore.contigStore[n].seq);
�� in.cargo = NULL;

�� addInterval(*tree, in);

�� }

output:
=======
Loading contigs file...
Found 40 contigs in genome file.
/Users/mat/cpp_develop/seqan-trunk/projects/library/seqan/sequence/string_base.hNAME: 1
LENGTH: 6844
:219 Assertion failed : static_cast<TStringPos>(pos) < static_cast<TStringPos>(length(me)) was: 0 >= 0 (Trying to access an element behind the last one!)

if i remove the "addInterval" statement i get the output for each contig...

thanks!

best,

mat
--------------030606010308030003090100-- From matthias.dodt@mdc-berlin.de Fri Nov 26 16:15:44 2010 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 <1PM01W-0003y5-8C>; Fri, 26 Nov 2010 16:15:42 +0100 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PM01W-0005Tt-5S>; Fri, 26 Nov 2010 16:15:42 +0100 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id E951D17C89D for ; Fri, 26 Nov 2010 16:15:41 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:in-reply-to:references:subject:subject :mime-version:user-agent:from:from:date:date:message-id:received :received:received:received; s=dkim1; t=1290784535; x= 1292598935; bh=m8sZKK5/IqCPbK0g6S7yoIxwH02hfx4mYOafaHYcW5o=; b=H KXHMeXfYl/M9WebsjrHA9kK/4mZFG2VXledw3lvfx7Bj8YfUKTw1uXAycqWhuOUF Dm2lXPLlJq7h7s+Vxp/XNJG+jqLVJAQCpN7VuAXcq+u+SK3qJ8Mjs2bOKQv1hiMI 1E0pKkbTVtnRJREucz0mO0fzT/KdnOE7EcnGPsYGhs= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id WZ-sfEUNwFiv for ; Fri, 26 Nov 2010 16:15:35 +0100 (CET) Received: from mdcmail.mdc-berlin.de (mab.citx.mdc-berlin.de [141.80.36.102]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Fri, 26 Nov 2010 16:15:35 +0100 (CET) Received: from mdcexcl.mdc-berlin.net ([141.80.184.16]) by mdcmail.mdc-berlin.de with Microsoft SMTPSVC(6.0.3790.4675); Fri, 26 Nov 2010 16:13:59 +0100 Received: from cd04-macpro.local ([141.80.188.98]) by mdcexcl.mdc-berlin.net with Microsoft SMTPSVC(6.0.3790.4675); Fri, 26 Nov 2010 16:13:58 +0100 Message-ID: <4CEFCEC8.9050202@mdc-berlin.de> Date: Fri, 26 Nov 2010 16:14:16 +0100 From: Mat User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; de; rv:1.9.2.12) Gecko/20101027 Lightning/1.0b2 Thunderbird/3.1.6 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: <4CEFAD8A.6090006@mdc-berlin.de> In-Reply-To: <4CEFAD8A.6090006@mdc-berlin.de> Content-Type: multipart/alternative; boundary="------------050102040002000805050207" X-OriginalArrivalTime: 26 Nov 2010 15:13:58.0906 (UTC) FILETIME=[8CDEBDA0:01CB8D7C] X-TM-AS-Product-Ver: SMEX-10.0.0.1412-6.500.1024-17792.000 X-TM-AS-Result: No--21.965800-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Originating-IP: 141.80.25.23 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1290784542-00000C0F-F3C999DA/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.030944, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.9 required=5.0 tests=HTML_40_50,HTML_MESSAGE, RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] problem with interval tree - assertion failed - how to use addInterval? X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 26 Nov 2010 15:15:44 -0000 This is a multi-part message in MIME format. --------------050102040002000805050207 Content-Type: text/plain; charset=ISO-8859-15; format=flowed Content-Transfer-Encoding: 7bit Hi, Okay if i so it like in the examples, it works but: How do i access "intervals" later in case i want to add an interval to the tree? then i would have to resize the "intervals" String? How does addInterval work? thanks! best, mat 2nd version >>> for(unsigned int n=0;n intervals; resize(intervals,1); TInterval in; intervals[0].i1 = 0; intervals[0].i2 = length(fragStore.contigStore[n].seq); gip::MappedFragment f; intervals[0].cargo = f; TIntervalTree *tree = new TIntervalTree(intervals); contigMap[fragStore.contigNameStore[n]] = tree; } <<< Am 11/26/10 1:52 PM, schrieb Mat: > Hey guys! > > I got a problem with the interval tree. I want to load contigs and > create intervals of the contigs sizes: > > //Interval tree construction > typedef int TValue; //position type > typedef gip::MappedFragment TCargo; // interval id type > typedef IntervalAndCargo TInterval;// interval type > typedef IntervalTree TIntervalTree;// interval > tree type > > std::cout << "Loading contigs file..." << std::endl; > if(!loadContigs(fragStore,genomeFileName)){ > std::cerr << "Error opening genome file!" << std::endl; > return -1; > } > > unsigned int numberOfContigs = length(fragStore.contigNameStore); > std::cout << "Found " << numberOfContigs << " contigs in genome > file." << std::endl; > > std::map contigMap; > > for(unsigned int n=0;n std::cout << "NAME: " << fragStore.contigNameStore[n] << > std::endl; > std::cout << "LENGTH: " << > length(fragStore.contigStore[n].seq) << std::endl; > TIntervalTree *tree = new TIntervalTree; > TInterval in; > in.i1 = 0; > in.i2 = length(fragStore.contigStore[n].seq); > in.cargo = NULL; > > addInterval(*tree, in); > > } > > output: > ======= > Loading contigs file... > Found 40 contigs in genome file. > /Users/mat/cpp_develop/seqan-trunk/projects/library/seqan/sequence/string_base.hNAME: > 1 > LENGTH: 6844 > :219 Assertion failed : static_cast(pos) < > static_cast(length(me)) was: 0 >= 0 (Trying to access an > element behind the last one!) > > if i remove the "addInterval" statement i get the output for each > contig... > > thanks! > > best, > > mat > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --------------050102040002000805050207 Content-Type: text/html; charset=ISO-8859-15 Content-Transfer-Encoding: 8bit Hi,

Okay if i so it like in the examples, it works but: How do i access "intervals" later in case i want to add an interval to the tree? then i would have to resize the "intervals" String? How does addInterval work?

thanks!

best,

mat

2nd version >>>

for(unsigned int n=0;n<numberOfContigs;++n){
�� std::cout << "NAME: " << fragStore.contigNameStore[n] << std::endl;
�� std::cout << "LENGTH: " << length(fragStore.contigStore[n].seq) << std::endl;

�� String<TInterval> intervals;
�� resize(intervals,1);

�� TInterval in;
�� intervals[0].i1 = 0;
�� intervals[0].i2 = length(fragStore.contigStore[n].seq);
�� gip::MappedFragment f;
�� intervals[0].cargo = f;

�� TIntervalTree *tree = new TIntervalTree(intervals);
�� contigMap[fragStore.contigNameStore[n]] = tree;
�� }

<<<

Am 11/26/10 1:52 PM, schrieb Mat:

Hey guys!

I got a problem with the interval tree. I want to load contigs and create intervals of the contigs sizes:

�� //Interval tree construction
�� typedef int TValue; //position type
�� typedef gip::MappedFragment TCargo; // interval id type
�� typedef IntervalAndCargo<TValue, TCargo*> TInterval;// interval type
�� typedef IntervalTree<TValue, TCargo*> TIntervalTree;// interval tree type

�� std::cout << "Loading contigs file..." << std::endl;
�� if(!loadContigs(fragStore,genomeFileName)){
�� std::cerr << "Error opening genome file!" << std::endl;
�� return -1;
�� }

�� unsigned int numberOfContigs = length(fragStore.contigNameStore);
�� std::cout << "Found " << numberOfContigs << " contigs in genome file." << std::endl;

�� std::map<CharString, TIntervalTree*> contigMap;

�� for(unsigned int n=0;n<numberOfContigs;++n){
�� std::cout << "NAME: " << fragStore.contigNameStore[n] << std::endl;
�� std::cout << "LENGTH: " << length(fragStore.contigStore[n].seq) << std::endl;
�� TIntervalTree *tree = new TIntervalTree;
�� TInterval in;
�� in.i1 = 0;
�� in.i2 = length(fragStore.contigStore[n].seq);
�� in.cargo = NULL;

�� addInterval(*tree, in);

