Details
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Type:
Improvement
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Status: Closed (View Workflow)
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Priority:
Minor
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 9.1.10 Major Release
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Fall 8 2021 Nov 29 - Dec 10, Fall 9 2021 Dec 13 - Dec 24, Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28
Description
When users create a bookmark, they can give the bookmark a name. Alternatively, they can accept a default bookmark name, the bookmarked location in the genome.
The interface for creating bookmarks contains a checkbox that when checked, deletes the name the user has entered. (See attached image.)
This is awkward and weird. For this task, remove the checkbox. Each time a user tries to create a bookmark, the window that opens should contain the so-called "default name" for the bookmark.
Describing the problem in more depth:
When the user clicks the bookmark icon in the Bookmarks tab, a window opens. The window contains a form with 4 components a user can interact with:
- a checkbox labeled "use default name"
- a single-line text entry field labeled "Name"
- a multi-line text entry field labeled "Notes"
- a radio button interface with two options: "position only" and "position and data"
When the window opens for the first time, the checkbox "use default name" is checked and a "default name" for the bookmark is filled in with the currently viewed location in IGB. (Note that if the user is looking at the start screen and has not yet loaded a genome, nothing is filled in to the "Name" field.)
Seeing this, the user may choose to delete the "default name" shown in "Name" and enter something they like better. Meanwhile, the checkbox "Use default name" is selected.
Seeing that the "use default name" option is checked, a user might think that they need to uncheck this option, since they have entered a non-default name into the Name field.
However, if the user then clicks the checkbox in order to "uncheck" the option "use default name," the name they just entered vanishes.
Some background: This design was meant to enable users to retrieve the so-called "default" bookmark name. However, I think this is unnecessary, because users will probably realize that if they truly want that option back, they can click "Cancel" and then click the bookmark-creation icon again. In other words, it is probably going to be quite easy for users to recover from an unintended deletion of the so-called "default" name.
Attachments
Issue Links
- relates to
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Sprint | Fall 8 2021 Nov 29 - Dec 10 [ 134 ] | Fall 9 2021 Dec 13 - Dec 24 [ 135 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Sprint | Fall 9 2021 Dec 13 - Dec 24 [ 135 ] | Fall 8 2021 Nov 29 - Dec 10 [ 134 ] |
| Rank | Ranked higher |
| Sprint | Fall 8 2021 Nov 29 - Dec 10 [ 134 ] | Fall 8 2021 Nov 29 - Dec 10, Fall 9 2021 Dec 13 - Dec 24 [ 134, 135 ] |
| Rank | Ranked higher |
| Story Points | 1.5 | 2 |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Attachment | igbman-Bookmarks-151221-1528-13.pdf [ 17026 ] |
| Attachment | ITD-Bookmarks-151221-1530-15.pdf [ 17027 ] |
To start: Identify the classes in the code base that implement the bookmarks popup window. Report the location in the location here.
The repository: https://bitbucket.org/lorainelab/integrated-genome-browser.
Also, reminder of the process:
- make a fork
- work on a branch named for the ticket
- submit PR
| Assignee | Omkar Marne [ omarne ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
When users create a bookmark, they can give the bookmark a name. Alternatively, they can accept a default bookmark name, the bookmarked location in the genome.
The interface for creating bookmarks contains a checkbox that when checked, deletes the name the user has entered. (See attached image.) This is awkward and weird. For this task, remove the checkbox. |
When users create a bookmark, they can give the bookmark a name. Alternatively, they can accept a default bookmark name, the bookmarked location in the genome.
The interface for creating bookmarks contains a checkbox that when checked, deletes the name the user has entered. (See attached image.) This is awkward and weird. For this task, remove the checkbox. Describing the problem in more depth: When the user clicks the bookmark icon in the Bookmarks tab, a dialog opens with three components: * |
| Description |
When users create a bookmark, they can give the bookmark a name. Alternatively, they can accept a default bookmark name, the bookmarked location in the genome.
The interface for creating bookmarks contains a checkbox that when checked, deletes the name the user has entered. (See attached image.) This is awkward and weird. For this task, remove the checkbox. Describing the problem in more depth: When the user clicks the bookmark icon in the Bookmarks tab, a dialog opens with three components: * |
When users create a bookmark, they can give the bookmark a name. Alternatively, they can accept a default bookmark name, the bookmarked location in the genome.
The interface for creating bookmarks contains a checkbox that when checked, deletes the name the user has entered. (See attached image.) This is awkward and weird. For this task, remove the checkbox. Describing the problem in more depth: When the user clicks the bookmark icon in the Bookmarks tab, a dialog opens with four components: * a checkbox labeled "use default name" * a single-line text entry field labeled "Name" * a multi-line text entry field labeled "Notes" * a radio button interface with two options: "position booka |
| Description |
When users create a bookmark, they can give the bookmark a name. Alternatively, they can accept a default bookmark name, the bookmarked location in the genome.
The interface for creating bookmarks contains a checkbox that when checked, deletes the name the user has entered. (See attached image.) This is awkward and weird. For this task, remove the checkbox. Describing the problem in more depth: When the user clicks the bookmark icon in the Bookmarks tab, a dialog opens with four components: * a checkbox labeled "use default name" * a single-line text entry field labeled "Name" * a multi-line text entry field labeled "Notes" * a radio button interface with two options: "position booka |
When users create a bookmark, they can give the bookmark a name. Alternatively, they can accept a default bookmark name, the bookmarked location in the genome.
The interface for creating bookmarks contains a checkbox that when checked, deletes the name the user has entered. (See attached image.) This is awkward and weird. For this task, remove the checkbox. Describing the problem in more depth: When the user clicks the bookmark icon in the Bookmarks tab, a window opens with four form components: * a checkbox labeled "use default name" * a single-line text entry field labeled "Name" * a multi-line text entry field labeled "Notes" * a radio button interface with two options: "position only" and "position and data" When the window opens for the first time, the checkbox "use default name" is checked and a "default name" for the bookmark is filled in with the currently viewed location in IGB. (Note that if the user is looking at the start screen and has not yet loaded a genome, nothing is filled in to the "Name" field.) Seeing this, the user may choose to delete the "default name" shown in "Name" and enter something they like better. Meanwhile, the checkbox "Use default name" is selected. Seeing that the "use default name" option is checked, a user might think that they need to uncheck this option, since they have entered a non-default name into the Name field. However, if the user then clicks the checkbox in order to "uncheck" the option "use default name," the name they just entered vanishes. What is the origin of this behavior? This design was meant to enable users to retrieve the so-called "default" bookmark name. However, I think this is unnecessary, because users will probably realize that if they truly want that option back, they can click "Cancel" and then click the bookmark-creation icon again. In other words, it is probably going to be quite easy for users to recover from an unintended deletion of the so-called "default" name. |
| Comment | [ Archive of user's guide bookmarks page: https://web.archive.org/web/20201126160332/https://wiki.transvar.org/display/igbman/Bookmarks ] |
| Description |
When users create a bookmark, they can give the bookmark a name. Alternatively, they can accept a default bookmark name, the bookmarked location in the genome.
The interface for creating bookmarks contains a checkbox that when checked, deletes the name the user has entered. (See attached image.) This is awkward and weird. For this task, remove the checkbox. Describing the problem in more depth: When the user clicks the bookmark icon in the Bookmarks tab, a window opens with four form components: * a checkbox labeled "use default name" * a single-line text entry field labeled "Name" * a multi-line text entry field labeled "Notes" * a radio button interface with two options: "position only" and "position and data" When the window opens for the first time, the checkbox "use default name" is checked and a "default name" for the bookmark is filled in with the currently viewed location in IGB. (Note that if the user is looking at the start screen and has not yet loaded a genome, nothing is filled in to the "Name" field.) Seeing this, the user may choose to delete the "default name" shown in "Name" and enter something they like better. Meanwhile, the checkbox "Use default name" is selected. Seeing that the "use default name" option is checked, a user might think that they need to uncheck this option, since they have entered a non-default name into the Name field. However, if the user then clicks the checkbox in order to "uncheck" the option "use default name," the name they just entered vanishes. What is the origin of this behavior? This design was meant to enable users to retrieve the so-called "default" bookmark name. However, I think this is unnecessary, because users will probably realize that if they truly want that option back, they can click "Cancel" and then click the bookmark-creation icon again. In other words, it is probably going to be quite easy for users to recover from an unintended deletion of the so-called "default" name. |
When users create a bookmark, they can give the bookmark a name. Alternatively, they can accept a default bookmark name, the bookmarked location in the genome.
