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JAL-1705 (new preference option to) hide introns when fetching genomic
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Mon, 11 Apr 2016 14:51:46 +0000
(15:51 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Mon, 11 Apr 2016 14:51:46 +0000
(15:51 +0100)
sequences
resources/lang/Messages.properties
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|
blob
|
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src/jalview/gui/Preferences.java
patch
|
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|
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src/jalview/gui/SequenceFetcher.java
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src/jalview/jbgui/GPreferences.java
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diff --git
a/resources/lang/Messages.properties
b/resources/lang/Messages.properties
index
05505a4
..
9a064b1
100644
(file)
--- a/
resources/lang/Messages.properties
+++ b/
resources/lang/Messages.properties
@@
-608,6
+608,7
@@
label.automatically_set_id_width = Automatically set ID width
label.figure_id_column_width = Figure ID column width
label.use_modeller_output = Use Modeller Output
label.wrap_alignment = Wrap Alignment
label.figure_id_column_width = Figure ID column width
label.use_modeller_output = Use Modeller Output
label.wrap_alignment = Wrap Alignment
+label.hide_introns = Hide Introns
label.right_align_ids = Right Align Ids
label.sequence_name_italics = Italic Sequence Ids
label.open_overview = Open Overview
label.right_align_ids = Right Align Ids
label.sequence_name_italics = Italic Sequence Ids
label.open_overview = Open Overview
@@
-1258,6
+1259,7
@@
label.biojs_html_export = BioJS
label.scale_as_cdna = Scale protein residues to codons
label.scale_protein_to_cdna = Scale Protein to cDNA
label.scale_protein_to_cdna_tip = Make protein residues same width as codons in split frame views
label.scale_as_cdna = Scale protein residues to codons
label.scale_protein_to_cdna = Scale Protein to cDNA
label.scale_protein_to_cdna_tip = Make protein residues same width as codons in split frame views
+label.hide_introns_tip = Hide intron columns after fetching genomic sequences
info.select_annotation_row = Select Annotation Row
info.enter_search_text_here = Enter Search Text Here
info.enter_search_text_to_enable = Enter Search Text to Enable
info.select_annotation_row = Select Annotation Row
info.enter_search_text_here = Enter Search Text Here
info.enter_search_text_to_enable = Enter Search Text to Enable
diff --git
a/src/jalview/gui/Preferences.java
b/src/jalview/gui/Preferences.java
index
c7e1332
..
8b33deb
100755
(executable)
--- a/
src/jalview/gui/Preferences.java
+++ b/
src/jalview/gui/Preferences.java
@@
-88,6
+88,8
@@
public class Preferences extends GPreferences
public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+ public static final String HIDE_INTRONS = "HIDE_INTRONS";
+
private static final int MIN_FONT_SIZE = 1;
private static final int MAX_FONT_SIZE = 30;
private static final int MIN_FONT_SIZE = 1;
private static final int MAX_FONT_SIZE = 30;
@@
-175,11
+177,11
@@
public class Preferences extends GPreferences
dasTab.add(dasSource, BorderLayout.CENTER);
wsPrefs = new WsPreferences();
wsTab.add(wsPrefs, BorderLayout.CENTER);
dasTab.add(dasSource, BorderLayout.CENTER);
wsPrefs = new WsPreferences();
wsTab.add(wsPrefs, BorderLayout.CENTER);
- int width = 500, height = 450;
+ int width = 500, height = 470;
if (new jalview.util.Platform().isAMac())
{
width = 570;
if (new jalview.util.Platform().isAMac())
{
width = 570;
- height = 480;
+ height = 500;
}
Desktop.addInternalFrame(frame,
}
Desktop.addInternalFrame(frame,
@@
-241,6
+243,7
@@
public class Preferences extends GPreferences
idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
+ hideIntrons.setSelected(Cache.getDefault(HIDE_INTRONS, true));
gapSymbolCB.addItem("-");
gapSymbolCB.addItem(".");
gapSymbolCB.addItem("-");
gapSymbolCB.addItem(".");
@@
-458,6
+461,8
@@
public class Preferences extends GPreferences
Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
Boolean.toString(wrap.isSelected()));
Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
Boolean.toString(wrap.isSelected()));
+ Cache.applicationProperties.setProperty(HIDE_INTRONS,
+ Boolean.toString(hideIntrons.isSelected()));
Cache.applicationProperties.setProperty("STARTUP_FILE",
startupFileTextfield.getText());
Cache.applicationProperties.setProperty("STARTUP_FILE",
startupFileTextfield.getText());
diff --git
a/src/jalview/gui/SequenceFetcher.java
b/src/jalview/gui/SequenceFetcher.java
index
784474e
..
b6ee041
100755
(executable)
--- a/
src/jalview/gui/SequenceFetcher.java
+++ b/
src/jalview/gui/SequenceFetcher.java
@@
-21,10
+21,12
@@
package jalview.gui;
import jalview.api.FeatureSettingsModelI;
package jalview.gui;
import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyI;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
@@
-156,9
+158,9
@@
public class SequenceFetcher extends JPanel implements Runnable
}
}
if (sfetch == null
}
}
if (sfetch == null
- || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
- || lastDasSourceRegistry != (jalview.bin.Cache
- .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
+ || dasRegistry != Cache.getDasSourceRegistry()
+ || lastDasSourceRegistry != (Cache.getDasSourceRegistry()
+ .getDasRegistryURL() + Cache
.getDasSourceRegistry().getLocalSourceString())
.hashCode())
{
.getDasSourceRegistry().getLocalSourceString())
.hashCode())
{
@@
-173,7
+175,7
@@
public class SequenceFetcher extends JPanel implements Runnable
.getString("status.init_sequence_database_fetchers"),
Thread.currentThread().hashCode());
}
.getString("status.init_sequence_database_fetchers"),
Thread.currentThread().hashCode());
}
- dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
+ dasRegistry = Cache.getDasSourceRegistry();
dasRegistry.refreshSources();
jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
dasRegistry.refreshSources();
jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
@@
-592,7
+594,8
@@
public class SequenceFetcher extends JPanel implements Runnable
}
} catch (Exception e)
{
}
} catch (Exception e)
{
- jalview.bin.Cache.log.info("Error retrieving " + item
+ Cache.log.info(
+ "Error retrieving " + item
+ " from " + proxy.getDbName(), e);
nextfetch.add(item);
}
+ " from " + proxy.getDbName(), e);
nextfetch.add(item);
}
@@
-833,8
+836,15
@@
public class SequenceFetcher extends JPanel implements Runnable
if (preferredFeatureColours != null)
{
if (preferredFeatureColours != null)
{
- af.viewport.applyFeaturesStyle(preferredFeatureColours);
+ af.getViewport().applyFeaturesStyle(preferredFeatureColours);
}
}
+ if (Cache.getDefault("HIDE_INTRONS", true))
+ {
+ af.avc.markColumnsContainingFeatures(true, false, false,
+ SequenceOntologyI.EXON);
+ af.getViewport().hideSelectedColumns();
+ }
+
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
@@
-843,7
+853,7
@@
public class SequenceFetcher extends JPanel implements Runnable
try
{
try
{
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+ af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
false));
} catch (Exception ex)
{
false));
} catch (Exception ex)
{
diff --git
a/src/jalview/jbgui/GPreferences.java
b/src/jalview/jbgui/GPreferences.java
index
b5c1804
..
0aafe50
100755
(executable)
--- a/
src/jalview/jbgui/GPreferences.java
+++ b/
src/jalview/jbgui/GPreferences.java
@@
-110,6
+110,8
@@
public class GPreferences extends JPanel
protected JCheckBox wrap = new JCheckBox();
protected JCheckBox wrap = new JCheckBox();
+ protected JCheckBox hideIntrons = new JCheckBox();
+
protected JComboBox<String> sortby = new JComboBox<String>();
protected JComboBox<String> sortAnnBy = new JComboBox<String>();
protected JComboBox<String> sortby = new JComboBox<String>();
protected JComboBox<String> sortAnnBy = new JComboBox<String>();
@@
-1149,7
+1151,7
@@
public class GPreferences extends JPanel
startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
startupCheckbox.setSelected(true);
startupFileTextfield.setFont(LABEL_FONT);
startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
startupCheckbox.setSelected(true);
startupFileTextfield.setFont(LABEL_FONT);
- startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
+ startupFileTextfield.setBounds(new Rectangle(173, 328, 330, 20));
startupFileTextfield.addMouseListener(new MouseAdapter()
{
@Override
startupFileTextfield.addMouseListener(new MouseAdapter()
{
@Override
@@
-1163,19
+1165,19
@@
public class GPreferences extends JPanel
});
sortby.setFont(LABEL_FONT);
});
sortby.setFont(LABEL_FONT);
- sortby.setBounds(new Rectangle(172, 260, 155, 21));
+ sortby.setBounds(new Rectangle(172, 280, 155, 20));
JLabel sortLabel = new JLabel();
sortLabel.setFont(LABEL_FONT);
sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
sortLabel.setText(MessageManager.getString("label.sort_by"));
sortAnnBy.setFont(LABEL_FONT);
JLabel sortLabel = new JLabel();
sortLabel.setFont(LABEL_FONT);
sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
sortLabel.setText(MessageManager.getString("label.sort_by"));
sortAnnBy.setFont(LABEL_FONT);
- sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
+ sortAnnBy.setBounds(new Rectangle(172, 305, 110, 20));
JLabel sortAnnLabel = new JLabel();
sortAnnLabel.setFont(LABEL_FONT);
sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
sortAutocalc.setFont(LABEL_FONT);
JLabel sortAnnLabel = new JLabel();
sortAnnLabel.setFont(LABEL_FONT);
sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
sortAutocalc.setFont(LABEL_FONT);
- sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
+ sortAutocalc.setBounds(new Rectangle(290, 305, 165, 20));
JPanel annsettingsPanel = new JPanel();
annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75));
JPanel annsettingsPanel = new JPanel();
annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75));
@@
-1219,6
+1221,12
@@
public class GPreferences extends JPanel
wrap.setHorizontalAlignment(SwingConstants.TRAILING);
wrap.setHorizontalTextPosition(SwingConstants.LEADING);
wrap.setText(MessageManager.getString("label.wrap_alignment"));
wrap.setHorizontalAlignment(SwingConstants.TRAILING);
wrap.setHorizontalTextPosition(SwingConstants.LEADING);
wrap.setText(MessageManager.getString("label.wrap_alignment"));
+ hideIntrons.setFont(LABEL_FONT);
+ hideIntrons.setHorizontalAlignment(SwingConstants.TRAILING);
+ hideIntrons.setHorizontalTextPosition(SwingConstants.LEADING);
+ hideIntrons.setText(MessageManager.getString("label.hide_introns"));
+ hideIntrons.setToolTipText(MessageManager
+ .getString("label.hide_introns_tip"));
rightAlign.setFont(LABEL_FONT);
rightAlign.setForeground(Color.black);
rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
rightAlign.setFont(LABEL_FONT);
rightAlign.setForeground(Color.black);
rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
@@
-1236,8
+1244,8
@@
public class GPreferences extends JPanel
openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
openoverv.setText(MessageManager.getString(("label.open_overview")));
JPanel jPanel2 = new JPanel();
openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
openoverv.setText(MessageManager.getString(("label.open_overview")));
JPanel jPanel2 = new JPanel();
- jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
- jPanel2.setLayout(new GridLayout(14, 1));
+ jPanel2.setBounds(new Rectangle(7, 17, 158, 330));
+ jPanel2.setLayout(new GridLayout(15, 1));
jPanel2.add(fullScreen);
jPanel2.add(openoverv);
jPanel2.add(seqLimit);
jPanel2.add(fullScreen);
jPanel2.add(openoverv);
jPanel2.add(seqLimit);
@@
-1249,6
+1257,7
@@
public class GPreferences extends JPanel
jPanel2.add(scaleProteinToCdna);
jPanel2.add(gapLabel);
jPanel2.add(wrap);
jPanel2.add(scaleProteinToCdna);
jPanel2.add(gapLabel);
jPanel2.add(wrap);
+ jPanel2.add(hideIntrons);
jPanel2.add(sortLabel);
jPanel2.add(sortAnnLabel);
jPanel2.add(startupCheckbox);
jPanel2.add(sortLabel);
jPanel2.add(sortAnnLabel);
jPanel2.add(startupCheckbox);