�� }

output:
=======
Loading contigs file...
Found 40 contigs in genome file.
/Users/mat/cpp_develop/seqan-trunk/projects/library/seqan/sequence/string_base.hNAME: 1
LENGTH: 6844
:219 Assertion failed : static_cast<TStringPos>(pos) < static_cast<TStringPos>(length(me)) was: 0 >= 0 (Trying to access an element behind the last one!)

if i remove the "addInterval" statement i get the output for each contig...

thanks!

best,

mat
_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev

--------------050102040002000805050207-- From Anne-Katrin.Emde@fu-berlin.de Fri Nov 26 14:12:37 2010 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 <1PLy6O-0008MS-SA>; Fri, 26 Nov 2010 14:12:36 +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 <1PLy6O-0004hB-Ok>; Fri, 26 Nov 2010 14:12:36 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PLy6O-00027r-GO>; Fri, 26 Nov 2010 14:12:36 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Fri, 26 Nov 2010 14:12:36 +0100 From: "Emde, Anne-Katrin" To: SeqAn Development Date: Fri, 26 Nov 2010 14:12:36 +0100 Thread-Topic: [Seqan-dev] problem with interval tree - assertion failed Thread-Index: AcuNaJvPIxiKqltGTtC4dZyjjQGwXAAAPfWg Message-ID: <6AB91D0276C1E744892C72E49C9DFFF77EACB79027@exchange6.fu-berlin.de> References: <4CEFAD8A.6090006@mdc-berlin.de> In-Reply-To: <4CEFAD8A.6090006@mdc-berlin.de> Accept-Language: de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: de-DE Content-Type: multipart/alternative; boundary="_000_6AB91D0276C1E744892C72E49C9DFFF77EACB79027exchange6fube_" MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1290777156-00000C0F-CEF81916/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.003778, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Mailman-Approved-At: Mon, 29 Nov 2010 09:32:52 +0100 Subject: Re: [Seqan-dev] problem with interval tree - assertion failed X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 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, 26 Nov 2010 13:12:38 -0000 --_000_6AB91D0276C1E744892C72E49C9DFFF77EACB79027exchange6fube_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Mat, there seems to be a problem with the addInterval function, when the interva= l tree is empty. I will fix that as soon as possible. However, in your case it would make sense to create a string of intervals, = and then construct the interval tree on the whole set of intervals at once.= This will be more efficient and may construct a more balanced tree. addInt= erval was originally meant to add intervals later on to an existing tree (a= nyway, it should of course also work on an empty tree!). You can see an example in demos/interval_tree.cpp. I'm copy&pasting the rel= evant part here: typedef CharString TCargo; // id type typedef int TValue; // position type typedef IntervalAndCargo TInterval; typedef IntervalTree TIntervalTree; String intervals; resize(intervals,3); // store gene annotation in intervals intervals[0].i1 =3D 5; intervals[0].i2 =3D 1000; intervals[0].cargo =3D "gene"; intervals[1].i1 =3D 50; intervals[1].i2 =3D 200; intervals[1].cargo =3D "exon"; intervals[2].i1 =3D 600; intervals[2].i2 =3D 800; intervals[2].cargo =3D "exon"; TIntervalTree tree(intervals); Best, Anne-Katrin ________________________________ From: Mat [mailto:matthias.dodt@mdc-berlin.de] Sent: Freitag, 26. November 2010 13:52 To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] problem with interval tree - assertion failed Hey guys! I got a problem with the interval tree. I want to load contigs and create i= ntervals of the contigs sizes: //Interval tree construction typedef int TValue; //position type typedef gip::MappedFragment TCargo; // interval id type typedef IntervalAndCargo TInterval;// interval type typedef IntervalTree TIntervalTree;// interval tree ty= pe std::cout << "Loading contigs file..." << std::endl; if(!loadContigs(fragStore,genomeFileName)){ std::cerr << "Error opening genome file!" << std::endl; return -1; } unsigned int numberOfContigs =3D length(fragStore.contigNameStore); std::cout << "Found " << numberOfContigs << " contigs in genome file." = << std::endl; std::map contigMap; for(unsigned int n=3D0;n(pos) < static_cast(length(me)) was: 0 >=3D 0 (Trying to access an element behind the last = one!) if i remove the "addInterval" statement i get the output for each contig... thanks! best, mat --_000_6AB91D0276C1E744892C72E49C9DFFF77EACB79027exchange6fube_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi Mat,

there seems to be a problem with the addInterval function, when the interval tree is empty. I w= ill fix that as soon as possible.

However, in your ca= se it would make sense to create a string of intervals, and then construct the interval tree on the whole set of intervals at once. This will be more efficient and may construct a more balanced tree. addInterval was originall= y meant to add intervals later on to an existing tree (anyway, it should of course also work on an empty tree!).

You can see an exam= ple in demos/interval_tree.cpp. I’m copy&pasting the relevant part here:=

&= nbsp; typedef CharString TCargo; // id type

&= nbsp; typedef int TValue; &n= bsp; // position type

&= nbsp; typedef IntervalAndCargo<TValue, TCargo> TInterval;=

&= nbsp; typedef IntervalTree<TValue, TCargo> TIntervalTree;=

&= nbsp; String<TInterval> intervals;

&= nbsp; resize(intervals,3);

&= nbsp; // store gene annotation in intervals

&= nbsp; intervals[0].i1 =3D 5; intervals[0].i2 =3D 1000;

&= nbsp; intervals[0].cargo =3D "gene";

&= nbsp; intervals[1].i1 =3D 50; intervals[1].i2 =3D 200;

&= nbsp; intervals[1].cargo =3D "exon";

&= nbsp; intervals[2].i1 =3D 600; intervals[2].i2 =3D 800;<= /p>

&= nbsp; intervals[2].cargo =3D "exon";

&= nbsp; TIntervalTree tree(intervals);

Best,

Anne-Katrin

= <= /span>

From: Mat [mailto:matthias.dodt@mdc-berlin.= de]
Sent: Freitag, 26. November = 2010 13:52
To: seqan-dev@lists.fu-berli= n.de
Subject: [Seqan-dev] problem= with interval tree - assertion failed

Hey guys!

I got a problem with the interval tree. I want to load contigs and create intervals of the contigs sizes:

    //Interval tree construction
    typedef int TValue; //position type
    typedef gip::MappedFragment TCargo; // interval id type<= br>     typedef IntervalAndCargo<TValue, TCargo*> TInterva= l;// interval type
    typedef IntervalTree<TValue, TCargo*> TIntervalTre= e;// interval tree type

    std::cout << "Loading contigs file..." << std::endl;
    if(!loadContigs(fragStore,genomeFileName)){
            std::cerr << "Error opening genome file!" << std::endl;
            return -1;
    }

    unsigned int numberOfContigs =3D length(fragStore.contigNameStore);
    std::cout << "Found " << numberOfContigs << " contigs in genome file." << std::endl;

    std::map<CharString, TIntervalTree*> contigMap;
    for(unsigned int n=3D0;n<numberOfContigs;++n){
        std::cout << "NAME: " << fragStore.contigNameStore[n] << std::endl;
        std::cout << "LENGTH: &quo= t; << length(fragStore.contigStore[n].seq) << std::endl;
        TIntervalTree *tree =3D new TInterval= Tree;
        TInterval in;
        in.i1 =3D 0;
        in.i2 =3D length(fragStore.contigStore[n].seq);
        in.cargo =3D NULL;

        addInterval(*tree, in);

     }

output:
=3D=3D=3D=3D=3D=3D=3D
Loading contigs file...
Found 40 contigs in genome file.
/Users/mat/cpp_develop/seqan-trunk/projects/library/seqan/sequence/string_b= ase.hNAME: 1
LENGTH: 6844
:219 Assertion failed : static_cast<TStringPos>(pos) < static_cast<TStringPos>(length(me)) was: 0 >=3D 0 (Trying to acces= s an element behind the last one!)

if i remove the "addInterval" statement i get the output for each contig...

thanks!

best,

mat

--_000_6AB91D0276C1E744892C72E49C9DFFF77EACB79027exchange6fube_-- From Anne-Katrin.Emde@fu-berlin.de Fri Nov 26 18:57:45 2010 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 <1PM2YK-000239-ML>; Fri, 26 Nov 2010 18:57:44 +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 <1PM2YK-0003zO-JC>; Fri, 26 Nov 2010 18:57:44 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from