The interface for creating bookmarks contains a checkbox that when checked, deletes the name the user has entered. (See attached image.) This is awkward and weird. For this task, remove the checkbox. Each time a user tries to create a bookmark, the window that opens should contain the so-called "default name" for the bookmark. Currently, the "default name" looks like: {quote} H_sapiens_Dec_2013, chr1 : 0 - 248,956,422 {quote} Note that the "default name" is getting constructed from the genome name (e.g., H_sapiens_Dec_2013), the currently viewed chromosome (e.g., chr1), and the currently visible region (e.g., 0 - 248,956,422) Describing the problem in more depth: When the user clicks the bookmark icon in the Bookmarks tab, a window opens with four form components: * a checkbox labeled "use default name" * a single-line text entry field labeled "Name" * a multi-line text entry field labeled "Notes" * a radio button interface with two options: "position only" and "position and data" When the window opens for the first time, the checkbox "use default name" is checked and a "default name" for the bookmark is filled in with the currently viewed location in IGB. (Note that if the user is looking at the start screen and has not yet loaded a genome, nothing is filled in to the "Name" field.) Seeing this, the user may choose to delete the "default name" shown in "Name" and enter something they like better. Meanwhile, the checkbox "Use default name" is selected. Seeing that the "use default name" option is checked, a user might think that they need to uncheck this option, since they have entered a non-default name into the Name field. However, if the user then clicks the checkbox in order to "uncheck" the option "use default name," the name they just entered vanishes. What is the origin of this behavior? This design was meant to enable users to retrieve the so-called "default" bookmark name. However, I think this is unnecessary, because users will probably realize that if they truly want that option back, they can click "Cancel" and then click the bookmark-creation icon again. In other words, it is probably going to be quite easy for users to recover from an unintended deletion of the so-called "default" name. |
| Description |
When users create a bookmark, they can give the bookmark a name. Alternatively, they can accept a default bookmark name, the bookmarked location in the genome.
The interface for creating bookmarks contains a checkbox that when checked, deletes the name the user has entered. (See attached image.) This is awkward and weird. For this task, remove the checkbox. Each time a user tries to create a bookmark, the window that opens should contain the so-called "default name" for the bookmark. Currently, the "default name" looks like: {quote} H_sapiens_Dec_2013, chr1 : 0 - 248,956,422 {quote} Note that the "default name" is getting constructed from the genome name (e.g., H_sapiens_Dec_2013), the currently viewed chromosome (e.g., chr1), and the currently visible region (e.g., 0 - 248,956,422) Describing the problem in more depth: When the user clicks the bookmark icon in the Bookmarks tab, a window opens with four form components: * a checkbox labeled "use default name" * a single-line text entry field labeled "Name" * a multi-line text entry field labeled "Notes" * a radio button interface with two options: "position only" and "position and data" When the window opens for the first time, the checkbox "use default name" is checked and a "default name" for the bookmark is filled in with the currently viewed location in IGB. (Note that if the user is looking at the start screen and has not yet loaded a genome, nothing is filled in to the "Name" field.) Seeing this, the user may choose to delete the "default name" shown in "Name" and enter something they like better. Meanwhile, the checkbox "Use default name" is selected. Seeing that the "use default name" option is checked, a user might think that they need to uncheck this option, since they have entered a non-default name into the Name field. However, if the user then clicks the checkbox in order to "uncheck" the option "use default name," the name they just entered vanishes. What is the origin of this behavior? This design was meant to enable users to retrieve the so-called "default" bookmark name. However, I think this is unnecessary, because users will probably realize that if they truly want that option back, they can click "Cancel" and then click the bookmark-creation icon again. In other words, it is probably going to be quite easy for users to recover from an unintended deletion of the so-called "default" name. |
When users create a bookmark, they can give the bookmark a name. Alternatively, they can accept a default bookmark name, the bookmarked location in the genome.
The interface for creating bookmarks contains a checkbox that when checked, deletes the name the user has entered. (See attached image.) This is awkward and weird. For this task, remove the checkbox. Each time a user tries to create a bookmark, the window that opens should contain the so-called "default name" for the bookmark. Describing the problem in more depth: When the user clicks the bookmark icon in the Bookmarks tab, a window opens with four form components: * a checkbox labeled "use default name" * a single-line text entry field labeled "Name" * a multi-line text entry field labeled "Notes" * a radio button interface with two options: "position only" and "position and data" When the window opens for the first time, the checkbox "use default name" is checked and a "default name" for the bookmark is filled in with the currently viewed location in IGB. (Note that if the user is looking at the start screen and has not yet loaded a genome, nothing is filled in to the "Name" field.) Seeing this, the user may choose to delete the "default name" shown in "Name" and enter something they like better. Meanwhile, the checkbox "Use default name" is selected. Seeing that the "use default name" option is checked, a user might think that they need to uncheck this option, since they have entered a non-default name into the Name field. However, if the user then clicks the checkbox in order to "uncheck" the option "use default name," the name they just entered vanishes. What is the origin of this behavior? This design was meant to enable users to retrieve the so-called "default" bookmark name. However, I think this is unnecessary, because users will probably realize that if they truly want that option back, they can click "Cancel" and then click the bookmark-creation icon again. In other words, it is probably going to be quite easy for users to recover from an unintended deletion of the so-called "default" name. |
| Description |
When users create a bookmark, they can give the bookmark a name. Alternatively, they can accept a default bookmark name, the bookmarked location in the genome.
The interface for creating bookmarks contains a checkbox that when checked, deletes the name the user has entered. (See attached image.) This is awkward and weird. For this task, remove the checkbox. Each time a user tries to create a bookmark, the window that opens should contain the so-called "default name" for the bookmark. Describing the problem in more depth: When the user clicks the bookmark icon in the Bookmarks tab, a window opens with four form components: * a checkbox labeled "use default name" * a single-line text entry field labeled "Name" * a multi-line text entry field labeled "Notes" * a radio button interface with two options: "position only" and "position and data" When the window opens for the first time, the checkbox "use default name" is checked and a "default name" for the bookmark is filled in with the currently viewed location in IGB. (Note that if the user is looking at the start screen and has not yet loaded a genome, nothing is filled in to the "Name" field.) Seeing this, the user may choose to delete the "default name" shown in "Name" and enter something they like better. Meanwhile, the checkbox "Use default name" is selected. Seeing that the "use default name" option is checked, a user might think that they need to uncheck this option, since they have entered a non-default name into the Name field. However, if the user then clicks the checkbox in order to "uncheck" the option "use default name," the name they just entered vanishes. What is the origin of this behavior? This design was meant to enable users to retrieve the so-called "default" bookmark name. However, I think this is unnecessary, because users will probably realize that if they truly want that option back, they can click "Cancel" and then click the bookmark-creation icon again. In other words, it is probably going to be quite easy for users to recover from an unintended deletion of the so-called "default" name. |
When users create a bookmark, they can give the bookmark a name. Alternatively, they can accept a default bookmark name, the bookmarked location in the genome.
The interface for creating bookmarks contains a checkbox that when checked, deletes the name the user has entered. (See attached image.) This is awkward and weird. For this task, remove the checkbox. Each time a user tries to create a bookmark, the window that opens should contain the so-called "default name" for the bookmark. Describing the problem in more depth: When the user clicks the bookmark icon in the Bookmarks tab, a window opens with four form components: * a checkbox labeled "use default name" * a single-line text entry field labeled "Name" * a multi-line text entry field labeled "Notes" * a radio button interface with two options: "position only" and "position and data" When the window opens for the first time, the checkbox "use default name" is checked and a "default name" for the bookmark is filled in with the currently viewed location in IGB. (Note that if the user is looking at the start screen and has not yet loaded a genome, nothing is filled in to the "Name" field.) Seeing this, the user may choose to delete the "default name" shown in "Name" and enter something they like better. Meanwhile, the checkbox "Use default name" is selected. Seeing that the "use default name" option is checked, a user might think that they need to uncheck this option, since they have entered a non-default name into the Name field. However, if the user then clicks the checkbox in order to "uncheck" the option "use default name," the name they just entered vanishes. Some background: This design was meant to enable users to retrieve the so-called "default" bookmark name. However, I think this is unnecessary, because users will probably realize that if they truly want that option back, they can click "Cancel" and then click the bookmark-creation icon again. In other words, it is probably going to be quite easy for users to recover from an unintended deletion of the so-called "default" name. |
I have identified the classes which implement the bookmarks popup window. Below are their names and location
- BookmarkEditor.java - This class is an implementation of the bookmark panel.
Location : plugins/Bookmark/src/main/java/com/affymetrix/igb/bookmarks/BookmarkEditor.java
- BookmarkAction.java : This class creates and adds new bookmark to the list.
Location : plugins/Bookmark/src/main/java/com/affymetrix/igb/bookmarks/action/BookmarkAction.java
- BookmarkManagerView.java : This class arranges bookmark hierarchy
Location : plugins/Bookmark/src/main/java/com/affymetrix/igb/bookmarks/BookmarkManagerView.java
- AddBookmarkAction.java -This class extends BookmarkAction.java
Location: plugins/Bookmark/src/main/java/com/affymetrix/igb/bookmarks/action/AddBookmarkAction.java
| Description |
When users create a bookmark, they can give the bookmark a name. Alternatively, they can accept a default bookmark name, the bookmarked location in the genome.
The interface for creating bookmarks contains a checkbox that when checked, deletes the name the user has entered. (See attached image.) This is awkward and weird. For this task, remove the checkbox. Each time a user tries to create a bookmark, the window that opens should contain the so-called "default name" for the bookmark. Describing the problem in more depth: When the user clicks the bookmark icon in the Bookmarks tab, a window opens with four form components: * a checkbox labeled "use default name" * a single-line text entry field labeled "Name" * a multi-line text entry field labeled "Notes" * a radio button interface with two options: "position only" and "position and data" When the window opens for the first time, the checkbox "use default name" is checked and a "default name" for the bookmark is filled in with the currently viewed location in IGB. (Note that if the user is looking at the start screen and has not yet loaded a genome, nothing is filled in to the "Name" field.) Seeing this, the user may choose to delete the "default name" shown in "Name" and enter something they like better. Meanwhile, the checkbox "Use default name" is selected. Seeing that the "use default name" option is checked, a user might think that they need to uncheck this option, since they have entered a non-default name into the Name field. However, if the user then clicks the checkbox in order to "uncheck" the option "use default name," the name they just entered vanishes. Some background: This design was meant to enable users to retrieve the so-called "default" bookmark name. However, I think this is unnecessary, because users will probably realize that if they truly want that option back, they can click "Cancel" and then click the bookmark-creation icon again. In other words, it is probably going to be quite easy for users to recover from an unintended deletion of the so-called "default" name. |
When users create a bookmark, they can give the bookmark a name. Alternatively, they can accept a default bookmark name, the bookmarked location in the genome.
The interface for creating bookmarks contains a checkbox that when checked, deletes the name the user has entered. (See attached image.) This is awkward and weird. For this task, remove the checkbox. Each time a user tries to create a bookmark, the window that opens should contain the so-called "default name" for the bookmark. Describing the problem in more depth: When the user clicks the bookmark icon in the Bookmarks tab, a window opens. The window contains a form with 4 components a user can interact with: * a checkbox labeled "use default name" * a single-line text entry field labeled "Name" * a multi-line text entry field labeled "Notes" * a radio button interface with two options: "position only" and "position and data" When the window opens for the first time, the checkbox "use default name" is checked and a "default name" for the bookmark is filled in with the currently viewed location in IGB. (Note that if the user is looking at the start screen and has not yet loaded a genome, nothing is filled in to the "Name" field.) Seeing this, the user may choose to delete the "default name" shown in "Name" and enter something they like better. Meanwhile, the checkbox "Use default name" is selected. Seeing that the "use default name" option is checked, a user might think that they need to uncheck this option, since they have entered a non-default name into the Name field. However, if the user then clicks the checkbox in order to "uncheck" the option "use default name," the name they just entered vanishes. Some background: This design was meant to enable users to retrieve the so-called "default" bookmark name. However, I think this is unnecessary, because users will probably realize that if they truly want that option back, they can click "Cancel" and then click the bookmark-creation icon again. In other words, it is probably going to be quite easy for users to recover from an unintended deletion of the so-called "default" name. |
Thank you for noting the classes.
Next question: Which method in which class creates the window that appears when a user selects Booksmarks > Add Bookmark ?
private BookmarkEditor() is the method in BookmarkEditor.java file that creates the window that appears when a user selects Bookmarks > Add Bookmark.
| Sprint | Fall 8 2021 Nov 29 - Dec 10, Fall 9 2021 Dec 13 - Dec 24 [ 134, 135 ] | Fall 8 2021 Nov 29 - Dec 10, Fall 9 2021 Dec 13 - Dec 24, Spring 1 2022 Jan 3 - Jan 14 [ 134, 135, 136 ] |
| Rank | Ranked higher |
| Attachment | New Bookmark Interface Outpu.png [ 17060 ] |
I have commented out the below lines ( between + symbol) from the BookmarkEditor.java file. I am getting the expected result. The checkbox option is gone and I am getting the default name in the Name field.
package com.affymetrix.igb.bookmarks; import com.affymetrix.genometry.SeqSpan; import com.affymetrix.genometry.util.ErrorHandler; import com.affymetrix.common.PreferenceUtils; import com.affymetrix.igb.bookmarks.model.Bookmark; import com.google.common.base.Optional; import java.util.logging.Level; import javax.swing.ButtonGroup; +_*/*import javax.swing.JCheckBox;*/*+ import javax.swing.JDialog; import javax.swing.JOptionPane; import javax.swing.JRadioButton; import javax.swing.JScrollPane; import javax.swing.JTextArea; import javax.swing.JTextField; import org.apache.commons.lang3.StringUtils; /** * This class is the implementation of bookmark editor panel. * * @author nick */ public class BookmarkEditor { private static BookmarkEditor singleton; private final JTextField nameField; private final JTextArea commentField; private final JRadioButton positionOnlyB; private final JRadioButton positionDataB; + /*private final JCheckBox useDefaultName;*/+ private final JOptionPane op; private SeqSpan span; private static final boolean defaultUseDefaultName = true; + /*private static final String PREF_USE_DEFAULT_NAME = "Use Default Name";*/+ private static final String default_bookmark_type = "Position and Data"; private static final String PREF_BOOKMARK_TYPE = "Bookmark type"; private BookmarkEditor() { nameField = new JTextField(40); commentField = new JTextArea(5, 8); commentField.setLineWrap(true); commentField.setWrapStyleWord(true); positionOnlyB = PreferenceUtils.createRadioButton("Position Only", "Position Only", PREF_BOOKMARK_TYPE, default_bookmark_type); positionDataB = PreferenceUtils.createRadioButton("Position and Data", "Position and Data", PREF_BOOKMARK_TYPE, default_bookmark_type); +/*useDefaultName = PreferenceUtils.createCheckBox(PREF_USE_DEFAULT_NAME, PREF_USE_DEFAULT_NAME, defaultUseDefaultName);*/ /*useDefaultName.addActionListener(evt -> setNameField());*/+ ButtonGroup group = new ButtonGroup(); group.add(positionOnlyB); group.add(positionDataB); JScrollPane scrollpane = new JScrollPane(commentField); scrollpane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); op = new JOptionPane(null, JOptionPane.PLAIN_MESSAGE, JOptionPane.CANCEL_OPTION, null, null); op.addPropertyChangeListener("value", evt -> addBookmark()); op.setMessage(new Object[]{"", "Name:", nameField, "Comment:", scrollpane, positionOnlyB, positionDataB}); } private static BookmarkEditor getInstance() { if (singleton == null) { singleton = new BookmarkEditor(); } return singleton; } /** * Used JDialog as display panel and initialized it. */ private void initDialog(SeqSpan span) { this.span = span; setNameField(); commentField.setText(""); JDialog dialog = op.createDialog("Enter Bookmark Information..."); dialog.setDefaultCloseOperation(JDialog.HIDE_ON_CLOSE); dialog.setResizable(true); dialog.setAlwaysOnTop(false); dialog.setModal(false); dialog.setVisible(true); dialog.pack(); } private void setNameField() { + /*if (useDefaultName.isSelected()){*/+ nameField.setText(BookmarkController.getDefaultBookmarkName(span)); +/*} else {*/+ +/*nameField.setText("");*/ /*}*/+ } private void addBookmark() { int result = JOptionPane.CANCEL_OPTION; if (op.getValue() != null && op.getValue() instanceof Integer) { result = (Integer) op.getValue(); } if (result == JOptionPane.OK_OPTION) { Optional<Bookmark> currentBookmark = BookmarkController.getCurrentBookmark( positionDataB.isSelected(), span); if (!currentBookmark.isPresent()) { ErrorHandler.errorPanel("Error", "Nothing to bookmark", Level.INFO); return; } Bookmark bookmark = currentBookmark.get(); String name = nameField.getText(); String comment = commentField.getText(); if (StringUtils.isBlank(name)) { name = "IGB BOOKMARK"; } bookmark.setName(name); bookmark.setComment(comment); BookmarkManagerView.getSingleton().insert(new BookmarkList(bookmark)); } } /** * Activate the panel and complete adding a bookmark by user's operation. */ public static void run(SeqSpan span) { getInstance().initDialog(span); } }
Dr. [~aloraine] Please see my changes here
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Omkar Marne [ omarne ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Ann Loraine [ aloraine ] | Omkar Marne [ omarne ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Dr. [~aloraine] Please find my pull request https://bitbucket.org/omarne/integrated-genome-browser/pull-requests/1
| Assignee | Omkar Marne [ omarne ] | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
The PR target branch needs to be the master branch on the team repository. Otherwise, I cannot merge it.
attn: Omkar Marne
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | Omkar Marne [ omarne ] |
My apologies Dr. [~aloraine]. Please find my pull requests https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/893/igbf-3008
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
PR is merged. Building master branch installers for deployment to BioViz Main pre-release IGB.
Master branch installers are built. Ran bioviz-playbook setup.yml to deploy the freshly built installers to bioviz.org. Ready for testing.
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Testing protocol:
- Please pull the latest changes made in the IGB.
- Open IGB local environment and select any of the genomes.
- Open bookmark tab. You'll see only the Name field, comment field, 2 radio buttons with OK and Cancel options. The checkbox option has been removed. Please see the attached snapshots 'Confusing interface' and 'New Bookmark Interface'.
- When you open the bookmark interface you should see the default genome name. Delete the default name and try giving the name of your choice.
- Once you add the bookmark name, close the interface.
- Reopen the bookmark interface, you should again see the default genome name.
- Also try to delete to the bookmark and check if the delete option works fine.
| Assignee | Omkar Marne [ omarne ] |
| Sprint | Fall 8 2021 Nov 29 - Dec 10, Fall 9 2021 Dec 13 - Dec 24, Spring 1 2022 Jan 3 - Jan 14 [ 134, 135, 136 ] | Fall 8 2021 Nov 29 - Dec 10, Fall 9 2021 Dec 13 - Dec 24, Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28 [ 134, 135, 136, 137 ] |
| Rank | Ranked higher |
Tested on Mac, working correctly with no errors in the log.
Closing ticket.
| Assignee | Omkar Marne [ omarne ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Fix Version/s | 9.1.10 Major Release [ 10700 ] |
User guide link to learn about how the bookmarking feature works from the user's perspective: https://wiki.bioviz.org/confluence/
See attached PDFs: