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  1. Jalview
  2. JAL-3905

old labels from alignment mouseovers not cleared in chimera view

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.11.2.0
    • Component/s: None
    • Labels:

      Description

      Moving the mouse across a linked sequence shows a label. Normally the previously shown label is removed before a new one shown but not in 2.11.2.0-rc1:

      Load examples/1GAQ.txt and view chain A in Chimera
      Open java console, and Move mouse across sequence.

      See output like below on console:
      1GAQ
      reading 690 atoms
      ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
      1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
      Default Van der Waals type for model set to Jmol
      690 atoms created
      ModelSet: autobonding; use autobond=false to not generate bonds automatically
      Time for creating model: 3 ms
      >>> SIFTS File already downloaded for 1GAQ
      Getting SIFTS mapping for 1GAQ|A: seq 1GAQ|A
      INFO org.apache.http.impl.client.DefaultHttpClient - I/O exception (java.net.SocketException) caught when processing request: Broken pipe (Write failed)
      INFO - I/O exception (java.net.SocketException) caught when processing request: Broken pipe (Write failed)
      INFO org.apache.http.impl.client.DefaultHttpClient - Retrying request
      INFO - Retrying request
      ERROR ext.edu.ucsf.rbvi.strucviz2.ChimeraManager - REST call '~rlabel #0:28.A' failed: Connect to /127.0.0.1:58300 timed out
      ERROR - REST call '~rlabel #0:28.A' failed: Connect to /127.0.0.1:58300 timed out
      ERROR ext.edu.ucsf.rbvi.strucviz2.ChimeraManager - REST call '~rlabel #0:23.A' failed: Connect to /127.0.0.1:58300 timed out
      ERROR - REST call '~rlabel #0:23.A' failed: Connect to /127.0.0.1:58300 timed out
      INFO org.apache.http.impl.client.DefaultHttpClient - I/O exception (java.net.SocketException) caught when processing request: Broken pipe (Write failed)
      INFO - I/O exception (java.net.SocketException) caught when processing request: Broken pipe (Write failed)
      INFO org.apache.http.impl.client.DefaultHttpClient - Retrying request
      INFO - Retrying request
      ERROR ext.edu.ucsf.rbvi.strucviz2.ChimeraManager - REST call '~rlabel #0:22.A' failed: Connect to /127.0.0.1:58300 timed out
      ERROR - REST call '~rlabel #0:22.A' failed: Connect to /127.0.0.1:58300 timed out
      ERROR ext.edu.ucsf.rbvi.strucviz2.ChimeraManager - REST call 'rlabel #0:29.A' failed: Connection reset by peer (connect failed)
      ERROR - REST call 'rlabel #0:29.A' failed: Connection reset by peer (connect failed)
      ERROR ext.edu.ucsf.rbvi.strucviz2.ChimeraManager - REST call '~rlabel #0:23.A' failed: Connect to /127.0.0.1:58300 timed out
      ERROR - REST call '~rlabel #0:23.A' failed: Connect to /127.0.0.1:58300 timed out
      ERROR ext.edu.ucsf.rbvi.strucviz2.ChimeraManager - REST call 'rlabel #0:27.A' failed: Connect to /127.0.0.1:58300 timed out
      ERROR - REST call 'rlabel #0:27.A' failed: Connect to /127.0.0.1:58300 timed out
      ERROR ext.edu.ucsf.rbvi.strucviz2.ChimeraManager - REST call '~rlabel #0:26.A' failed: Connect to /127.0.0.1:58300 timed out
      ERROR - REST call '~rlabel #0:26.A' failed: Connect to /127.0.0.1:58300 timed out
      ERROR ext.edu.ucsf.rbvi.strucviz2.ChimeraManager - REST call '~rlabel #0:28.A' failed: Connect to /127.0.0.1:58300 timed out
      ERROR - REST call '~rlabel #0:28.A' failed: Connect to /127.0.0.1:58300 timed out

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            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
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              Created:
              Updated:
              Resolved: