From 9f96765fbbdc8fd6c4826c66b9181ece76ac99e7 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 11 Oct 2013 09:48:14 +0100
Subject: [PATCH] tidy
---
.../genebuilder/gff/PropertiesPanel.java | 289 ++++++------------
1 file changed, 89 insertions(+), 200 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java b/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java
index 905ce19d2..6d8fed748 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java
@@ -106,7 +106,6 @@ public class PropertiesPanel extends JPanel
boolean showTimeLastModified)
{
super(new FlowLayout(FlowLayout.LEFT));
-
this.showNames = showNames;
this.showOptions = showOptions;
this.showParent = showParent;
@@ -114,7 +113,6 @@ public class PropertiesPanel extends JPanel
setBackground(Color.WHITE);
updateFromFeature(feature);
- //makeBorder();
}
/**
@@ -148,47 +146,44 @@ public class PropertiesPanel extends JPanel
JPanel gridPanel = new JPanel(new GridBagLayout());
gridPanel.setBackground(Color.white);
- int nrow = 0;
-
if(showNames)
{
- addNames(c, gridPanel, nrow++);
- nrow = addSynonyms(c, gridPanel, nrow);
+ addNames(c, gridPanel);
+ addSynonyms(c, gridPanel);
}
if(showParent)
- addParent(c, gridPanel, nrow++);
+ {
+ addParent(c, gridPanel, "Parent");
+ addParent(c, gridPanel, "Derives_from");
+ }
// phase of translation wrt / codon_start
if(feature.getEntry().getEntryInformation().isValidQualifier(
feature.getKey(), "codon_start"))
- addPhaseComponent(c, gridPanel, nrow++);
+ addPhaseComponent(c, gridPanel);
// partial/obsolete options
if(showOptions)
- addOptions(c, gridPanel, nrow);
+ addOptions(c, gridPanel);
// add buttons and timelastmodified
if(showTimeLastModified)
- addTimeLastModified(c, gridPanel, nrow);
+ addTimeLastModified(c, gridPanel);
return gridPanel;
}
/**
* Add uniquename and name to the panel.
- * @param cellDimension
* @param c
* @param gridPanel
- * @param nrows
*/
- private void addNames(GridBagConstraints c,
- JPanel gridPanel,
- int nrows)
+ private void addNames(GridBagConstraints c, JPanel gridPanel)
{
Qualifier idQualifier = gffQualifiers.getQualifierByName("ID");
Qualifier nameQualifier = gffQualifiers.getQualifierByName("Name");
- final String uniquename = (String)idQualifier.getValues().get(0);
+ final String uniquename = idQualifier.getValues().get(0);
uniquenameTextField = new JTextField(uniquename);
uniquenameTextField.setPreferredSize(calcPreferredMaxTextFieldWidth());
uniquenameTextField.setCaretPosition(0);
@@ -199,7 +194,7 @@ public class PropertiesPanel extends JPanel
idField.setPreferredSize(calcPreferredLabelWidth());
c.gridx = 0;
- c.gridy = nrows;
+ c.gridy++;
c.ipadx = 5;
c.anchor = GridBagConstraints.EAST;
gridPanel.add(idField, c);
@@ -214,11 +209,11 @@ public class PropertiesPanel extends JPanel
Qualifier timeQualifier = gffQualifiers.getQualifierByName("timelastmodified");
String time = null;
if (timeQualifier != null)
- time = (String) timeQualifier.getValues().get(0);
+ time = timeQualifier.getValues().get(0);
String parent = getParentString();
String tt = "feature_id=" +
- (String) featIdQualifier.getValues().get(0) +
+ featIdQualifier.getValues().get(0) +
(parent == null ? "" : "\n"+parent)+
(time == null ? "" : "\n"+time);
@@ -271,21 +266,16 @@ public class PropertiesPanel extends JPanel
*/
private String getParentString()
{
- Qualifier parentQualifier = gffQualifiers.getQualifierByName("Parent");
- if(parentQualifier != null &&
- parentQualifier.getValues().size() == 1)
- {
- StringVector parents = parentQualifier.getValues();
- return "Parent: "+parents.get(0);
- }
+ Qualifier parentQual = gffQualifiers.getQualifierByName("Parent");
+ if(parentQual != null &&
+ parentQual.getValues().size() == 1)
+ return "Parent: "+parentQual.getValues().get(0);
+
+ Qualifier derivesFromQual = gffQualifiers.getQualifierByName("Derives_from");
+ if(derivesFromQual != null &&
+ derivesFromQual.getValues().size() == 1)
+ return "Derives from: "+derivesFromQual.getValues().get(0);
- Qualifier derivesFromQualifier = gffQualifiers.getQualifierByName("Derives_from");
- if(derivesFromQualifier != null &&
- derivesFromQualifier.getValues().size() == 1)
- {
- StringVector derivesFroms = derivesFromQualifier.getValues();
- return "Derives from: "+derivesFroms.get(0);
- }
return null;
}
@@ -293,27 +283,25 @@ public class PropertiesPanel extends JPanel
* Add Parent or Derives_from.
* @param c
* @param gridPanel
- * @param nrows
*/
private void addParent(GridBagConstraints c,
JPanel gridPanel,
- int nrows)
+ String parentName)
{
- Qualifier parentQualifier = gffQualifiers.getQualifierByName("Parent");
+ Qualifier parentQualifier = gffQualifiers.getQualifierByName(parentName);
if(parentQualifier != null &&
parentQualifier.getValues().size() == 1)
{
- StringVector parents = parentQualifier.getValues();
- JLabel parentField = new JLabel("Parent");
+ JLabel parentField = new JLabel(parentName);
parentField.setFont(getFont().deriveFont(Font.BOLD));
c.gridx = 0;
- c.gridy = nrows;
+ c.gridy++;
c.ipadx = 5;
c.fill = GridBagConstraints.NONE;
c.anchor = GridBagConstraints.EAST;
gridPanel.add(parentField, c);
- JTextField parent = new JTextField(" "+(String) parents.get(0));
+ JTextField parent = new JTextField(" "+ parentQualifier.getValues().get(0));
parent.setPreferredSize(calcPreferredMaxTextFieldWidth());
parent.setBorder(BorderFactory.createEmptyBorder());
c.gridx = 1;
@@ -321,28 +309,6 @@ public class PropertiesPanel extends JPanel
gridPanel.add(parent, c);
return;
}
-
- Qualifier derivesFromQualifier = gffQualifiers.getQualifierByName("Derives_from");
- if(derivesFromQualifier != null &&
- derivesFromQualifier.getValues().size() == 1)
- {
- StringVector derivesFroms = derivesFromQualifier.getValues();
- JLabel derivesFromsField = new JLabel("Derives from");
- derivesFromsField.setFont(getFont().deriveFont(Font.BOLD));
- c.gridx = 0;
- c.gridy = nrows;
- c.ipadx = 5;
- c.fill = GridBagConstraints.NONE;
- c.anchor = GridBagConstraints.EAST;
- gridPanel.add(derivesFromsField, c);
-
- JTextField parent = new JTextField(" "+(String) derivesFroms.get(0));
- parent.setPreferredSize(calcPreferredMaxTextFieldWidth());
- parent.setBorder(BorderFactory.createEmptyBorder());
- c.gridx = 1;
- c.anchor = GridBagConstraints.WEST;
- gridPanel.add(parent, c);
- }
}
/**
@@ -350,37 +316,28 @@ public class PropertiesPanel extends JPanel
* @param c
* @param gridPanel
* @param nrows
- * @return
*/
- private int addSynonyms(GridBagConstraints c, JPanel gridPanel, int nrows)
+ private void addSynonyms(GridBagConstraints c, JPanel gridPanel)
{
- int maxSynonymWidth = 0;
- int maxLabelWidth = new JLabel("previous_systematic_id ").getPreferredSize().width;
-
- for(int i=0; i<gffQualifiers.size(); i++)
+ for(Qualifier qualifier: gffQualifiers)
{
- final Qualifier qualifier = (Qualifier)gffQualifiers.get(i);
if( ChadoTransactionManager.isSynonymTag(qualifier.getName(),
(GFFStreamFeature)feature.getEmblFeature()) &&
isSystematicId(qualifier.getName()))
{
- addSynonymComponent(qualifier, c, gridPanel, nrows++,
- maxLabelWidth, maxSynonymWidth);
+ addSynonymComponent(qualifier, c, gridPanel);
}
}
- for(int i=0; i<gffQualifiers.size(); i++)
+ for(Qualifier qualifier: gffQualifiers)
{
- final Qualifier qualifier = (Qualifier)gffQualifiers.get(i);
if( ChadoTransactionManager.isSynonymTag(qualifier.getName(),
(GFFStreamFeature)feature.getEmblFeature()) &&
!isSystematicId(qualifier.getName()))
{
- addSynonymComponent(qualifier, c, gridPanel, nrows++,
- maxLabelWidth, maxSynonymWidth);
+ addSynonymComponent(qualifier, c, gridPanel);
}
}
- return nrows;
}
@@ -388,21 +345,20 @@ public class PropertiesPanel extends JPanel
* Add partial and obsolete options to the panel.
* @param c
* @param gridPanel
- * @param nrows
*/
- private void addOptions(GridBagConstraints c, JPanel gridPanel, int nrows)
+ private void addOptions(GridBagConstraints c, JPanel gridPanel)
{
- Qualifier isPartialQualfier5;
- Qualifier isPartialQualfier3;
+ final Qualifier isPartialQualfier5;
+ final Qualifier isPartialQualfier3;
if(feature.isForwardFeature())
{
- isPartialQualfier5 = gffQualifiers.getQualifierByName("Start_range");
- isPartialQualfier3 = gffQualifiers.getQualifierByName("End_range");
+ isPartialQualfier5 = gffQualifiers.getQualifierByName("Start_range");
+ isPartialQualfier3 = gffQualifiers.getQualifierByName("End_range");
}
else
{
- isPartialQualfier3 = gffQualifiers.getQualifierByName("Start_range");
- isPartialQualfier5 = gffQualifiers.getQualifierByName("End_range");
+ isPartialQualfier3 = gffQualifiers.getQualifierByName("Start_range");
+ isPartialQualfier5 = gffQualifiers.getQualifierByName("End_range");
}
Box optionsBox = Box.createHorizontalBox();
@@ -417,7 +373,6 @@ public class PropertiesPanel extends JPanel
checkPartial();
}
});
-
optionsBox.add(partialField5prime);
partialField3prime = new JCheckBox("partial 3'",
@@ -432,15 +387,10 @@ public class PropertiesPanel extends JPanel
});
optionsBox.add(partialField3prime);
- Qualifier obsoleteQualifier = gffQualifiers.getQualifierByName("isObsolete");
- boolean isObsolete;
- if(obsoleteQualifier == null)
- isObsolete = false;
- else
- isObsolete = Boolean.parseBoolean((String) obsoleteQualifier.getValues().get(0));
- obsoleteField = new JCheckBox("obsolete", isObsolete);
+ Qualifier obsoleteQual = gffQualifiers.getQualifierByName("isObsolete");
+ obsoleteField = new JCheckBox("obsolete", (obsoleteQual == null ? false :
+ Boolean.parseBoolean(obsoleteQual.getValues().get(0))));
obsoleteField.setPreferredSize(calcPreferred(obsoleteField.getPreferredSize().width));
-
obsoleteField.setOpaque(false);
obsoleteField.addActionListener(new ActionListener()
{
@@ -459,22 +409,21 @@ public class PropertiesPanel extends JPanel
c.gridx = 0;
c.anchor = GridBagConstraints.WEST;
c.gridwidth = GridBagConstraints.REMAINDER;
- c.gridy = nrows;
+ c.gridy++;
gridPanel.add(optionsBox, c);
c.gridwidth = 1;
}
- private void addTimeLastModified(GridBagConstraints c, JPanel gridPanel, int nrows)
+ private void addTimeLastModified(GridBagConstraints c, JPanel gridPanel)
{
Qualifier timeQualifier = gffQualifiers.getQualifierByName("timelastmodified");
if (timeQualifier != null)
{
- String time = (String) timeQualifier.getValues().get(0);
- JLabel timeLabel = new JLabel(time);
+ JLabel timeLabel = new JLabel(timeQualifier.getValues().get(0));
timeLabel.setEnabled(false);
timeLabel.setToolTipText("time last modified");
- c.gridy = ++nrows;
+ c.gridy++;
c.gridx = 4;
c.gridwidth = GridBagConstraints.REMAINDER;
c.anchor = GridBagConstraints.EAST;
@@ -492,9 +441,8 @@ public class PropertiesPanel extends JPanel
gffQualifiers = new QualifierVector();
final QualifierVector qualifiers = feature.getQualifiers();
- for(int i = 0 ; i < qualifiers.size(); ++i)
+ for(Qualifier qualifier: qualifiers)
{
- Qualifier qualifier = (Qualifier)qualifiers.elementAt(i);
if(isPropertiesTag(qualifier, feature))
gffQualifiers.addElement(qualifier.copy());
}
@@ -506,16 +454,15 @@ public class PropertiesPanel extends JPanel
}
/**
- * Get the latest (edited) controlled vocab qualifiers
+ * Get the latest (edited) property qualifiers
* @return
*/
public QualifierVector getGffQualifiers(final Feature feature)
{
// check editable components for changes
-
Qualifier idQualifier = gffQualifiers.getQualifierByName("ID");
if(showNames &&
- !((String)(idQualifier.getValues().get(0))).equals(uniquenameTextField.getText()))
+ !idQualifier.getValues().get(0).equals(uniquenameTextField.getText()))
{
if(!uniquenameTextField.getText().equals(""))
{
@@ -539,7 +486,7 @@ public class PropertiesPanel extends JPanel
{
Qualifier nameQualifier = gffQualifiers.getQualifierByName("Name");
if( (nameQualifier != null &&
- !((String)(nameQualifier.getValues().get(0))).equals(primaryNameTextField.getText())) ||
+ !nameQualifier.getValues().get(0).equals(primaryNameTextField.getText())) ||
(primaryNameTextField != null && !primaryNameTextField.getText().equals("")))
{
gffQualifiers.remove(nameQualifier);
@@ -552,7 +499,6 @@ public class PropertiesPanel extends JPanel
if(phaseButtonGroup != null)
{
String selectionCmd = phaseButtonGroup.getSelection().getActionCommand();
-
Qualifier phaseQualifier = gffQualifiers.getQualifierByName("codon_start");
if(phaseQualifier == null)
{
@@ -564,7 +510,7 @@ public class PropertiesPanel extends JPanel
}
else
{
- String oldPhase = (String)phaseQualifier.getValues().get(0);
+ String oldPhase = phaseQualifier.getValues().get(0);
if(!oldPhase.equals(phaseButtonGroup))
{
gffQualifiers.remove(phaseQualifier);
@@ -582,7 +528,7 @@ public class PropertiesPanel extends JPanel
{
if(showOptions)
{
- String isObsoleteOld = (String) isObsoleteQualifier.getValues().get(0);
+ String isObsoleteOld = isObsoleteQualifier.getValues().get(0);
String isObsoleteNew = Boolean.toString(obsoleteField.isSelected());
if (!isObsoleteNew.equals(isObsoleteOld))
@@ -660,11 +606,8 @@ public class PropertiesPanel extends JPanel
public static void updateObsoleteSettings(GFFStreamFeature gffFeature)
{
Qualifier isObsoleteQualifier = gffFeature.getQualifierByName("isObsolete");
- String isObsoleteNew = (String) isObsoleteQualifier.getValues().get(0);
- if(isObsoleteNew.equals("true"))
- gffFeature.setVisible(false);
- else
- gffFeature.setVisible(true);
+ String isObsoleteNew = isObsoleteQualifier.getValues().get(0);
+ gffFeature.setVisible(!isObsoleteNew.equals("true"));
if(gffFeature.getChadoGene() == null)
return;
@@ -674,7 +617,6 @@ public class PropertiesPanel extends JPanel
if(children.size() > 0)
{
Qualifier idQualifier = gffFeature.getQualifierByName("ID");
-
int select = JOptionPane.showConfirmDialog(null,
"Make children of "+idQualifier.getValues().get(0)+"\n"+
(isObsoleteNew.equals("true") ? "obsolete?" : "not obsolete?"),
@@ -803,9 +745,7 @@ public class PropertiesPanel extends JPanel
private boolean isSystematicId(final String synonymType)
{
- if(synonymType.indexOf("systematic_id") > -1)
- return true;
- return false;
+ return (synonymType.indexOf("systematic_id") > -1);
}
private void removeSynonym(String synonymName, String qualifierValue)
@@ -819,7 +759,7 @@ public class PropertiesPanel extends JPanel
StringVector values =
gffQualifiers.getQualifierByName(synonymName).getValues();
-
+
if(values.size()==1)
gffQualifiers.removeQualifierByName(synonymName);
else
@@ -836,7 +776,6 @@ public class PropertiesPanel extends JPanel
repaint();
}
-
private void addSynonym()
{
final Vector<CvTerm> synonyms = DatabaseDocument.getCvterms("",
@@ -848,9 +787,7 @@ public class PropertiesPanel extends JPanel
"Select synonym type",
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE,
- null,
- options,
- options[1]);
+ null, options, options[1]);
if(select == 0)
return;
@@ -887,23 +824,6 @@ public class PropertiesPanel extends JPanel
synonymQualifier.addValue(newSynonymValue);
final StringVector newValues = synonymQualifier.getValues();
-
- /*
- final StringVector newValues = new StringVector();
- for(int i=0; i<values.size(); i++)
- {
- String thisValue = (String) values.get(i);
- StringVector str = StringVector.getStrings(thisValue, ";");
- String synonymValue = (String) str.get(0);
-
- if(isSystematicId(synonymName) && !synonymValue.equals(newSynonymValue))
- if(current.isSelected() && !thisValue.endsWith(";current=false"))
- thisValue = thisValue + ";current=false";
-
- newValues.add(thisValue);
- }
- */
-
int index = gffQualifiers.indexOfQualifierWithName(synonymName);
if(index == -1)
gffQualifiers.setQualifier(new Qualifier(synonymName,newValues));
@@ -922,46 +842,19 @@ public class PropertiesPanel extends JPanel
* @param c
* @param gridPanel
*/
- private void addPhaseComponent(final GridBagConstraints c, final JPanel gridPanel, int nrows)
+ private void addPhaseComponent(final GridBagConstraints c, final JPanel gridPanel)
{
- Qualifier qualifierCodonStart = gffQualifiers.getQualifierByName("codon_start");
phaseButtonGroup = new ButtonGroup();
-
- JRadioButton phase1 = new JRadioButton("1");
- phase1.setOpaque(false);
- phase1.setActionCommand("1");
- phaseButtonGroup.add(phase1);
- JRadioButton phase2 = new JRadioButton("2");
- phase2.setOpaque(false);
- phase2.setActionCommand("2");
- phaseButtonGroup.add(phase2);
- JRadioButton phase3 = new JRadioButton("3");
- phase3.setOpaque(false);
- phase3.setActionCommand("3");
- phaseButtonGroup.add(phase3);
- JRadioButton phaseNone = new JRadioButton("Default");
+
+ JRadioButton phaseNone = new JRadioButton("Default", true);
phaseNone.setOpaque(false);
phaseNone.setActionCommand("");
phaseButtonGroup.add(phaseNone);
-
- if(qualifierCodonStart == null)
- phaseNone.setSelected(true);
- else
- {
- int codon_start = feature.getCodonStart();
- empty = false;
- switch (codon_start)
- {
- case 1: phase1.setSelected(true); break;
- case 2: phase2.setSelected(true); break;
- case 3: phase3.setSelected(true); break;
- default: phaseNone.setSelected(true);break;
- }
- }
-
+ int codon_start = feature.getCodonStart();
+
Box xBox = Box.createHorizontalBox();
c.gridx = 0;
- c.gridy = nrows;
+ c.gridy++;
c.anchor = GridBagConstraints.EAST;
c.fill = GridBagConstraints.NONE;
c.ipadx = 5;
@@ -969,9 +862,22 @@ public class PropertiesPanel extends JPanel
JLabel lab = new JLabel("Codon Start");
lab.setFont(getFont().deriveFont(Font.BOLD));
gridPanel.add(lab, c);
- xBox.add(phase1);
- xBox.add(phase2);
- xBox.add(phase3);
+
+ Qualifier qualifierCodonStart = gffQualifiers.getQualifierByName("codon_start");
+ for(int i=1; i<4; i++)
+ {
+ String s = Integer.toString(i);
+ JRadioButton phase = new JRadioButton(s);
+ phase.setOpaque(false);
+ phase.setActionCommand(s);
+ phaseButtonGroup.add(phase);
+ if(qualifierCodonStart != null && i == codon_start)
+ {
+ empty = false;
+ phase.setSelected(true);
+ }
+ xBox.add(phase);
+ }
xBox.add(phaseNone);
xBox.add(Box.createHorizontalGlue());
c.gridx = 1;
@@ -987,17 +893,10 @@ public class PropertiesPanel extends JPanel
* @param qualifier
* @param c
* @param gridPanel
- * @param nrows
- * @param maxLabelWidth
- * @param maxSynonymWidth
- * @return
*/
private void addSynonymComponent(final Qualifier qualifier,
final GridBagConstraints c,
- final JPanel gridPanel,
- final int nrows,
- final int maxLabelWidth,
- int maxSynonymWidth)
+ final JPanel gridPanel)
{
empty = false;
final StringVector values = qualifier.getValues();
@@ -1011,29 +910,25 @@ public class PropertiesPanel extends JPanel
sysidField.setPreferredSize(calcPreferredLabelWidth());
c.gridx = 0;
- c.gridy = nrows;
+ c.gridy++;
c.ipadx = 5;
c.anchor = GridBagConstraints.EAST;
gridPanel.add(sysidField, c);
c.gridx = 1;
- c.ipadx = 5;
c.anchor = GridBagConstraints.WEST;
Box synBox = Box.createHorizontalBox();
- for (int i = 0; i < values.size(); i++)
+ for (final String val: values)
{
- final String val = (String) values.get(i);
- String strings[] = val.split(";");
-
- JLabel syn = new JLabel(" "+(String) strings[0] + ";");
+ String strs[] = val.split(";");
+ JLabel syn = new JLabel(" "+ strs[0] + ";");
syn.setPreferredSize(calcPreferred(syn.getPreferredSize().width));
- if (strings.length > 1
- && ((String) strings[1]).indexOf("current=false") > -1)
+ if (strs.length > 1 && strs[1].indexOf("current=false") > -1)
syn.setEnabled(false);
synBox.add(syn);
-
+
ActionListener removeAction = new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -1041,8 +936,7 @@ public class PropertiesPanel extends JPanel
removeSynonym(qualifier.getName(), val);
}
};
- RemoveButton remove = new RemoveButton(removeAction);
- synBox.add(remove);
+ synBox.add(new RemoveButton(removeAction));
}
c.gridwidth = GridBagConstraints.REMAINDER;
@@ -1059,11 +953,6 @@ public class PropertiesPanel extends JPanel
{
return empty;
}
-
- public void setEmpty(boolean empty)
- {
- this.empty = empty;
- }
public void setObsoleteChanged(boolean obsoleteChanged)
{
@@ -1092,7 +981,7 @@ public class PropertiesPanel extends JPanel
return d;
}
- public void makeBorder()
+ protected void makeBorder()
{
Border grayline = BorderFactory.createLineBorder(Color.gray);
setBorder(BorderFactory.createTitledBorder(grayline,
--
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