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  1. Bug Repository
  2. BUG-571

please add ability to copy protein sequence

          Details

          • Type: Bug
          • Status: Closed (View Workflow)
          • Priority: Major
          • Resolution: Fixed
          • Labels:
            None
          • Environment:

            IGB 6.7

            Description

            Please add a new feature to the Sequence Viewer. Hopefully this can be added to IGB 6.7 in addition to IGB 7.0?

            If Anuj is available, maybe he could work on this? Whatever you would like to do is fine.

            What we need is a way for users to copy the translations to the clipboard so that they can then run the sequences in blastp search.

            The way this would work is:

            • Under Edit menu, there is a new option "Copy translation to clipboard" with sub-options for each frame:

            +1 Translation
            +2 Translation
            +3 Translation
            -1 Translation
            -2 Translation
            -3 Translation

            Only one Translation can be copied to the clipboard at a time.

            Also, no selection is necessary. The translation for whatever genomic or cDNA sequence being shown in the viewer is copied to the clipboard.

            Also, under Edit menu, there is an option:

            "Copy annotated translation to clipboard" with no sub-menus.

            This option is active only if the feature being shown has an annotated translation. When the user chooses this option, only the annotated translation is copied. (This starts with ATG and ends with a stop code, e.g., TAG)

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                Issue Links

                relates to

                Task - A task that needs to be done. BUG-608 Sequence viewer bugs

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

                  Activity

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                  anuj Anuj Puram (Inactive) added a comment - - edited

                  Added in v12454 (IGB 7.0)

                  Show
                  anuj Anuj Puram (Inactive) added a comment - - edited Added in v12454 (IGB 7.0)
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                  anuj Anuj Puram (Inactive) added a comment - - edited

                  Added in 6_7 branch in v12455

                  Show
                  anuj Anuj Puram (Inactive) added a comment - - edited Added in 6_7 branch in v12455
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                  ann.loraine Ann Loraine added a comment -

                  Please test.

                  Show
                  ann.loraine Ann Loraine added a comment - Please test.
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  currently the +1 and -1 translation is returning the same results, which is wrong. (the same is happening for the +2/ -2 and +3/ -3)

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - currently the +1 and -1 translation is returning the same results, which is wrong. (the same is happening for the +2/ -2 and +3/ -3)
                  Hide
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Also - I got this exception:

                  Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: -1
                  at com.affymetrix.genoviz.util.DNAUtils.translate(DNAUtils.java:1090)
                  at com.affymetrix.genoviz.util.DNAUtils.translate(DNAUtils.java:943)
                  at com.affymetrix.genoviz.util.DNAUtils.translate(DNAUtils.java:919)
                  at com.affymetrix.igb.view.AbstractSequenceViewer.copyTransAction(AbstractSequenceViewer.java:655)
                  at com.affymetrix.igb.view.CopyTransFromSeqViewerAction.actionPerformed(AbstractSequenceViewer.java:861)
                  at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
                  at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
                  at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
                  at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
                  at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
                  at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
                  at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)
                  at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
                  at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
                  at java.awt.Component.processMouseEvent(Component.java:6382)
                  at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)
                  at java.awt.Component.processEvent(Component.java:6147)
                  at java.awt.Container.processEvent(Container.java:2083)
                  at java.awt.Component.dispatchEventImpl(Component.java:4744)
                  at java.awt.Container.dispatchEventImpl(Container.java:2141)
                  at java.awt.Component.dispatchEvent(Component.java:4572)
                  at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619)
                  at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4280)
                  at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210)
                  at java.awt.Container.dispatchEventImpl(Container.java:2127)
                  at java.awt.Window.dispatchEventImpl(Window.java:2489)
                  at java.awt.Component.dispatchEvent(Component.java:4572)
                  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:704)
                  at java.awt.EventQueue.access$400(EventQueue.java:82)
                  at java.awt.EventQueue$2.run(EventQueue.java:663)
                  at java.awt.EventQueue$2.run(EventQueue.java:661)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
                  at java.awt.EventQueue$3.run(EventQueue.java:677)
                  at java.awt.EventQueue$3.run(EventQueue.java:675)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
                  at java.awt.EventQueue.dispatchEvent(EventQueue.java:674)
                  at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
                  at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
                  at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
                  at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - Also - I got this exception: Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: -1 at com.affymetrix.genoviz.util.DNAUtils.translate(DNAUtils.java:1090) at com.affymetrix.genoviz.util.DNAUtils.translate(DNAUtils.java:943) at com.affymetrix.genoviz.util.DNAUtils.translate(DNAUtils.java:919) at com.affymetrix.igb.view.AbstractSequenceViewer.copyTransAction(AbstractSequenceViewer.java:655) at com.affymetrix.igb.view.CopyTransFromSeqViewerAction.actionPerformed(AbstractSequenceViewer.java:861) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) at javax.swing.AbstractButton.doClick(AbstractButton.java:389) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809) at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272) at java.awt.Component.processMouseEvent(Component.java:6382) at javax.swing.JComponent.processMouseEvent(JComponent.java:3275) at java.awt.Component.processEvent(Component.java:6147) at java.awt.Container.processEvent(Container.java:2083) at java.awt.Component.dispatchEventImpl(Component.java:4744) at java.awt.Container.dispatchEventImpl(Container.java:2141) at java.awt.Component.dispatchEvent(Component.java:4572) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4280) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210) at java.awt.Container.dispatchEventImpl(Container.java:2127) at java.awt.Window.dispatchEventImpl(Window.java:2489) at java.awt.Component.dispatchEvent(Component.java:4572) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:704) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:663) at java.awt.EventQueue$2.run(EventQueue.java:661) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) at java.awt.EventQueue$3.run(EventQueue.java:677) at java.awt.EventQueue$3.run(EventQueue.java:675) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:674) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
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                  fwang4 Fuquan Wang (Inactive) added a comment -

                  Fixed in 13224

                  Show
                  fwang4 Fuquan Wang (Inactive) added a comment - Fixed in 13224

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      ann.loraine Ann Loraine
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                      Dates

                      • Created:
                        Updated:
                        Resolved: