From matthias.dodt@mdc-berlin.de Mon Feb 07 16:31:36 2011 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 <1PmT3v-0001Bt-Aw>; Mon, 07 Feb 2011 16:31:35 +0100 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PmT3v-0003My-79>; Mon, 07 Feb 2011 16:31:35 +0100 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id D3EFC6321A for ; Mon, 7 Feb 2011 16:31:34 +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=1297092689; x=1298907089; bh=Gat3 BdxaPPmg77oMCr/Twwhad1CTGiyEMmB7GmCm3hU=; b=fSwUbF1xcp3mTGzUGhAs i5K3c4UC0/fXOSrEqBvFP1V2rERE32bWDeIS2PrjA/PVa2WGQickYKxJP5Ok5otE 6PEskCaZVLTGU0/Ysz0MTtlFLBNu5ca11bTWU9hBp5zAW3RXnuj9p+tMMCSUY7uj QblSubHdm6Wl+mR+EoJocNc= X-Virus-Scanned: amavisd-new at bbbm.mdc-berlin.de Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id djZ2Vo44i+Cq for ; Mon, 7 Feb 2011 16:31:29 +0100 (CET) Received: from mdcmail.mdc-berlin.de (mab.citx.mdc-berlin.de [141.80.36.102]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Mon, 7 Feb 2011 16:31:29 +0100 (CET) Received: from mdcexcl.mdc-berlin.net ([141.80.184.16]) by mdcmail.mdc-berlin.de with Microsoft SMTPSVC(6.0.3790.4675); Mon, 7 Feb 2011 16:31:23 +0100 Received: from cd04-macpro.local ([141.80.188.98]) by mdcexcl.mdc-berlin.net with Microsoft SMTPSVC(6.0.3790.4675); Mon, 7 Feb 2011 16:31:22 +0100 Message-ID: <4D5010F3.1020306@mdc-berlin.de> Date: Mon, 07 Feb 2011 16:34:11 +0100 From: Mat User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; de; rv:1.9.2.13) Gecko/20101207 Lightning/1.0b2 Thunderbird/3.1.7 MIME-Version: 1.0 To: SeqAn Development Content-Type: multipart/alternative; boundary="------------080001060301040401060200" X-OriginalArrivalTime: 07 Feb 2011 15:31:22.0225 (UTC) FILETIME=[12E45610:01CBC6DC] X-TM-AS-Product-Ver: SMEX-10.0.0.1412-6.500.1024-17940.007 X-TM-AS-Result: No--3.186700-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Originating-IP: 141.80.25.20 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1297092695-00003B05-E6C5D68A/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.045464, 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=0.9 required=5.0 tests=HTML_40_50,HTML_MESSAGE, RATWARE_GECKO_BUILD Subject: [Seqan-dev] Using EdgeProperties and VertexProperties 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: Mon, 07 Feb 2011 15:31:36 -0000 This is a multi-part message in MIME format. --------------080001060301040401060200 Content-Type: text/plain; charset=ISO-8859-15; format=flowed Content-Transfer-Encoding: 7bit Hey guys! I would like to create a .dot file of my graph using the write(strmWrite, *graph, *vertexPropertyMap,*edgePropertyMap,DotDrawing()); method. The two maps are defined as follows: seqan::String *vertexPropertyMap = new seqan::String(); seqan::String *edgePropertyMap = new seqan::String(); VertexProperty and EdgeProperty are two custom classes... Now if i use the DotDrawing() method i get the message "cannot convert form VertexProperty to char"... So i guess i would have to implement my own "_streamPut" method for these classes in seqans "cstream.h", so something like: inline void _streamPut(::std::FILE * target, const EdgeProperty e) { SEQAN_CHECKPOINT //putc(e.toChar(), target); } or is there an easier way to do that? Thanks! best, mat --------------080001060301040401060200 Content-Type: text/html; charset=ISO-8859-15 Content-Transfer-Encoding: 8bit Hey guys!

I would like to create a .dot file of my graph using the

write(strmWrite, *graph, *vertexPropertyMap,*edgePropertyMap,DotDrawing());

method.

The two maps are defined as follows:

seqan::String<VertexProperty> *vertexPropertyMap = new seqan::String<VertexProperty>();
seqan::String<EdgeProperty> *edgePropertyMap = new seqan::String<EdgeProperty>();

VertexProperty and EdgeProperty are two custom classes...

Now if i use the DotDrawing() method i get the message "cannot convert form VertexProperty to char"...

So i guess i would have to implement my own "_streamPut" method for these classes in seqans "cstream.h", so something like:

inline void _streamPut(::std::FILE * target,
           const EdgeProperty e)
{
SEQAN_CHECKPOINT
    //putc(e.toChar(), target);
}

or is there an easier way to do that?

Thanks!

best,

mat
 --------------080001060301040401060200-- From Tobias.Rausch@fu-berlin.de Tue Feb 08 10:06:07 2011 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 <1PmjWQ-0001iV-Fo>; Tue, 08 Feb 2011 10:06:06 +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 <1PmjWQ-0004tZ-Aw>; Tue, 08 Feb 2011 10:06:06 +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 <1PmjWP-00054n-W7>; Tue, 08 Feb 2011 10:06:06 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Tue, 8 Feb 2011 10:06:05 +0100 From: "Rausch, Tobias" To: SeqAn Development Date: Tue, 8 Feb 2011 10:02:35 +0100 Thread-Topic: [Seqan-dev] Using EdgeProperties and VertexProperties Thread-Index: AcvG3B46VIKTepASSiKkVl9eSQD9/wAks76U Message-ID: <6AB91D0276C1E744892C72E49C9DFFF77EB8525487@exchange6.fu-berlin.de> References: <4D5010F3.1020306@mdc-berlin.de> In-Reply-To: <4D5010F3.1020306@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: text/plain; charset="us-ascii" 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::1297155966-00003B05-7DCA72A4/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.042236, 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 Subject: Re: [Seqan-dev] Using EdgeProperties and VertexProperties 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, 08 Feb 2011 09:06:07 -0000 Hey Mat, In the write function in graph_types/graph_drawing.h, for each vertex and e= dge property the following call is used: _streamWrite(file, getProperty(nodeMap, *itVertex)); _streamWrite(file, getProperty(edgeMap, *itEdge)); Best, Tobias ________________________________________ From: Mat [matthias.dodt@mdc-berlin.de] Sent: Monday, February 07, 2011 4:34 PM To: SeqAn Development Subject: [Seqan-dev] Using EdgeProperties and VertexProperties Hey guys! I would like to create a .dot file of my graph using the write(strmWrite, *graph, *vertexPropertyMap,*edgePropertyMap,DotDrawing()); method. The two maps are defined as follows: seqan::String *vertexPropertyMap =3D new seqan::String(); seqan::String *edgePropertyMap =3D new seqan::String(); VertexProperty and EdgeProperty are two custom classes... Now if i use the DotDrawing() method i get the message "cannot convert form= VertexProperty to char"... So i guess i would have to implement my own "_streamPut" method for these c= lasses in seqans "cstream.h", so something like: inline void _streamPut(::std::FILE * target, const EdgeProperty e) { SEQAN_CHECKPOINT //putc(e.toChar(), target); } or is there an easier way to do that? Thanks! best, mat From matthias.dodt@mdc-berlin.de Tue Feb 08 10:17:42 2011 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 <1Pmjhd-00025d-7H>; Tue, 08 Feb 2011 10:17:41 +0100 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Pmjhd-0006MS-3y>; Tue, 08 Feb 2011 10:17:41 +0100 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id DF9AA62D85 for ; Tue, 8 Feb 2011 10:17:40 +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=1297156654; x= 1298971054; bh=LpzjTzYzZJ8PiX1+aQBBZx3g6VhDGnOVvk2IxOYP8tU=; b=i cQVqSyraIVj6NoLCA8/mKrC3FrNHIrdrajUjD7GktJun3bFVOEvaO9CX/nBm54xZ 8KHTaTZdkP/yvDf40KYlG9vUXYwftSkjKKK86rAZB11/VLFR7VWHKMQLuvGDYFjc UWGs5PgklU7nUryUh7BYMhmmx8tEzzgYQ0RV+Y64N8= X-Virus-Scanned: amavisd-new at bbbm.mdc-berlin.de Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id XVTiMAd2uNUY for ; Tue, 8 Feb 2011 10:17:34 +0100 (CET) Received: from mdcmail.mdc-berlin.de (mab.citx.mdc-berlin.de [141.80.36.102]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Tue, 8 Feb 2011 10:17:34 +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, 8 Feb 2011 10:17:21 +0100 Received: from cd04-macpro.local ([141.80.188.98]) by mdcexcl.mdc-berlin.net with Microsoft SMTPSVC(6.0.3790.4675); Tue, 8 Feb 2011 10:17:21 +0100 Message-ID: <4D510ACB.2040409@mdc-berlin.de> Date: Tue, 08 Feb 2011 10:20:11 +0100 From: Mat User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; de; rv:1.9.2.13) Gecko/20101207 Lightning/1.0b2 Thunderbird/3.1.7 MIME-Version: 1.0 To: SeqAn Development References: <4D5010F3.1020306@mdc-berlin.de> <6AB91D0276C1E744892C72E49C9DFFF77EB8525487@exchange6.fu-berlin.de> In-Reply-To: <6AB91D0276C1E744892C72E49C9DFFF77EB8525487@exchange6.fu-berlin.de> Content-Type: multipart/alternative; boundary="------------060409080406040701000505" X-OriginalArrivalTime: 08 Feb 2011 09:17:21.0088 (UTC) FILETIME=[FD585400:01CBC770] X-TM-AS-Product-Ver: SMEX-10.0.0.1412-6.500.1024-17940.007 X-TM-AS-Result: No--14.120300-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Originating-IP: 141.80.25.20 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1297156661-00003B05-570D2E6E/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.056674, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.9 required=5.0 tests=HTML_30_40,HTML_MESSAGE, HTML_TITLE_EMPTY,RATWARE_GECKO_BUILD Subject: Re: [Seqan-dev] Using EdgeProperties and VertexProperties 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, 08 Feb 2011 09:17:42 -0000 This is a multi-part message in MIME format. --------------060409080406040701000505 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi Tobias! Yes, this basically means the output works only for build-in types i guess- getProperty will return the object stored in the map... so i would have to write my own "write" specialization i guess... I was wondering if its possible to avoid that. I have various attributes per node and edge- so it wouldnt work to just use a map of int's for example- best, mat Am 2/8/11 10:02 AM, schrieb Rausch, Tobias: > Hey Mat, > > In the write function in graph_types/graph_drawing.h, for each vertex and edge property the following call is used: > > _streamWrite(file, getProperty(nodeMap, *itVertex)); > > _streamWrite(file, getProperty(edgeMap, *itEdge)); > > > Best, Tobias > > > > ________________________________________ > From: Mat [matthias.dodt@mdc-berlin.de] > Sent: Monday, February 07, 2011 4:34 PM > To: SeqAn Development > Subject: [Seqan-dev] Using EdgeProperties and VertexProperties > > Hey guys! > > I would like to create a .dot file of my graph using the > > write(strmWrite, *graph, *vertexPropertyMap,*edgePropertyMap,DotDrawing()); > > method. > > The two maps are defined as follows: > > seqan::String *vertexPropertyMap = new seqan::String(); > seqan::String *edgePropertyMap = new seqan::String(); > > VertexProperty and EdgeProperty are two custom classes... > > Now if i use the DotDrawing() method i get the message "cannot convert form VertexProperty to char"... > > So i guess i would have to implement my own "_streamPut" method for these classes in seqans "cstream.h", so something like: > > inline void _streamPut(::std::FILE * target, > const EdgeProperty e) > { > SEQAN_CHECKPOINT > //putc(e.toChar(), target); > } > > or is there an easier way to do that? > > Thanks! > > best, > > mat > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --------------060409080406040701000505 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Tobias!

Yes, this basically means the output works only for build-in types i guess-

getProperty will return the object stored in the map... so i would have to write my own "write" specialization i guess...

I was wondering if its possible to avoid that. I have various attributes per node and edge- so it wouldnt work to just use a map of int's for example-

best,

mat

Am 2/8/11 10:02 AM, schrieb Rausch, Tobias: 
Hey Mat,

In the write function in graph_types/graph_drawing.h, for each vertex and edge property the following call is used:

_streamWrite(file, getProperty(nodeMap, *itVertex));

_streamWrite(file, getProperty(edgeMap, *itEdge));


Best, Tobias



________________________________________
From: Mat [matthias.dodt@mdc-berlin.de]
Sent: Monday, February 07, 2011 4:34 PM
To: SeqAn Development
Subject: [Seqan-dev] Using EdgeProperties and VertexProperties

Hey guys!

I would like to create a .dot file of my graph using the

write(strmWrite, *graph, *vertexPropertyMap,*edgePropertyMap,DotDrawing());

method.

The two maps are defined as follows:

seqan::String<VertexProperty> *vertexPropertyMap = new seqan::String<VertexProperty>();
seqan::String<EdgeProperty> *edgePropertyMap = new seqan::String<EdgeProperty>();

VertexProperty and EdgeProperty are two custom classes...

Now if i use the DotDrawing() method i get the message "cannot convert form VertexProperty to char"...

So i guess i would have to implement my own "_streamPut" method for these classes in seqans "cstream.h", so something like:

inline void _streamPut(::std::FILE * target,
           const EdgeProperty e)
{
SEQAN_CHECKPOINT
    //putc(e.toChar(), target);
}

or is there an easier way to do that?

Thanks!

best,

mat

_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev
--------------060409080406040701000505-- From carbaj1@hotmail.com Wed Feb 09 14:01:38 2011 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 <1Pn9fs-0006yN-RK>; Wed, 09 Feb 2011 14:01:36 +0100 Received: from col0-omc2-s14.col0.hotmail.com ([65.55.34.88]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Pn9fs-00079o-Cr>; Wed, 09 Feb 2011 14:01:36 +0100 Received: from COL122-W19 ([65.55.34.72]) by col0-omc2-s14.col0.hotmail.com with Microsoft SMTPSVC(6.0.3790.4675); Wed, 9 Feb 2011 05:01:33 -0800 Message-ID: Content-Type: multipart/alternative; boundary="_df8537d4-eb0b-4e19-ab89-c1d7b8ad2c9e_" From: Julio Cesar Carbajal To: Date: Wed, 9 Feb 2011 13:01:33 +0000 Importance: Normal In-Reply-To: <6AB91D0276C1E744892C72E49C9DFFF77EB8525487@exchange6.fu-berlin.de> References: <4D5010F3.1020306@mdc-berlin.de>, <6AB91D0276C1E744892C72E49C9DFFF77EB8525487@exchange6.fu-berlin.de> MIME-Version: 1.0 X-OriginalArrivalTime: 09 Feb 2011 13:01:33.0496 (UTC) FILETIME=[7A04A380:01CBC859] X-Originating-IP: 65.55.34.88 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1297256496-00003B05-1DDD16FB/0-0/0-0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.497104, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.-Berlin.DE X-Spam-Level: xxx X-Spam-Status: No, score=3.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,FU_BOGO_UNSURE,HTML_20_30,HTML_MESSAGE, SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] how to read fasta files to uses in Hoorspol program 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: Wed, 09 Feb 2011 13:01:38 -0000 --_df8537d4-eb0b-4e19-ab89-c1d7b8ad2c9e_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hey=2C Could you help me. How to read fasta files to uses in Hoorspol program or modify de find_exact= program. Julio=20 > From: Tobias.Rausch@fu-berlin.de > To: seqan-dev@lists.fu-berlin.de > Date: Tue=2C 8 Feb 2011 10:02:35 +0100 > Subject: Re: [Seqan-dev] Using EdgeProperties and VertexProperties >=20 > Hey Mat=2C >=20 > In the write function in graph_types/graph_drawing.h=2C for each vertex a= nd edge property the following call is used: >=20 > _streamWrite(file=2C getProperty(nodeMap=2C *itVertex))=3B >=20 > _streamWrite(file=2C getProperty(edgeMap=2C *itEdge))=3B >=20 >=20 > Best=2C Tobias >=20 >=20 >=20 > ________________________________________ > From: Mat [matthias.dodt@mdc-berlin.de] > Sent: Monday=2C February 07=2C 2011 4:34 PM > To: SeqAn Development > Subject: [Seqan-dev] Using EdgeProperties and VertexProperties >=20 > Hey guys! >=20 > I would like to create a .dot file of my graph using the >=20 > write(strmWrite=2C *graph=2C *vertexPropertyMap=2C*edgePropertyMap=2CDotD= rawing())=3B >=20 > method. >=20 > The two maps are defined as follows: >=20 > seqan::String *vertexPropertyMap =3D new seqan::String()=3B > seqan::String *edgePropertyMap =3D new seqan::String()=3B >=20 > VertexProperty and EdgeProperty are two custom classes... >=20 > Now if i use the DotDrawing() method i get the message "cannot convert fo= rm VertexProperty to char"... >=20 > So i guess i would have to implement my own "_streamPut" method for these= classes in seqans "cstream.h"=2C so something like: >=20 > inline void _streamPut(::std::FILE * target=2C > const EdgeProperty e) > { > SEQAN_CHECKPOINT > //putc(e.toChar()=2C target)=3B > } >=20 > or is there an easier way to do that? >=20 > Thanks! >=20 > best=2C >=20 > mat >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev = --_df8537d4-eb0b-4e19-ab89-c1d7b8ad2c9e_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hey=2C

Could you help me.

How to read fasta files to uses in = Hoorspol program or modify de find_exact program.

Julio

>= =3B From: Tobias.Rausch@fu-berlin.de
>=3B To: seqan-dev@lists.fu-berli= n.de
>=3B Date: Tue=2C 8 Feb 2011 10:02:35 +0100
>=3B Subject: Re= : [Seqan-dev] Using EdgeProperties and VertexProperties
>=3B
>= =3B Hey Mat=2C
>=3B
>=3B In the write function in graph_types/gr= aph_drawing.h=2C for each vertex and edge property the following call is us= ed:
>=3B
>=3B _streamWrite(file=2C getProperty(nodeMap=2C *itVer= tex))=3B
>=3B
>=3B _streamWrite(file=2C getProperty(edgeMap=2C *= itEdge))=3B
>=3B
>=3B
>=3B Best=2C Tobias
>=3B
&g= t=3B
>=3B
>=3B ________________________________________
>= =3B From: Mat [matthias.dodt@mdc-berlin.de]
>=3B Sent: Monday=2C Febru= ary 07=2C 2011 4:34 PM
>=3B To: SeqAn Development
>=3B Subject: [= Seqan-dev] Using EdgeProperties and VertexProperties
>=3B
>=3B H= ey guys!
>=3B
>=3B I would like to create a .dot file of my grap= h using the
>=3B
>=3B write(strmWrite=2C *graph=2C *vertexProper= tyMap=2C*edgePropertyMap=2CDotDrawing())=3B
>=3B
>=3B method.>=3B
>=3B The two maps are defined as follows:
>=3B
>= =3B seqan::String<=3BVertexProperty>=3B *vertexPropertyMap =3D new seqa= n::String<=3BVertexProperty>=3B()=3B
>=3B seqan::String<=3BEdgeP= roperty>=3B *edgePropertyMap =3D new seqan::String<=3BEdgeProperty>= =3B()=3B
>=3B
>=3B VertexProperty and EdgeProperty are two custo= m classes...
>=3B
>=3B Now if i use the DotDrawing() method i ge= t the message "cannot convert form VertexProperty to char"...
>=3B >=3B So i guess i would have to implement my own "_streamPut" method for= these classes in seqans "cstream.h"=2C so something like:
>=3B
&g= t=3B inline void _streamPut(::std::FILE * target=2C
>=3B co= nst EdgeProperty e)
>=3B {
>=3B SEQAN_CHECKPOINT
>=3B //= putc(e.toChar()=2C target)=3B
>=3B }
>=3B
>=3B or is there = an easier way to do that?
>=3B
>=3B Thanks!
>=3B
>=3B= best=2C
>=3B
>=3B mat
>=3B
>=3B ____________________= ___________________________
>=3B seqan-dev mailing list
>=3B seqa= n-dev@lists.fu-berlin.de
>=3B https://lists.fu-berlin.de/listinfo/seqa= n-dev
= --_df8537d4-eb0b-4e19-ab89-c1d7b8ad2c9e_-- From Anne-Katrin.Emde@fu-berlin.de Wed Feb 09 14:27:29 2011 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 <1PnA4t-0007uh-V1>; Wed, 09 Feb 2011 14:27:28 +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 <1PnA4t-0004tf-T1>; Wed, 09 Feb 2011 14:27:27 +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 <1PnA4t-0002RR-NR>; Wed, 09 Feb 2011 14:27:27 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Wed, 9 Feb 2011 14:27:27 +0100 From: "Emde, Anne-Katrin" To: SeqAn Development Date: Wed, 9 Feb 2011 14:22:35 +0100 Thread-Topic: [Seqan-dev] how to read fasta files to uses in Hoorspol program Thread-Index: AcvIWX8Gvq1m3+PVQHCSnelQ99uVJQAAurlS Message-ID: <6AB91D0276C1E744892C72E49C9DFFF77EB8408063@exchange6.fu-berlin.de> References: <4D5010F3.1020306@mdc-berlin.de>, <6AB91D0276C1E744892C72E49C9DFFF77EB8525487@exchange6.fu-berlin.de>, In-Reply-To: Accept-Language: de-DE Content-Language: de-DE X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: de-DE Content-Type: text/plain; charset="iso-8859-1" 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::1297258047-00003B05-4F0B64E6/0-0/0-0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.455540, 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=-1.3 required=5.0 tests=ALL_TRUSTED,FU_BOGO_UNSURE Cc: "carbaj1@hotmail.com" Subject: Re: [Seqan-dev] how to read fasta files to uses in Hoorspol program 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: Wed, 09 Feb 2011 13:27:29 -0000 Hi Julio, you can use the FileReader data structure to load sequences from Fasta file= s. So for example, if you pass the Fasta filenames via the command line: String haystack =3D String >(argv[1])= ; String needle =3D String >(argv[2]); Take a look at file_format.cpp for more options on reading Fasta sequences. Cheers, Anne-Katrin ----------------------------------------------- Anne-Katrin Emde +49 30 83875240 emde@inf.fu-berlin.de Algorithmic Bioinformatics Department of Computer Science Freie Universit=E4t Berlin ---------------------------------------------- ________________________________________ Von: Julio Cesar Carbajal [carbaj1@hotmail.com] Gesendet: Mittwoch, 9. Februar 2011 14:01 An: seqan-dev@lists.fu-berlin.de Betreff: [Seqan-dev] how to read fasta files to uses in Hoorspol program Hey, Could you help me. How to read fasta files to uses in Hoorspol program or modify de find_exact= program. Julio > From: Tobias.Rausch@fu-berlin.de > To: seqan-dev@lists.fu-berlin.de > Date: Tue, 8 Feb 2011 10:02:35 +0100 > Subject: Re: [Seqan-dev] Using EdgeProperties and VertexProperties > > Hey Mat, > > In the write function in graph_types/graph_drawing.h, for each vertex and= edge property the following call is used: > > _streamWrite(file, getProperty(nodeMap, *itVertex)); > > _streamWrite(file, getProperty(edgeMap, *itEdge)); > > > Best, Tobias > > > > ________________________________________ > From: Mat [matthias.dodt@mdc-berlin.de] > Sent: Monday, February 07, 2011 4:34 PM > To: SeqAn Development > Subject: [Seqan-dev] Using EdgeProperties and VertexProperties > > Hey guys! > > I would like to create a .dot file of my graph using the > > write(strmWrite, *graph, *vertexPropertyMap,*edgePropertyMap,DotDrawing()= ); > > method. > > The two maps are defined as follows: > > seqan::String *vertexPropertyMap =3D new seqan::String(); > seqan::String *edgePropertyMap =3D new seqan::String(); > > VertexProperty and EdgeProperty are two custom classes... > > Now if i use the DotDrawing() method i get the message "cannot convert fo= rm VertexProperty to char"... > > So i guess i would have to implement my own "_streamPut" method for these= classes in seqans "cstream.h", so something like: > > inline void _streamPut(::std::FILE * target, > const EdgeProperty e) > { > SEQAN_CHECKPOINT > //putc(e.toChar(), target); > } > > or is there an easier way to do that? > > Thanks! > > best, > > mat > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From carbaj1@hotmail.com Thu Feb 10 17:45:27 2011 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 <1PnZe2-0003j8-Gr>; Thu, 10 Feb 2011 17:45:26 +0100 Received: from col0-omc2-s9.col0.hotmail.com ([65.55.34.83]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1PnZe2-0002Q1-8H>; Thu, 10 Feb 2011 17:45:26 +0100 Received: from COL122-W3 ([65.55.34.71]) by col0-omc2-s9.col0.hotmail.com with Microsoft SMTPSVC(6.0.3790.4675); Thu, 10 Feb 2011 08:45:23 -0800 Message-ID: Content-Type: multipart/alternative; boundary="_18f9d79f-532b-4c48-a4c6-2e1aae4b9172_" From: Julio Cesar Carbajal To: Tobias R. Date: Thu, 10 Feb 2011 16:45:22 +0000 Importance: Normal In-Reply-To: References: MIME-Version: 1.0 X-OriginalArrivalTime: 10 Feb 2011 16:45:23.0017 (UTC) FILETIME=[E90CAB90:01CBC941] X-Originating-IP: 65.55.34.83 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1297356326-00003B05-D666DF5C/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.417213, 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 X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,HTML_40_50,HTML_MESSAGE,SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] Help me 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, 10 Feb 2011 16:45:27 -0000 --_18f9d79f-532b-4c48-a4c6-2e1aae4b9172_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello=20 Please=2C help me. I have problem using a external file such as lagan1.fasta (Escherichia coli= ) with demo program: find_exact.cpp. During the running of the program=2C the program no count occurrences of ne= edle in the haystack. Could you say me how to solve this problem. Thanks. Julio /// THE CODE OF MY PROBLEM #include #include #include #include #include #include using namespace seqan=3B int main()=20 { // Open a file using a file reader string. String my_haystack =3D String > ("lagan= 1.fasta")=3B String my_needle =3D "GATC"=3B Finder > finder(my_haystack)=3B Pattern=2C Horspool> pattern(my_needle)=3B =20 // proof printing: correct printing ::std::cout << my_haystack << "\n\n\n"=3B =20 ::std::cout << my_needle << "\n"=3B =20 // the problem: no count the find position of my_needle within the my_hayst= ack. // How to solve this problem? while (find(finder=2C pattern))=20 { ::std::cout << position(finder) << "=2C"=3B =20 } =20 ::std::cout << ::std::endl=3B // fstrm.close()=3B return (0)=3B } = --_18f9d79f-532b-4c48-a4c6-2e1aae4b9172_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello


Please=2C help me.

I have problem using a external= file such as lagan1.fasta (Escherichia coli) with demo program: find_exact= .cpp.
During the running of the program=2C the program no count occurren= ces of needle in the haystack.


Could you say me how to solve thi= s problem.


Thanks.

Julio


/// THE CODE OF MY PR= OBLEM

#include <=3Biostream>=3B
#include <=3Bseqan/find.h&g= t=3B

#include <=3Bfstream>=3B
#include <=3Bcstdio>=3B
=
#include <=3Bseqan/sequence.h>=3B
#include <=3Bseqan/file.h>= =3B


using namespace seqan=3B

int main()
{

// O= pen a file using a file reader string.
 =3B =3B =3B String&l= t=3Bchar>=3B my_haystack =3D String<=3Bchar=2C FileReader<=3BFasta>= =3B >=3B ("lagan1.fasta")=3B

 =3B =3B =3B String<=3B= char>=3B my_needle =3D "GATC"=3B

 =3B =3B =3B Finder&l= t=3BString<=3Bchar>=3B >=3B finder(my_haystack)=3B
 =3B = =3B =3B Pattern<=3BString<=3Bchar>=3B=2C Horspool>=3B pattern(m= y_needle)=3B
 =3B =3B =3B
// proof printing: correct pri= nting
 =3B =3B =3B ::std::cout <=3B<=3B my_haystack <= =3B<=3B "\n\n\n"=3B =3B
 =3B =3B =3B ::std::cout <= =3B<=3B my_needle <=3B<=3B "\n"=3B =3B =3B =3B

//= the problem: no count the find position of my_needle within the my_haystac= k.
// How to solve this problem?

 =3B =3B =3B while (= find(finder=2C pattern))
 =3B =3B =3B {
 =3B =3B=  =3B  =3B =3B =3B ::std::cout <=3B<=3B position(finder)= <=3B<=3B "=2C"=3B =3B
 =3B =3B =3B } =3B = =3B =3B  =3B =3B =3B  =3B =3B =3B  =3B = =3B =3B  =3B =3B =3B  =3B =3B =3B  =3B
<= br> =3B =3B =3B ::std::cout <=3B<=3B ::std::endl=3B

=
 =3B =3B =3B // fstrm.close()=3B
 =3B =3B = =3B return (0)=3B
}


= --_18f9d79f-532b-4c48-a4c6-2e1aae4b9172_-- From Knut.Reinert@fu-berlin.de Thu Feb 10 17:57:07 2011 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 <1PnZpK-000466-KK>; Thu, 10 Feb 2011 17:57:06 +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 <1PnZpK-0000y3-Hl>; Thu, 10 Feb 2011 17:57:06 +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 <1PnZpK-0001yE-CQ>; Thu, 10 Feb 2011 17:57:06 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Thu, 10 Feb 2011 17:57:06 +0100 From: "Reinert, Knut" To: SeqAn Development Date: Thu, 10 Feb 2011 17:57:07 +0100 Thread-Topic: [Seqan-dev] Help me Thread-Index: AcvJQ4wNtlthYoHBQJWnxzKYbQFfJg== 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/14.2.0.101115 acceptlanguage: en-US, de-DE Content-Type: multipart/signed; protocol="application/pkcs7-signature"; micalg=sha1; boundary="B_3380205427_32959312" MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-ZEDAT-Hint: A X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1297357026-00003B05-A3216E6D/3291807941-0/0-1 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000001, 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=-1.7 required=5.0 tests=ALL_TRUSTED, FU_XPURGATE_SUSP, HTML_50_60,HTML_MESSAGE Subject: Re: [Seqan-dev] Help me 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, 10 Feb 2011 16:57:07 -0000 --B_3380205427_32959312 Content-type: multipart/alternative; boundary="B_3380205427_32940248" --B_3380205427_32940248 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi Julio, Can yo specify more closely your problem? When I compile your program and start it it outputs the correct matches. What do you mean by "no count occurrences". If you need to count the number of occurrences, you just have to increment a counter in the while loop. darwin10.0 : ./find_exact CAGCCGGATCGGGATCTATC GATC 6,12, Knut Von: Julio Cesar Carbajal Antworten an: SeqAn Development Datum: Thu, 10 Feb 2011 17:45:22 +0100 An: "Tobias R." Betreff: [Seqan-dev] Help me > Hello > > > Please, help me. > > I have problem using a external file such as lagan1.fasta (Escherichia coli) > with demo program: find_exact.cpp. > During the running of the program, the program no count occurrences of needle > in the haystack. > > > Could you say me how to solve this problem. > > > Thanks. > > Julio > > > /// THE CODE OF MY PROBLEM > > #include > #include > > #include > #include > > #include > #include > > > using namespace seqan; > > int main() > { > > // Open a file using a file reader string. > String my_haystack = String > > ("lagan1.fasta"); > > String my_needle = "GATC"; > > Finder > finder(my_haystack); > Pattern, Horspool> pattern(my_needle); > > // proof printing: correct printing > ::std::cout << my_haystack << "\n\n\n"; > ::std::cout << my_needle << "\n"; > > // the problem: no count the find position of my_needle within the > my_haystack. > // How to solve this problem? > > while (find(finder, pattern)) > { > ::std::cout << position(finder) << ","; > } > > ::std::cout << ::std::endl; > > > // fstrm.close(); > return (0); > } > > > --B_3380205427_32940248 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable
Hi Julio,

Can yo specify more closely your problem?

Wh= en I compile your program and start it it outputs the correct matches.
=
What do you mean by "no count occurrences".
If you need to co= unt the number of occurrences, you just have to increment a counter in the w= hile loop.


 darwin10.0 : .= /find_exact 
CAGCCGGATCGGGATCTATC

GATC
6,12,

Knut
<= div>
Von: Julio Cesar Carbajal = <carbaj1@hotmail.com>
Antworten an: SeqAn Development <seqan-dev@lists.fu-berlin.de>= ;
Datum: Thu, 10 Feb 2011 17:45:22= +0100
An: "Tobias R." <seqan-dev@lists.fu-berlin.de><= br>Betreff: [Seqan-dev] Help me

Hello


Please, help me.

I have problem using a external f= ile such as lagan1.fasta (Escherichia coli) with demo program: find_exact.cp= p.
During the running of the program, the program no count occurrences of= needle in the haystack.


Could you say me how to solve this probl= em.


Thanks.

Julio


/// THE CODE OF MY PROBLEM
#include <iostream>
#include <seqan/find.h>

#incl= ude <fstream>
#include <cstdio>

#include <seqan/seq= uence.h>
#include <seqan/file.h>


using namespace seqa= n;

int main()
{

// Open a file using a file reader string.=
    String<char> my_haystack =3D String<char, File= Reader<Fasta> > ("lagan1.fasta");

    String&= lt;char> my_needle =3D "GATC";

    Finder<String&l= t;char> > finder(my_haystack);
    Pattern<String= <char>, Horspool> pattern(my_needle);
   
// = proof printing: correct printing
    ::std::cout << = my_haystack << "\n\n\n"; 
    ::std::cout <= < my_needle << "\n";   

// the problem: no c= ount the find position of my_needle within the my_haystack.
// How to sol= ve this problem?

    while (find(finder, pattern))     {
        ::std::cout &= lt;< position(finder) << ","; 
    } &= nbsp;               &= nbsp;       

    ::std::cout = << ::std::endl;


    // fstrm.close();
&nb= sp;   return (0);
}


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Date: Fri, 11 Feb 2011 14:42:39 +0000 Importance: Normal In-Reply-To: References: MIME-Version: 1.0 X-OriginalArrivalTime: 11 Feb 2011 14:42:39.0213 (UTC) FILETIME=[EE4B19D0:01CBC9F9] X-Originating-IP: 65.55.34.81 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1297435362-00003B05-1BBEC8C4/0-0/0-0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.495340, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.-Berlin.DE X-Spam-Level: xxx X-Spam-Status: No, score=3.3 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,FU_BOGO_UNSURE,HTML_40_50,HTML_MESSAGE, SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] Specific problem 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, 11 Feb 2011 14:42:44 -0000 --_3c6fdf28-9e50-4e8e-93c4-d6aff6204966_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello. Forgive me. I am using a external file such as lagan1.fasta (Escherichia coli) with dem= o program: find_exact.cpp. During the running of the program=2C the program NO PRINT occurrences of ne= edle in the haystack. /// // the problem: NO PRINT the find position of my_needle within the my_hayst= ack. // How to solve this problem? while (find(finder=2C pattern)) { ::std::cout << position(finder) << "=2C"=3B=20 } =20 /// =20 I am doing this=2C because it is my intention to measure the run time execu= tion of Horspool algorithm=2C with different size of my_needle for this situation. Could you say me how to solve this problem.=20 Thanks.=20 Julio. = --_3c6fdf28-9e50-4e8e-93c4-d6aff6204966_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello.

Forgive me.

I am using a external file such as lagan1.= fasta (Escherichia coli) with demo program: find_exact.cpp.
During the r= unning of the program=2C the program NO PRINT occurrences of needle in the = haystack.

///
// the problem: NO PRINT the find position of my_ne= edle within the my_haystack.
// How to solve this problem?

 = =3B =3B =3B while (find(finder=2C pattern))
 =3B =3B&nbs= p=3B {
 =3B =3B =3B =3B =3B =3B =3B ::std::c= out <=3B<=3B position(finder) <=3B<=3B "=2C"=3B
 =3B = =3B =3B } =3B =3B  =3B
///
 =3B =3B =3B&n= bsp=3B  =3B
I am doing this=2C because it is my intention to measure= the run time execution of Horspool algorithm=2C
with different size of = my_needle for this situation.


Could you say me how to solve this= problem.


Thanks.

Julio.
= --_3c6fdf28-9e50-4e8e-93c4-d6aff6204966_-- From Knut.Reinert@fu-berlin.de Fri Feb 11 15:57:09 2011 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 <1PnuQm-0005GG-VF>; Fri, 11 Feb 2011 15:57:09 +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 <1PnuQm-0003AV-Sf>; Fri, 11 Feb 2011 15:57:08 +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 <1PnuQm-0004gR-Kq>; Fri, 11 Feb 2011 15:57:08 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Fri, 11 Feb 2011 15:57:08 +0100 From: "Reinert, Knut" To: SeqAn Development Date: Fri, 11 Feb 2011 15:57:07 +0100 Thread-Topic: [Seqan-dev] Specific problem Thread-Index: AcvJ+/RB0WBzOt6kSmeAW6j3Vc9EHA== 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/14.2.0.101115 acceptlanguage: en-US, de-DE Content-Type: multipart/signed; protocol="application/pkcs7-signature"; micalg=sha1; boundary="B_3380284627_1527652" 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::1297436228-00003B05-591E7C70/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000115, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=ALL_TRUSTED,HTML_50_60, HTML_MESSAGE Subject: Re: [Seqan-dev] Specific problem 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, 11 Feb 2011 14:57:09 -0000 --B_3380284627_1527652 Content-type: multipart/alternative; boundary="B_3380284627_1528941" --B_3380284627_1528941 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, I took your program and compiled it. I provided it with a file lagan1.fasta (with content > test CAGCCGGATCGGGATCTATC The program works fine as you can see. It outputs positions 6 and 12. darwin10.0 : ./find_exact CAGCCGGATCGGGATCTATC GATC 6,12, Knut Von: Julio Cesar Carbajal Antworten an: SeqAn Development Datum: Fri, 11 Feb 2011 15:42:39 +0100 An: "Tobias R." Betreff: [Seqan-dev] Specific problem > Hello. > > Forgive me. > > I am using a external file such as lagan1.fasta (Escherichia coli) with demo > program: find_exact.cpp. > During the running of the program, the program NO PRINT occurrences of needle > in the haystack. > > /// > // the problem: NO PRINT the find position of my_needle within the > my_haystack. > // How to solve this problem? > > while (find(finder, pattern)) > { > ::std::cout << position(finder) << ","; > } > /// > > I am doing this, because it is my intention to measure the run time execution > of Horspool algorithm, > with different size of my_needle for this situation. > > > Could you say me how to solve this problem. > > > Thanks. > > Julio. > --B_3380284627_1528941 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable
Hi,

I took your program and compiled it. I provided it with a file lagan1.fasta= (with content 

> test
CAGCCGGATC= GGGATCTATC


The program works fine as= you can see. It outputs positions 6 and 12.

<= div> darwin10.0 : ./find_exact 
CAGCCGGATCGGGATCTATC


GATC
6,12,
Knut

=
Von:= Julio Cesar Carbajal <carba= j1@hotmail.com>
Antworten an: SeqAn Development <seqan= -dev@lists.fu-berlin.de>
Datum: Fri, 11 Feb 2011 15:42:39 +0100
An: <= /span> "Tobias R." <seqan-d= ev@lists.fu-berlin.de>
Betreff: [Seqan-dev] Specific problem

Hello.

Forgive me.

I am using a external file such as lagan1.= fasta (Escherichia coli) with demo program: find_exact.cpp.
During the ru= nning of the program, the program NO PRINT occurrences of needle in the hays= tack.

///
// the problem: NO PRINT the find position of my_needle = within the my_haystack.
// How to solve this problem?

  =   while (find(finder, pattern))
    {
  =       ::std::cout << position(finder) <<= ; ",";
    }    
///
  &nb= sp;   
I am doing this, because it is my intention to measure t= he run time execution of Horspool algorithm,
with different size of my_ne= edle for this situation.


Could you say me how to solve this probl= em.


Thanks.

Julio.
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