#21 oligotm does not accept floats

open
nobody
5
2014-03-25
2007-07-11
Jan van Haarst
No

Right now oligotm does not accepts floats for the concentration values, it would be nice if it would.

Related

Feature Requests: #21

Discussion

  • benpruitt
    benpruitt
    2014-03-19

    This is still an issue with the current release (2.3.6). The command line argument parsing requires the monovalent cation concentration and dna concentration to be integers (see oligotm_main.c lines 131, 167), while the divalent cation concentration and dntp concentrations can be floats (lines 143 and 155). The function that oligotm_main wraps, oligotm, takes doubles for all of these values. It also appears that all of the calculations in oligotm and its helper functions are floating point calculations, so any sort of cast/conversion to an int isn't an optimization. It would be really helpful if this could be corrected or explained.

     
    • Steve Rozen
      Steve Rozen
      2014-03-19

      Ok, thanks. Just to confirm, your are talking about the oligotm main, the
      command line arguments, correct?

      On Wed, Mar 19, 2014 at 12:02 PM, benpruitt benpruitt@users.sf.net wrote:

      This is still an issue with the current release (2.3.6). The command line
      argument parsing requires the monovalent cation concentration and dna
      concentration to be integers (see oligotm_main.c lines 131, 167), while the
      divalent cation concentration and dntp concentrations can be floats (lines
      143 and 155). The function that oligotm_main wraps, oligotm, takes doubles
      for all of these values. It also appears that all of the calculations in
      oligotm and its helper functions are floating point calculations, so any
      sort of cast/conversion to an int isn't an optimization. It would be really
      helpful if this could be corrected or explained.


      Status: open
      Group:
      Labels: interface improvements
      Created: Wed Jul 11, 2007 12:37 PM UTC by Jan van Haarst
      Last Updated: Tue Feb 05, 2013 02:44 AM UTC
      Owner: nobody

      Right now oligotm does not accepts floats for the concentration values, it
      would be nice if it would.


      Sent from sourceforge.net because you indicated interest in
      https://sourceforge.net/p/primer3/feature-requests/21/

      To unsubscribe from further messages, please visit
      https://sourceforge.net/auth/subscriptions/

      --
      Steve

      ================================
      Steven G. ROZEN, Ph.D.
      Associate Professor and Director, Centre for Computational Biology
      DUKE-NUS GRADUATE MEDICAL SCHOOL SINGAPORE
      8 College Road
      169857 Singapore
      Republic of Singapore
      steve.rozen (at) duke-nus.edu.sg
      +65 9857 3213
      https://www.duke-nus.edu.sg/content/rozen-steve
      ================================
      -

       

      Related

      Feature Requests: #21

      Attachments
      • benpruitt
        benpruitt
        2014-03-19

        Yes that is correct.

        On Wed, Mar 19, 2014 at 12:35 AM, Steve Rozen steverozen@users.sf.net
        wrote:

        Ok, thanks. Just to confirm, your are talking about the oligotm main, the
        command line arguments, correct?
        On Wed, Mar 19, 2014 at 12:02 PM, benpruitt benpruitt@users.sf.net wrote:

        This is still an issue with the current release (2.3.6). The command line
        argument parsing requires the monovalent cation concentration and dna
        concentration to be integers (see oligotm_main.c lines 131, 167), while the
        divalent cation concentration and dntp concentrations can be floats (lines
        143 and 155). The function that oligotm_main wraps, oligotm, takes doubles
        for all of these values. It also appears that all of the calculations in
        oligotm and its helper functions are floating point calculations, so any
        sort of cast/conversion to an int isn't an optimization. It would be really
        helpful if this could be corrected or explained.


        Status: open
        Group:
        Labels: interface improvements
        Created: Wed Jul 11, 2007 12:37 PM UTC by Jan van Haarst
        Last Updated: Tue Feb 05, 2013 02:44 AM UTC
        Owner: nobody

        Right now oligotm does not accepts floats for the concentration values, it
        would be nice if it would.


        Sent from sourceforge.net because you indicated interest in
        https://sourceforge.net/p/primer3/feature-requests/21/

        To unsubscribe from further messages, please visit
        https://sourceforge.net/auth/subscriptions/

        --
        Steve
        ================================
        Steven G. ROZEN, Ph.D.
        Associate Professor and Director, Centre for Computational Biology
        DUKE-NUS GRADUATE MEDICAL SCHOOL SINGAPORE
        8 College Road
        169857 Singapore
        Republic of Singapore
        steve.rozen (at) duke-nus.edu.sg
        +65 9857 3213
        https://www.duke-nus.edu.sg/content/rozen-steve
        ================================
        -


        2:02 PM, benpruitt benpruitt@users.sf.net wrote:

        This is still an issue with the current release (2.3.6). The command line
        argument parsing requires the monovalent cation concentration and dna
        concentration to be integers (see oligotm_main.c lines 131, 167), while the
        divalent cation concentration and dntp concentrations can be floats (lines
        143 and 155). The function that oligotm_main wraps, oligotm, takes doubles
        for all of these values. It also appears that all of the calculations in
        oligotm and its helper functions are floating point calculations, so any
        sort of cast/conversion to an int isn't an optimization. It would be really
        helpful if this could be corrected or explained.


