[IGBF-399] Refactor SeqMapView by introducing new abstractions to reduce complexity of this class - JIRA UNCC

Details

Type: Improvement
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
2
Epic Link:
Technical Debt Reduction
Sprint:
Sprint 12, Sprint 15

Description

We should not have a class that is ~3000 lines. There is an obvious failure to apply the single responsibility principle to in this location of the code. Please spend some time refactoring this code.

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David Norris (Inactive) created issue - 06/Feb/15 5:53 AM

David Norris (Inactive) made changes - 06/Feb/15 5:53 AM

Field	Original Value	New Value
Rank		Ranked higher

David Norris (Inactive) made changes - 06/Feb/15 5:53 AM

Status

Open [ 1 ]

In Progress [ 3 ]

David Norris (Inactive) made changes - 09/Feb/15 4:31 AM

Sprint

Sprint 12 [ 17 ]

Sprint 12, Sprint 13 [ 17, 18 ]

David Norris (Inactive) made changes - 09/Feb/15 4:31 AM

Rank

Ranked higher

David Norris (Inactive) made changes - 10/Feb/15 5:30 AM

Status

In Progress [ 3 ]

Needs Testing [ 10002 ]

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Tarun Mall (Inactive) added a comment - 10/Feb/15 5:49 AM

commit 00d6e030ab90a720b6771591ad8933c01a710f16
Merge: d317e8c 34b8ef0
Author: hillrunner2008 <Hillrunner2008@gmail.com>
Date: Tue Feb 10 10:29:52 2015 -0500

Merged in c2tarun/integrated-genome-browser/IGBF-323 (pull request #206)

Code refactoring of SeqMapView done.

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Tarun Mall (Inactive) added a comment - 10/Feb/15 5:49 AM commit 00d6e030ab90a720b6771591ad8933c01a710f16 Merge: d317e8c 34b8ef0 Author: hillrunner2008 <Hillrunner2008@gmail.com> Date: Tue Feb 10 10:29:52 2015 -0500 Merged in c2tarun/integrated-genome-browser/ IGBF-323 (pull request #206) Code refactoring of SeqMapView done.

Mason Meyer (Inactive) made changes - 10/Feb/15 6:33 AM

Status

Needs Testing [ 10002 ]

Testing In Progress [ 10003 ]

Mason Meyer (Inactive) made changes - 10/Feb/15 6:34 AM

Assignee

Tarun Mall [ tmall ]

Mason Meyer [ mason ]

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Mason Meyer (Inactive) added a comment - 10/Feb/15 8:58 AM - edited

While testing I noticed that the foreground color was not being respected. The foreground color should change the color of the annotations/reads but it changed the track label instead.

Also, a null pointer exception was generated when changing the color settings under the Annotation tab (see exception below).

Moving back to To-Do column.

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at com.affymetrix.igb.action.ChangeColorActionA.performAction(ChangeColorActionA.java:97)
at com.affymetrix.igb.shared.Actions.setLabelColor(Actions.java:44)
at com.affymetrix.igb.shared.StylePanelImpl.labelColorComboBoxActionPerformedA(StylePanelImpl.java:85)
at com.affymetrix.igb.shared.StylePanel.labelColorComboBoxActionPerformed(StylePanel.java:146)
at com.affymetrix.igb.shared.StylePanel$$Lambda$125/987834065.actionPerformed(Unknown Source)
at com.jidesoft.combobox.AbstractComboBox.fireActionEvent(Unknown Source)
at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source)
at com.jidesoft.combobox.ColorComboBox.setSelectedItem(Unknown Source)
at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source)
at com.jidesoft.combobox.AbstractComboBox$3.itemStateChanged(Unknown Source)
at com.jidesoft.combobox.PopupPanel.fireItemStateChanged(Unknown Source)
at com.jidesoft.combobox.PopupPanel.setSelectedObject(Unknown Source)
at com.jidesoft.combobox.PopupPanel.setSelectedObject(Unknown Source)
at com.jidesoft.combobox.ColorChooserPanel.setSelectedColor(Unknown Source)
at com.jidesoft.combobox.ColorChooserPanel$d_.actionPerformed(Unknown Source)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
at com.jidesoft.plaf.basic.BasicJideButtonListener.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$400(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

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Mason Meyer (Inactive) added a comment - 10/Feb/15 8:58 AM - edited While testing I noticed that the foreground color was not being respected. The foreground color should change the color of the annotations/reads but it changed the track label instead. Also, a null pointer exception was generated when changing the color settings under the Annotation tab (see exception below). Moving back to To-Do column. Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.action.ChangeColorActionA.performAction(ChangeColorActionA.java:97) at com.affymetrix.igb.shared.Actions.setLabelColor(Actions.java:44) at com.affymetrix.igb.shared.StylePanelImpl.labelColorComboBoxActionPerformedA(StylePanelImpl.java:85) at com.affymetrix.igb.shared.StylePanel.labelColorComboBoxActionPerformed(StylePanel.java:146) at com.affymetrix.igb.shared.StylePanel$$Lambda$125/987834065.actionPerformed(Unknown Source) at com.jidesoft.combobox.AbstractComboBox.fireActionEvent(Unknown Source) at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source) at com.jidesoft.combobox.ColorComboBox.setSelectedItem(Unknown Source) at com.jidesoft.combobox.AbstractComboBox.setSelectedItem(Unknown Source) at com.jidesoft.combobox.AbstractComboBox$3.itemStateChanged(Unknown Source) at com.jidesoft.combobox.PopupPanel.fireItemStateChanged(Unknown Source) at com.jidesoft.combobox.PopupPanel.setSelectedObject(Unknown Source) at com.jidesoft.combobox.PopupPanel.setSelectedObject(Unknown Source) at com.jidesoft.combobox.ColorChooserPanel.setSelectedColor(Unknown Source) at com.jidesoft.combobox.ColorChooserPanel$d_.actionPerformed(Unknown Source) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source) at com.jidesoft.plaf.basic.BasicJideButtonListener.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$400(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source)

Mason Meyer (Inactive) made changes - 10/Feb/15 8:58 AM

Assignee

Mason Meyer [ mason ]

Tarun Mall [ tmall ]

Mason Meyer (Inactive) made changes - 10/Feb/15 8:59 AM

Status

Testing In Progress [ 10003 ]

Open [ 1 ]

David Norris (Inactive) made changes - 10/Feb/15 10:57 AM

Status

Open [ 1 ]

Needs Testing [ 10002 ]

Mason Meyer (Inactive) made changes - 12/Feb/15 5:35 AM

Status

Needs Testing [ 10002 ]

Testing In Progress [ 10003 ]

Mason Meyer (Inactive) made changes - 12/Feb/15 6:42 AM

Assignee

Tarun Mall [ tmall ]

Mason Meyer [ mason ]

Mason Meyer (Inactive) made changes - 20/Feb/15 9:58 AM

Sprint

Sprint 12, Sprint 13 [ 17, 18 ]

Sprint 12 [ 17 ]

Mason Meyer (Inactive) made changes - 20/Feb/15 9:58 AM

Sprint

Sprint 12 [ 17 ]

Sprint 12, Sprint 14 [ 17, 19 ]

Mason Meyer (Inactive) made changes - 20/Feb/15 9:58 AM

Rank

Ranked higher

Ann Loraine made changes - 03/Mar/15 3:35 PM

Epic Link

IGBF-99 [ 14534 ]

Mason Meyer (Inactive) made changes - 06/Mar/15 11:21 AM

Sprint

Sprint 12, Sprint 14 [ 17, 19 ]

Sprint 12 [ 17 ]

Mason Meyer (Inactive) made changes - 06/Mar/15 11:21 AM

Sprint

Sprint 12 [ 17 ]

Sprint 12, Sprint 15 [ 17, 20 ]

Mason Meyer (Inactive) made changes - 06/Mar/15 11:21 AM

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Mason Meyer (Inactive) added a comment - 11/Mar/15 11:07 AM

My testing verifies that IGB is still stable and operating as expected after the refactoring. Since this story is resolved it will now be closed.

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Mason Meyer (Inactive) added a comment - 11/Mar/15 11:07 AM My testing verifies that IGB is still stable and operating as expected after the refactoring. Since this story is resolved it will now be closed.

Mason Meyer (Inactive) made changes - 11/Mar/15 11:50 AM

Resolution		Done [ 10000 ]
Status	Testing In Progress [ 10003 ]	Closed [ 6 ]

Ann Loraine made changes - 27/Aug/19 4:58 PM

Workflow

Loraine Lab Workflow [ 15656 ]

Fall 2019 Workflow Update [ 19350 ]

Ann Loraine made changes - 16/Oct/19 5:49 PM

Workflow

Fall 2019 Workflow Update [ 19350 ]

Revised Fall 2019 Workflow Update [ 21467 ]

People

Assignee:

Mason Meyer (Inactive)

Reporter:

David Norris (Inactive)

Votes:

0 Vote for this issue

Watchers:

3 Start watching this issue

Dates

Created:

06/Feb/15 5:53 AM

Updated:

11/Mar/15 11:50 AM

Resolved:

11/Mar/15 11:50 AM