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Commit 9f96765f authored by tcarver's avatar tcarver
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tidy

parent 2f0a27d1
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uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java
+ 89
− 200
View file @ 9f96765f
...@@ -106,7 +106,6 @@ public class PropertiesPanel extends JPanel ...@@ -106,7 +106,6 @@ public class PropertiesPanel extends JPanel
boolean showTimeLastModified) boolean showTimeLastModified)
{ {
super(new FlowLayout(FlowLayout.LEFT)); super(new FlowLayout(FlowLayout.LEFT));
this.showNames = showNames; this.showNames = showNames;
this.showOptions = showOptions; this.showOptions = showOptions;
this.showParent = showParent; this.showParent = showParent;
...@@ -114,7 +113,6 @@ public class PropertiesPanel extends JPanel ...@@ -114,7 +113,6 @@ public class PropertiesPanel extends JPanel
setBackground(Color.WHITE); setBackground(Color.WHITE);
updateFromFeature(feature); updateFromFeature(feature);
//makeBorder();
} }
/** /**
...@@ -148,47 +146,44 @@ public class PropertiesPanel extends JPanel ...@@ -148,47 +146,44 @@ public class PropertiesPanel extends JPanel
JPanel gridPanel = new JPanel(new GridBagLayout()); JPanel gridPanel = new JPanel(new GridBagLayout());
gridPanel.setBackground(Color.white); gridPanel.setBackground(Color.white);
int nrow = 0;
if(showNames) if(showNames)
{ {
addNames(c, gridPanel, nrow++); addNames(c, gridPanel);
nrow = addSynonyms(c, gridPanel, nrow); addSynonyms(c, gridPanel);
} }
if(showParent) if(showParent)
addParent(c, gridPanel, nrow++); {
addParent(c, gridPanel, "Parent");
addParent(c, gridPanel, "Derives_from");
}
// phase of translation wrt / codon_start // phase of translation wrt / codon_start
if(feature.getEntry().getEntryInformation().isValidQualifier( if(feature.getEntry().getEntryInformation().isValidQualifier(
feature.getKey(), "codon_start")) feature.getKey(), "codon_start"))
addPhaseComponent(c, gridPanel, nrow++); addPhaseComponent(c, gridPanel);
// partial/obsolete options // partial/obsolete options
if(showOptions) if(showOptions)
addOptions(c, gridPanel, nrow); addOptions(c, gridPanel);
// add buttons and timelastmodified // add buttons and timelastmodified
if(showTimeLastModified) if(showTimeLastModified)
addTimeLastModified(c, gridPanel, nrow); addTimeLastModified(c, gridPanel);
return gridPanel; return gridPanel;
} }
/** /**
* Add uniquename and name to the panel. * Add uniquename and name to the panel.
* @param cellDimension
* @param c * @param c
* @param gridPanel * @param gridPanel
* @param nrows
*/ */
private void addNames(GridBagConstraints c, private void addNames(GridBagConstraints c, JPanel gridPanel)
JPanel gridPanel,
int nrows)
{ {
Qualifier idQualifier = gffQualifiers.getQualifierByName("ID"); Qualifier idQualifier = gffQualifiers.getQualifierByName("ID");
Qualifier nameQualifier = gffQualifiers.getQualifierByName("Name"); 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 = new JTextField(uniquename);
uniquenameTextField.setPreferredSize(calcPreferredMaxTextFieldWidth()); uniquenameTextField.setPreferredSize(calcPreferredMaxTextFieldWidth());
uniquenameTextField.setCaretPosition(0); uniquenameTextField.setCaretPosition(0);
...@@ -199,7 +194,7 @@ public class PropertiesPanel extends JPanel ...@@ -199,7 +194,7 @@ public class PropertiesPanel extends JPanel
idField.setPreferredSize(calcPreferredLabelWidth()); idField.setPreferredSize(calcPreferredLabelWidth());
c.gridx = 0; c.gridx = 0;
c.gridy = nrows; c.gridy++;
c.ipadx = 5; c.ipadx = 5;
c.anchor = GridBagConstraints.EAST; c.anchor = GridBagConstraints.EAST;
gridPanel.add(idField, c); gridPanel.add(idField, c);
...@@ -214,11 +209,11 @@ public class PropertiesPanel extends JPanel ...@@ -214,11 +209,11 @@ public class PropertiesPanel extends JPanel
Qualifier timeQualifier = gffQualifiers.getQualifierByName("timelastmodified"); Qualifier timeQualifier = gffQualifiers.getQualifierByName("timelastmodified");
String time = null; String time = null;
if (timeQualifier != null) if (timeQualifier != null)
time = (String) timeQualifier.getValues().get(0); time = timeQualifier.getValues().get(0);
String parent = getParentString(); String parent = getParentString();
String tt = "feature_id=" + String tt = "feature_id=" +
(String) featIdQualifier.getValues().get(0) + featIdQualifier.getValues().get(0) +
(parent == null ? "" : "\n"+parent)+ (parent == null ? "" : "\n"+parent)+
(time == null ? "" : "\n"+time); (time == null ? "" : "\n"+time);
...@@ -271,21 +266,16 @@ public class PropertiesPanel extends JPanel ...@@ -271,21 +266,16 @@ public class PropertiesPanel extends JPanel
*/ */
private String getParentString() private String getParentString()
{ {
Qualifier parentQualifier = gffQualifiers.getQualifierByName("Parent"); Qualifier parentQual = gffQualifiers.getQualifierByName("Parent");
if(parentQualifier != null && if(parentQual != null &&
parentQualifier.getValues().size() == 1) parentQual.getValues().size() == 1)
{ return "Parent: "+parentQual.getValues().get(0);
StringVector parents = parentQualifier.getValues();
return "Parent: "+parents.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; return null;
} }
...@@ -293,27 +283,25 @@ public class PropertiesPanel extends JPanel ...@@ -293,27 +283,25 @@ public class PropertiesPanel extends JPanel
* Add Parent or Derives_from. * Add Parent or Derives_from.
* @param c * @param c
* @param gridPanel * @param gridPanel
* @param nrows
*/ */
private void addParent(GridBagConstraints c, private void addParent(GridBagConstraints c,
JPanel gridPanel, JPanel gridPanel,
int nrows) String parentName)
{ {
Qualifier parentQualifier = gffQualifiers.getQualifierByName("Parent"); Qualifier parentQualifier = gffQualifiers.getQualifierByName(parentName);
if(parentQualifier != null && if(parentQualifier != null &&
parentQualifier.getValues().size() == 1) parentQualifier.getValues().size() == 1)
{ {
StringVector parents = parentQualifier.getValues(); JLabel parentField = new JLabel(parentName);
JLabel parentField = new JLabel("Parent");
parentField.setFont(getFont().deriveFont(Font.BOLD)); parentField.setFont(getFont().deriveFont(Font.BOLD));
c.gridx = 0; c.gridx = 0;
c.gridy = nrows; c.gridy++;
c.ipadx = 5; c.ipadx = 5;
c.fill = GridBagConstraints.NONE; c.fill = GridBagConstraints.NONE;
c.anchor = GridBagConstraints.EAST; c.anchor = GridBagConstraints.EAST;
gridPanel.add(parentField, c); gridPanel.add(parentField, c);
JTextField parent = new JTextField(" "+(String) parents.get(0)); JTextField parent = new JTextField(" "+ parentQualifier.getValues().get(0));
parent.setPreferredSize(calcPreferredMaxTextFieldWidth()); parent.setPreferredSize(calcPreferredMaxTextFieldWidth());
parent.setBorder(BorderFactory.createEmptyBorder()); parent.setBorder(BorderFactory.createEmptyBorder());
c.gridx = 1; c.gridx = 1;
...@@ -321,28 +309,6 @@ public class PropertiesPanel extends JPanel ...@@ -321,28 +309,6 @@ public class PropertiesPanel extends JPanel
gridPanel.add(parent, c); gridPanel.add(parent, c);
return; 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 ...@@ -350,37 +316,28 @@ public class PropertiesPanel extends JPanel
* @param c * @param c
* @param gridPanel * @param gridPanel
* @param nrows * @param nrows
* @return
*/ */
private int addSynonyms(GridBagConstraints c, JPanel gridPanel, int nrows) private void addSynonyms(GridBagConstraints c, JPanel gridPanel)
{ {
int maxSynonymWidth = 0; for(Qualifier qualifier: gffQualifiers)
int maxLabelWidth = new JLabel("previous_systematic_id ").getPreferredSize().width;
for(int i=0; i<gffQualifiers.size(); i++)
{ {
final Qualifier qualifier = (Qualifier)gffQualifiers.get(i);
if( ChadoTransactionManager.isSynonymTag(qualifier.getName(), if( ChadoTransactionManager.isSynonymTag(qualifier.getName(),
(GFFStreamFeature)feature.getEmblFeature()) && (GFFStreamFeature)feature.getEmblFeature()) &&
isSystematicId(qualifier.getName())) isSystematicId(qualifier.getName()))
{ {
addSynonymComponent(qualifier, c, gridPanel, nrows++, addSynonymComponent(qualifier, c, gridPanel);
maxLabelWidth, maxSynonymWidth);
} }
} }
for(int i=0; i<gffQualifiers.size(); i++) for(Qualifier qualifier: gffQualifiers)
{ {
final Qualifier qualifier = (Qualifier)gffQualifiers.get(i);
if( ChadoTransactionManager.isSynonymTag(qualifier.getName(), if( ChadoTransactionManager.isSynonymTag(qualifier.getName(),
(GFFStreamFeature)feature.getEmblFeature()) && (GFFStreamFeature)feature.getEmblFeature()) &&
!isSystematicId(qualifier.getName())) !isSystematicId(qualifier.getName()))
{ {
addSynonymComponent(qualifier, c, gridPanel, nrows++, addSynonymComponent(qualifier, c, gridPanel);
maxLabelWidth, maxSynonymWidth);
} }
} }
return nrows;
} }
...@@ -388,21 +345,20 @@ public class PropertiesPanel extends JPanel ...@@ -388,21 +345,20 @@ public class PropertiesPanel extends JPanel
* Add partial and obsolete options to the panel. * Add partial and obsolete options to the panel.
* @param c * @param c
* @param gridPanel * @param gridPanel
* @param nrows
*/ */
private void addOptions(GridBagConstraints c, JPanel gridPanel, int nrows) private void addOptions(GridBagConstraints c, JPanel gridPanel)
{ {
Qualifier isPartialQualfier5; final Qualifier isPartialQualfier5;
Qualifier isPartialQualfier3; final Qualifier isPartialQualfier3;
if(feature.isForwardFeature()) if(feature.isForwardFeature())
{ {
isPartialQualfier5 = gffQualifiers.getQualifierByName("Start_range"); isPartialQualfier5 = gffQualifiers.getQualifierByName("Start_range");
isPartialQualfier3 = gffQualifiers.getQualifierByName("End_range"); isPartialQualfier3 = gffQualifiers.getQualifierByName("End_range");
} }
else else
{ {
isPartialQualfier3 = gffQualifiers.getQualifierByName("Start_range"); isPartialQualfier3 = gffQualifiers.getQualifierByName("Start_range");
isPartialQualfier5 = gffQualifiers.getQualifierByName("End_range"); isPartialQualfier5 = gffQualifiers.getQualifierByName("End_range");
} }
Box optionsBox = Box.createHorizontalBox(); Box optionsBox = Box.createHorizontalBox();
...@@ -417,7 +373,6 @@ public class PropertiesPanel extends JPanel ...@@ -417,7 +373,6 @@ public class PropertiesPanel extends JPanel
checkPartial(); checkPartial();
} }
}); });
optionsBox.add(partialField5prime); optionsBox.add(partialField5prime);
partialField3prime = new JCheckBox("partial 3'", partialField3prime = new JCheckBox("partial 3'",
...@@ -432,15 +387,10 @@ public class PropertiesPanel extends JPanel ...@@ -432,15 +387,10 @@ public class PropertiesPanel extends JPanel
}); });
optionsBox.add(partialField3prime); optionsBox.add(partialField3prime);
Qualifier obsoleteQualifier = gffQualifiers.getQualifierByName("isObsolete"); Qualifier obsoleteQual = gffQualifiers.getQualifierByName("isObsolete");
boolean isObsolete; obsoleteField = new JCheckBox("obsolete", (obsoleteQual == null ? false :
if(obsoleteQualifier == null) Boolean.parseBoolean(obsoleteQual.getValues().get(0))));
isObsolete = false;
else
isObsolete = Boolean.parseBoolean((String) obsoleteQualifier.getValues().get(0));
obsoleteField = new JCheckBox("obsolete", isObsolete);
obsoleteField.setPreferredSize(calcPreferred(obsoleteField.getPreferredSize().width)); obsoleteField.setPreferredSize(calcPreferred(obsoleteField.getPreferredSize().width));
obsoleteField.setOpaque(false); obsoleteField.setOpaque(false);
obsoleteField.addActionListener(new ActionListener() obsoleteField.addActionListener(new ActionListener()
{ {
...@@ -459,22 +409,21 @@ public class PropertiesPanel extends JPanel ...@@ -459,22 +409,21 @@ public class PropertiesPanel extends JPanel
c.gridx = 0; c.gridx = 0;
c.anchor = GridBagConstraints.WEST; c.anchor = GridBagConstraints.WEST;
c.gridwidth = GridBagConstraints.REMAINDER; c.gridwidth = GridBagConstraints.REMAINDER;
c.gridy = nrows; c.gridy++;
gridPanel.add(optionsBox, c); gridPanel.add(optionsBox, c);
c.gridwidth = 1; c.gridwidth = 1;
} }
private void addTimeLastModified(GridBagConstraints c, JPanel gridPanel, int nrows) private void addTimeLastModified(GridBagConstraints c, JPanel gridPanel)
{ {
Qualifier timeQualifier = gffQualifiers.getQualifierByName("timelastmodified"); Qualifier timeQualifier = gffQualifiers.getQualifierByName("timelastmodified");
if (timeQualifier != null) if (timeQualifier != null)
{ {
String time = (String) timeQualifier.getValues().get(0); JLabel timeLabel = new JLabel(timeQualifier.getValues().get(0));
JLabel timeLabel = new JLabel(time);
timeLabel.setEnabled(false); timeLabel.setEnabled(false);
timeLabel.setToolTipText("time last modified"); timeLabel.setToolTipText("time last modified");
c.gridy = ++nrows; c.gridy++;
c.gridx = 4; c.gridx = 4;
c.gridwidth = GridBagConstraints.REMAINDER; c.gridwidth = GridBagConstraints.REMAINDER;
c.anchor = GridBagConstraints.EAST; c.anchor = GridBagConstraints.EAST;
...@@ -492,9 +441,8 @@ public class PropertiesPanel extends JPanel ...@@ -492,9 +441,8 @@ public class PropertiesPanel extends JPanel
gffQualifiers = new QualifierVector(); gffQualifiers = new QualifierVector();
final QualifierVector qualifiers = feature.getQualifiers(); 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)) if(isPropertiesTag(qualifier, feature))
gffQualifiers.addElement(qualifier.copy()); gffQualifiers.addElement(qualifier.copy());
} }
...@@ -506,16 +454,15 @@ public class PropertiesPanel extends JPanel ...@@ -506,16 +454,15 @@ public class PropertiesPanel extends JPanel
} }
/** /**
* Get the latest (edited) controlled vocab qualifiers * Get the latest (edited) property qualifiers
* @return * @return
*/ */
public QualifierVector getGffQualifiers(final Feature feature) public QualifierVector getGffQualifiers(final Feature feature)
{ {
// check editable components for changes // check editable components for changes
Qualifier idQualifier = gffQualifiers.getQualifierByName("ID"); Qualifier idQualifier = gffQualifiers.getQualifierByName("ID");
if(showNames && if(showNames &&
!((String)(idQualifier.getValues().get(0))).equals(uniquenameTextField.getText())) !idQualifier.getValues().get(0).equals(uniquenameTextField.getText()))
{ {
if(!uniquenameTextField.getText().equals("")) if(!uniquenameTextField.getText().equals(""))
{ {
...@@ -539,7 +486,7 @@ public class PropertiesPanel extends JPanel ...@@ -539,7 +486,7 @@ public class PropertiesPanel extends JPanel
{ {
Qualifier nameQualifier = gffQualifiers.getQualifierByName("Name"); Qualifier nameQualifier = gffQualifiers.getQualifierByName("Name");
if( (nameQualifier != null && if( (nameQualifier != null &&
!((String)(nameQualifier.getValues().get(0))).equals(primaryNameTextField.getText())) || !nameQualifier.getValues().get(0).equals(primaryNameTextField.getText())) ||
(primaryNameTextField != null && !primaryNameTextField.getText().equals(""))) (primaryNameTextField != null && !primaryNameTextField.getText().equals("")))
{ {
gffQualifiers.remove(nameQualifier); gffQualifiers.remove(nameQualifier);
...@@ -552,7 +499,6 @@ public class PropertiesPanel extends JPanel ...@@ -552,7 +499,6 @@ public class PropertiesPanel extends JPanel
if(phaseButtonGroup != null) if(phaseButtonGroup != null)
{ {
String selectionCmd = phaseButtonGroup.getSelection().getActionCommand(); String selectionCmd = phaseButtonGroup.getSelection().getActionCommand();
Qualifier phaseQualifier = gffQualifiers.getQualifierByName("codon_start"); Qualifier phaseQualifier = gffQualifiers.getQualifierByName("codon_start");
if(phaseQualifier == null) if(phaseQualifier == null)
{ {
...@@ -564,7 +510,7 @@ public class PropertiesPanel extends JPanel ...@@ -564,7 +510,7 @@ public class PropertiesPanel extends JPanel
} }
else else
{ {
String oldPhase = (String)phaseQualifier.getValues().get(0); String oldPhase = phaseQualifier.getValues().get(0);
if(!oldPhase.equals(phaseButtonGroup)) if(!oldPhase.equals(phaseButtonGroup))
{ {
gffQualifiers.remove(phaseQualifier); gffQualifiers.remove(phaseQualifier);
...@@ -582,7 +528,7 @@ public class PropertiesPanel extends JPanel ...@@ -582,7 +528,7 @@ public class PropertiesPanel extends JPanel
{ {
if(showOptions) if(showOptions)
{ {
String isObsoleteOld = (String) isObsoleteQualifier.getValues().get(0); String isObsoleteOld = isObsoleteQualifier.getValues().get(0);
String isObsoleteNew = Boolean.toString(obsoleteField.isSelected()); String isObsoleteNew = Boolean.toString(obsoleteField.isSelected());
if (!isObsoleteNew.equals(isObsoleteOld)) if (!isObsoleteNew.equals(isObsoleteOld))
...@@ -660,11 +606,8 @@ public class PropertiesPanel extends JPanel ...@@ -660,11 +606,8 @@ public class PropertiesPanel extends JPanel
public static void updateObsoleteSettings(GFFStreamFeature gffFeature) public static void updateObsoleteSettings(GFFStreamFeature gffFeature)
{ {
Qualifier isObsoleteQualifier = gffFeature.getQualifierByName("isObsolete"); Qualifier isObsoleteQualifier = gffFeature.getQualifierByName("isObsolete");
String isObsoleteNew = (String) isObsoleteQualifier.getValues().get(0); String isObsoleteNew = isObsoleteQualifier.getValues().get(0);
if(isObsoleteNew.equals("true")) gffFeature.setVisible(!isObsoleteNew.equals("true"));
gffFeature.setVisible(false);
else
gffFeature.setVisible(true);
if(gffFeature.getChadoGene() == null) if(gffFeature.getChadoGene() == null)
return; return;
...@@ -674,7 +617,6 @@ public class PropertiesPanel extends JPanel ...@@ -674,7 +617,6 @@ public class PropertiesPanel extends JPanel
if(children.size() > 0) if(children.size() > 0)
{ {
Qualifier idQualifier = gffFeature.getQualifierByName("ID"); Qualifier idQualifier = gffFeature.getQualifierByName("ID");
int select = JOptionPane.showConfirmDialog(null, int select = JOptionPane.showConfirmDialog(null,
"Make children of "+idQualifier.getValues().get(0)+"\n"+ "Make children of "+idQualifier.getValues().get(0)+"\n"+
(isObsoleteNew.equals("true") ? "obsolete?" : "not obsolete?"), (isObsoleteNew.equals("true") ? "obsolete?" : "not obsolete?"),
...@@ -803,9 +745,7 @@ public class PropertiesPanel extends JPanel ...@@ -803,9 +745,7 @@ public class PropertiesPanel extends JPanel
private boolean isSystematicId(final String synonymType) private boolean isSystematicId(final String synonymType)
{ {
if(synonymType.indexOf("systematic_id") > -1) return (synonymType.indexOf("systematic_id") > -1);
return true;
return false;
} }
private void removeSynonym(String synonymName, String qualifierValue) private void removeSynonym(String synonymName, String qualifierValue)
...@@ -819,7 +759,7 @@ public class PropertiesPanel extends JPanel ...@@ -819,7 +759,7 @@ public class PropertiesPanel extends JPanel
StringVector values = StringVector values =
gffQualifiers.getQualifierByName(synonymName).getValues(); gffQualifiers.getQualifierByName(synonymName).getValues();
if(values.size()==1) if(values.size()==1)
gffQualifiers.removeQualifierByName(synonymName); gffQualifiers.removeQualifierByName(synonymName);
else else
...@@ -836,7 +776,6 @@ public class PropertiesPanel extends JPanel ...@@ -836,7 +776,6 @@ public class PropertiesPanel extends JPanel
repaint(); repaint();
} }
private void addSynonym() private void addSynonym()
{ {
final Vector<CvTerm> synonyms = DatabaseDocument.getCvterms("", final Vector<CvTerm> synonyms = DatabaseDocument.getCvterms("",
...@@ -848,9 +787,7 @@ public class PropertiesPanel extends JPanel ...@@ -848,9 +787,7 @@ public class PropertiesPanel extends JPanel
"Select synonym type", "Select synonym type",
JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE, JOptionPane.QUESTION_MESSAGE,
null, null, options, options[1]);
options,
options[1]);
if(select == 0) if(select == 0)
return; return;
...@@ -887,23 +824,6 @@ public class PropertiesPanel extends JPanel ...@@ -887,23 +824,6 @@ public class PropertiesPanel extends JPanel
synonymQualifier.addValue(newSynonymValue); synonymQualifier.addValue(newSynonymValue);
final StringVector newValues = synonymQualifier.getValues(); 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); int index = gffQualifiers.indexOfQualifierWithName(synonymName);
if(index == -1) if(index == -1)
gffQualifiers.setQualifier(new Qualifier(synonymName,newValues)); gffQualifiers.setQualifier(new Qualifier(synonymName,newValues));
...@@ -922,46 +842,19 @@ public class PropertiesPanel extends JPanel ...@@ -922,46 +842,19 @@ public class PropertiesPanel extends JPanel
* @param c * @param c
* @param gridPanel * @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(); phaseButtonGroup = new ButtonGroup();
JRadioButton phase1 = new JRadioButton("1"); JRadioButton phaseNone = new JRadioButton("Default", true);
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");
phaseNone.setOpaque(false); phaseNone.setOpaque(false);
phaseNone.setActionCommand(""); phaseNone.setActionCommand("");
phaseButtonGroup.add(phaseNone); phaseButtonGroup.add(phaseNone);
int codon_start = feature.getCodonStart();
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;
}
}
Box xBox = Box.createHorizontalBox(); Box xBox = Box.createHorizontalBox();
c.gridx = 0; c.gridx = 0;
c.gridy = nrows; c.gridy++;
c.anchor = GridBagConstraints.EAST; c.anchor = GridBagConstraints.EAST;
c.fill = GridBagConstraints.NONE; c.fill = GridBagConstraints.NONE;
c.ipadx = 5; c.ipadx = 5;
...@@ -969,9 +862,22 @@ public class PropertiesPanel extends JPanel ...@@ -969,9 +862,22 @@ public class PropertiesPanel extends JPanel
JLabel lab = new JLabel("Codon Start"); JLabel lab = new JLabel("Codon Start");
lab.setFont(getFont().deriveFont(Font.BOLD)); lab.setFont(getFont().deriveFont(Font.BOLD));
gridPanel.add(lab, c); gridPanel.add(lab, c);
xBox.add(phase1);
xBox.add(phase2); Qualifier qualifierCodonStart = gffQualifiers.getQualifierByName("codon_start");
xBox.add(phase3); 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(phaseNone);
xBox.add(Box.createHorizontalGlue()); xBox.add(Box.createHorizontalGlue());
c.gridx = 1; c.gridx = 1;
...@@ -987,17 +893,10 @@ public class PropertiesPanel extends JPanel ...@@ -987,17 +893,10 @@ public class PropertiesPanel extends JPanel
* @param qualifier * @param qualifier
* @param c * @param c
* @param gridPanel * @param gridPanel
* @param nrows
* @param maxLabelWidth
* @param maxSynonymWidth
* @return
*/ */
private void addSynonymComponent(final Qualifier qualifier, private void addSynonymComponent(final Qualifier qualifier,
final GridBagConstraints c, final GridBagConstraints c,
final JPanel gridPanel, final JPanel gridPanel)
final int nrows,
final int maxLabelWidth,
int maxSynonymWidth)
{ {
empty = false; empty = false;
final StringVector values = qualifier.getValues(); final StringVector values = qualifier.getValues();
...@@ -1011,29 +910,25 @@ public class PropertiesPanel extends JPanel ...@@ -1011,29 +910,25 @@ public class PropertiesPanel extends JPanel
sysidField.setPreferredSize(calcPreferredLabelWidth()); sysidField.setPreferredSize(calcPreferredLabelWidth());
c.gridx = 0; c.gridx = 0;
c.gridy = nrows; c.gridy++;
c.ipadx = 5; c.ipadx = 5;
c.anchor = GridBagConstraints.EAST; c.anchor = GridBagConstraints.EAST;
gridPanel.add(sysidField, c); gridPanel.add(sysidField, c);
c.gridx = 1; c.gridx = 1;
c.ipadx = 5;
c.anchor = GridBagConstraints.WEST; c.anchor = GridBagConstraints.WEST;
Box synBox = Box.createHorizontalBox(); 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 strs[] = val.split(";");
String strings[] = val.split(";"); JLabel syn = new JLabel(" "+ strs[0] + ";");
JLabel syn = new JLabel(" "+(String) strings[0] + ";");
syn.setPreferredSize(calcPreferred(syn.getPreferredSize().width)); syn.setPreferredSize(calcPreferred(syn.getPreferredSize().width));
if (strings.length > 1 if (strs.length > 1 && strs[1].indexOf("current=false") > -1)
&& ((String) strings[1]).indexOf("current=false") > -1)
syn.setEnabled(false); syn.setEnabled(false);
synBox.add(syn); synBox.add(syn);
ActionListener removeAction = new ActionListener() ActionListener removeAction = new ActionListener()
{ {
public void actionPerformed(ActionEvent e) public void actionPerformed(ActionEvent e)
...@@ -1041,8 +936,7 @@ public class PropertiesPanel extends JPanel ...@@ -1041,8 +936,7 @@ public class PropertiesPanel extends JPanel
removeSynonym(qualifier.getName(), val); removeSynonym(qualifier.getName(), val);
} }
}; };
RemoveButton remove = new RemoveButton(removeAction); synBox.add(new RemoveButton(removeAction));
synBox.add(remove);
} }
c.gridwidth = GridBagConstraints.REMAINDER; c.gridwidth = GridBagConstraints.REMAINDER;
...@@ -1059,11 +953,6 @@ public class PropertiesPanel extends JPanel ...@@ -1059,11 +953,6 @@ public class PropertiesPanel extends JPanel
{ {
return empty; return empty;
} }
public void setEmpty(boolean empty)
{
this.empty = empty;
}
public void setObsoleteChanged(boolean obsoleteChanged) public void setObsoleteChanged(boolean obsoleteChanged)
{ {
...@@ -1092,7 +981,7 @@ public class PropertiesPanel extends JPanel ...@@ -1092,7 +981,7 @@ public class PropertiesPanel extends JPanel
return d; return d;
} }
public void makeBorder() protected void makeBorder()
{ {
Border grayline = BorderFactory.createLineBorder(Color.gray); Border grayline = BorderFactory.createLineBorder(Color.gray);
setBorder(BorderFactory.createTitledBorder(grayline, setBorder(BorderFactory.createTitledBorder(grayline,
......
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