        Status: open
        Group:
        Labels: interface improvements
        Created: Wed Jul 11, 2007 12:37 PM UTC by Jan van Haarst
        Last Updated: Tue Feb 05, 2013 02:44 AM UTC
        Owner: nobody

        Right now oligotm does not accepts floats for the concentration values, it
        would be nice if it would.


        Sent from sourceforge.net because you indicated interest in
        https://sourceforge.net/p/primer3/feature-requests/21/

        To unsubscribe from further messages, please visit
        https://sourceforge.net/auth/subscriptions/

        --
        Steve
        ================================
        Steven G. ROZEN, Ph.D.
        Associate Professor and Director, Centre for Computational Biology
        DUKE-NUS GRADUATE MEDICAL SCHOOL SINGAPORE
        8 College Road
        169857 Singapore
        Republic of Singapore
        steve.rozen (at) duke-nus.edu.sg
        +65 9857 3213
        https://www.duke-nus.edu.sg/content/rozen-steve
        ================================
        -


        ument parsing requires the monovalent cation concentration and dna

        concentration to be integers (see oligotm_main.c lines 131, 167), while the
        divalent cation concentration and dntp concentrations can be floats (lines
        143 and 155). The function that oligotm_main wraps, oligotm, takes doubles
        for all of these values. It also appears that all of the calculations in
        oligotm and its helper functions are floating point calculations, so any
        sort of cast/conversion to an int isn't an optimization. It would be really
        helpful if this could be corrected or explained.


        Status: open
        Group:
        Labels: interface improvements
        Created: Wed Jul 11, 2007 12:37 PM UTC by Jan van Haarst
        Last Updated: Tue Feb 05, 2013 02:44 AM UTC
        Owner: nobody

        Right now oligotm does not accepts floats for the concentration values, it
        would be nice if it would.


        Sent from sourceforge.net because you indicated interest in
        https://sourceforge.net/p/primer3/feature-requests/21/

        To unsubscribe from further messages, please visit
        https://sourceforge.net/auth/subscriptions/

        --
        Steve
        ================================
        Steven G. ROZEN, Ph.D.
        Associate Professor and Director, Centre for Computational Biology
        DUKE-NUS GRADUATE MEDICAL SCHOOL SINGAPORE
        8 College Road
        169857 Singapore
        Republic of Singapore
        steve.rozen (at) duke-nus.edu.sg
        +65 9857 3213
        https://www.duke-nus.edu.sg/content/rozen-steve
        ================================
        -


        ), while the

        divalent cation concentration and dntp concentrations can be floats (lines
        143 and 155). The function that oligotm_main wraps, oligotm, takes doubles
        for all of these values. It also appears that all of the calculations in
        oligotm and its helper functions are floating point calculations, so any
        sort of cast/conversion to an int isn't an optimization. It would be really
        helpful if this could be corrected or explained.


        Status: open
        Group:
        Labels: interface improvements
        Created: Wed Jul 11, 2007 12:37 PM UTC by Jan van Haarst
        Last Updated: Tue Feb 05, 2013 02:44 AM UTC
        Owner: nobody

        Right now oligotm does not accepts floats for the concentration values, it
        would be nice if it would.


        Sent from sourceforge.net because you indicated interest in
        https://sourceforge.net/p/primer3/feature-requests/21/

        To unsubscribe from further messages, please visit
        https://sourceforge.net/auth/subscriptions/

        --
        Steve
        ================================
        Steven G. ROZEN, Ph.D.
        Associate Professor and Director, Centre for Computational Biology
        DUKE-NUS GRADUATE MEDICAL SCHOOL SINGAPORE
        8 College Road
        169857 Singapore
        Republic of Singapore
        steve.rozen (at) duke-nus.edu.sg
        +65 9857 3213
        https://www.duke-nus.edu.sg/content/rozen-steve
        ================================
        -


        main wraps, oligotm, takes doubles

        for all of these values. It also appears that all of the calculations in
        oligotm and its helper functions are floating point calculations, so any
        sort of cast/conversion to an int isn't an optimization. It would be really
        helpful if this could be corrected or explained.


        Status: open
        Group:
        Labels: interface improvements
        Created: Wed Jul 11, 2007 12:37 PM UTC by Jan van Haarst
        Last Updated: Tue Feb 05, 2013 02:44 AM UTC
        Owner: nobody

        Right now oligotm does not accepts floats for the concentration values, it
        would be nice if it would.


        Sent from sourceforge.net because you indicated interest in
        https://sourceforge.net/p/primer3/feature-requests/21/

        To unsubscribe from further messages, please visit
        https://sourceforge.net/auth/subscriptions/

        --
        Steve
        ================================
        Steven G. ROZEN, Ph.D.
        Associate Professor and Director, Centre for Computational Biology
        DUKE-NUS GRADUATE MEDICAL SCHOOL SINGAPORE
        8 College Road
        169857 Singapore
        Republic of Singapore
        steve.rozen (at) duke-nus.edu.sg
        +65 9857 3213
        https://www.duke-nus.edu.sg/content/rozen-steve
        ================================
        -


        er functions are floating point calculations, so any

        sort of cast/conversion to an int isn't an optimization. It would be really
        helpful if this could be corrected or explained.


        Status: open
        Group:
        Labels: interface improvements
        Created: Wed Jul 11, 2007 12:37 PM UTC by Jan van Haarst
        Last Updated: Tue Feb 05, 2013 02:44 AM UTC
        Owner: nobody

        Right now oligotm does not accepts floats for the concentration values, it
        would be nice if it would.


        Sent from sourceforge.net because you indicated interest in
        https://sourceforge.net/p/primer3/feature-requests/21/

        To unsubscribe from further messages, please visit
        https://sourceforge.net/auth/subscriptions/

        --
        Steve
        ================================
        Steven G. ROZEN, Ph.D.
        Associate Professor and Director, Centre for Computational Biology
        DUKE-NUS GRADUATE MEDICAL SCHOOL SINGAPORE
        8 College Road
        169857 Singapore
        Republic of Singapore
        steve.rozen (at) duke-nus.edu.sg
        +65 9857 3213
        https://www.duke-nus.edu.sg/content/rozen-steve
        ================================
        -


        helpful if this could be corrected or explained.


        Status: open
        Group:
        Labels: interface improvements
        Created: Wed Jul 11, 2007 12:37 PM UTC by Jan van Haarst
        Last Updated: Tue Feb 05, 2013 02:44 AM UTC
        Owner: nobody

        Right now oligotm does not accepts floats for the concentration values, it
        would be nice if it would.


        Sent from sourceforge.net because you indicated interest in
        https://sourceforge.net/p/primer3/feature-requests/21/

        To unsubscribe from further messages, please visit
        https://sourceforge.net/auth/subscriptions/

        --
        Steve
        ================================
        Steven G. ROZEN, Ph.D.
        Associate Professor and Director, Centre for Computational Biology
        DUKE-NUS GRADUATE MEDICAL SCHOOL SINGAPORE
        8 College Road
        169857 Singapore
        Republic of Singapore
        steve.rozen (at) duke-nus.edu.sg
        +65 9857 3213
        https://www.duke-nus.edu.sg/content/rozen-steve
        ================================
        -


        e.net/p/primer3/feature-requests/21/> oligotm does not

        accept floats*

        Status: open
        Group:
        Labels: interface improvements
        Created: Wed Jul 11, 2007 12:37 PM UTC by Jan van Haarst
        Last Updated: Tue Feb 05, 2013 02:44 AM UTC
        Owner: nobody

        Right now oligotm does not accepts floats for the concentration values, it
        would be nice if it would.


        Sent from sourceforge.net because you indicated interest in
        https://sourceforge.net/p/primer3/feature-requests/21/

        To unsubscribe from further messages, please visit
        https://sourceforge.net/auth/subscriptions/

        --
        Steve
        ================================
        Steven G. ROZEN, Ph.D.
        Associate Professor and Director, Centre for Computational Biology
        DUKE-NUS GRADUATE MEDICAL SCHOOL SINGAPORE
        8 College Road
        169857 Singapore
        Republic of Singapore
        steve.rozen (at) duke-nus.edu.sg
        +65 9857 3213
        https://www.duke-nus.edu.sg/content/rozen-steve
        ================================
        -


        ents

        Created: Wed Jul 11, 2007 12:37 PM UTC by Jan van Haarst
        Last Updated: Tue Feb 05, 2013 02:44 AM UTC
        Owner: nobody

        Right now oligotm does not accepts floats for the concentration values, it
        would be nice if it would.


        Sent from sourceforge.net because you indicated interest in
        https://sourceforge.net/p/primer3/feature-requests/21/

        To unsubscribe from further messages, please visit
        https://sourceforge.net/auth/subscriptions/

        --
        Steve
        ================================
        Steven G. ROZEN, Ph.D.
        Associate Professor and Director, Centre for Computational Biology
        DUKE-NUS GRADUATE MEDICAL SCHOOL SINGAPORE
        8 College Road
        169857 Singapore
        Republic of Singapore
        steve.rozen (at) duke-nus.edu.sg
        +65 9857 3213
        https://www.duke-nus.edu.sg/content/rozen-steve
        ================================
        -


        Right now oligotm does not accepts floats for the concentration values, it
        would be nice if it would.


        Sent from sourceforge.net because you indicated interest in
        https://sourceforge.net/p/primer3/feature-requests/21/

        To unsubscribe from further messages, please visit
        https://sourceforge.net/auth/subscriptions/

        --
        Steve
        ================================
        Steven G. ROZEN, Ph.D.
        Associate Professor and Director, Centre for Computational Biology
        DUKE-NUS GRADUATE MEDICAL SCHOOL SINGAPORE
        8 College Road
        169857 Singapore
        Republic of Singapore
        steve.rozen (at) duke-nus.edu.sg
        +65 9857 3213
        https://www.duke-nus.edu.sg/content/rozen-steve
        ================================
        -



        Sent from sourceforge.net because you indicated interest in
        https://sourceforge.net/p/primer3/feature-requests/21/

        To unsubscribe from further messages, please visit
        https://sourceforge.net/auth/subscriptions/

        --
        Steve
        ================================
        Steven G. ROZEN, Ph.D.
        Associate Professor and Director, Centre for Computational Biology
        DUKE-NUS GRADUATE MEDICAL SCHOOL SINGAPORE
        8 College Road
        169857 Singapore
        Republic of Singapore
        steve.rozen (at) duke-nus.edu.sg
        +65 9857 3213
        https://www.duke-nus.edu.sg/content/rozen-steve
        ================================
        -


        [feature-requests:#21] oligotm does not accept floats
        Status: open
        Group:
        Labels: interface improvements
        Created: Wed Jul 11, 2007 12:37 PM UTC by Jan van Haarst
        Last Updated: Wed Mar 19, 2014 04:02 AM UTC
        Owner: nobody
        Right now oligotm does not accepts floats for the concentration values, it would be nice if it would.


        Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/primer3/feature-requests/21/
        To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

         

        Related

        Feature Requests: #21

        • Steve Rozen
          Steve Rozen
          2014-03-22

          We have updated the code, tests, and release notes. Are you able to get the
          updated code directly from the repository?

          On Wed, Mar 19, 2014 at 4:22 PM, benpruitt benpruitt@users.sf.net wrote:

          Yes that is correct.

          On Wed, Mar 19, 2014 at 12:35 AM, Steve Rozen steverozen@users.sf.net
          wrote:

          Ok, thanks. Just to confirm, your are talking about the oligotm main, the
          command line arguments, correct?
          On Wed, Mar 19, 2014 at 12:02 PM, benpruitt benpruitt@users.sf.net wrote:

          This is still an issue with the current release (2.3.6). The command line

           
          Attachments
  • benpruitt
    benpruitt
    2014-03-25

    I am, thanks for the quick fix.

     
    • Steve Rozen
      Steve Rozen
      2014-03-25

      Ok, good. We will not push a release at this point, then.

      On Tue, Mar 25, 2014 at 12:19 PM, benpruitt benpruitt@users.sf.net wrote:

      I am, thanks for the quick fix.


      [feature-requests:#21] oligotm does not accept floats

      Status: open
      Group:
      Labels: interface improvements
      Created: Wed Jul 11, 2007 12:37 PM UTC by Jan van Haarst
      Last Updated: Wed Mar 19, 2014 04:02 AM UTC
      Owner: nobody

      Right now oligotm does not accepts floats for the concentration values, it
      would be nice if it would.


      Sent from sourceforge.net because you indicated interest in
      https://sourceforge.net/p/primer3/feature-requests/21/

      To unsubscribe from further messages, please visit
      https://sourceforge.net/auth/subscriptions/

      --
      Steve

      ================================
      Steven G. ROZEN, Ph.D.
      Associate Professor and Director, Centre for Computational Biology
      DUKE-NUS GRADUATE MEDICAL SCHOOL SINGAPORE
      8 College Road
      169857 Singapore
      Republic of Singapore
      steve.rozen (at) duke-nus.edu.sg
      +65 9857 3213
      https://www.duke-nus.edu.sg/content/rozen-steve
      ================================
      -

       

      Related

      Feature Requests: #21