X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=46f574e03ec4d9f4c3b9f8183582c6aa80079767;hb=9e926ac4305fd9dff38b6e079e55b4f50664d544;hp=2f12eef1a607cf0a455a59d156d5ebb77fd1287a;hpb=268dfe33ea14bbcdfb0671a1ec8acc5e9c423426;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 2f12eef..46f574e 100644 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -41,6 +41,7 @@ import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; +import java.util.ArrayList; import java.util.Arrays; import java.util.Comparator; import java.util.List; @@ -63,8 +64,8 @@ import javax.swing.event.DocumentListener; * @author $author$ * @version $Revision$ */ -public class FeatureRenderer extends - jalview.renderer.seqfeatures.FeatureRenderer +public class FeatureRenderer + extends jalview.renderer.seqfeatures.FeatureRenderer { /* * defaults for creating a new feature are the last created @@ -179,15 +180,15 @@ public class FeatureRenderer extends final JSpinner end = new JSpinner(); start.setPreferredSize(new Dimension(80, 20)); end.setPreferredSize(new Dimension(80, 20)); - final FeatureRenderer me = this; final JLabel colour = new JLabel(); colour.setOpaque(true); // colour.setBorder(BorderFactory.createEtchedBorder()); colour.setMaximumSize(new Dimension(30, 16)); colour.addMouseListener(new MouseAdapter() { - FeatureColourChooser fcc = null; - + /* + * open colour chooser on click in colour panel + */ @Override public void mousePressed(MouseEvent evt) { @@ -199,33 +200,31 @@ public class FeatureRenderer extends if (col != null) { fcol = new FeatureColour(col); - updateColourButton(mainPanel, colour, new FeatureColour(col)); + updateColourButton(mainPanel, colour, fcol); } } else { - if (fcc == null) + /* + * variable colour dialog - on OK, refetch the updated + * feature colour and update this display + */ + final String ft = features.get(featureIndex).getType(); + final String type = ft == null ? lastFeatureAdded : ft; + FeatureTypeSettings fcc = new FeatureTypeSettings( + FeatureRenderer.this, type); + fcc.setRequestFocusEnabled(true); + fcc.requestFocus(); + fcc.addActionListener(new ActionListener() { - final String ft = features.get(featureIndex).getType(); - final String type = ft == null ? lastFeatureAdded : ft; - fcc = new FeatureColourChooser(me, type); - fcc.setRequestFocusEnabled(true); - fcc.requestFocus(); - - fcc.addActionListener(new ActionListener() + @Override + public void actionPerformed(ActionEvent e) { - - @Override - public void actionPerformed(ActionEvent e) - { - fcol = fcc.getLastColour(); - fcc = null; - setColour(type, fcol); - updateColourButton(mainPanel, colour, fcol); - } - }); - - } + fcol = FeatureRenderer.this.getFeatureStyle(ft); + setColour(type, fcol); + updateColourButton(mainPanel, colour, fcol); + } + }); } } }); @@ -234,20 +233,26 @@ public class FeatureRenderer extends if (!create && features.size() > 1) { /* - * more than one feature at selected position - add a drop-down - * to choose the feature to amend + * more than one feature at selected position - + * add a drop-down to choose the feature to amend + * space pad text if necessary to make entries distinct */ gridPanel = new JPanel(new GridLayout(4, 1)); JPanel choosePanel = new JPanel(); - choosePanel.add(new JLabel(MessageManager - .getString("label.select_feature") - + ":")); - final JComboBox overlaps = new JComboBox(); + choosePanel.add(new JLabel( + MessageManager.getString("label.select_feature") + ":")); + final JComboBox overlaps = new JComboBox<>(); + List added = new ArrayList<>(); for (SequenceFeature sf : features) { - String text = sf.getType() + "/" + sf.getBegin() + "-" - + sf.getEnd() + " (" + sf.getFeatureGroup() + ")"; + String text = String.format("%s/%d-%d (%s)", sf.getType(), + sf.getBegin(), sf.getEnd(), sf.getFeatureGroup()); + while (added.contains(text)) + { + text += " "; + } overlaps.addItem(text); + added.add(text); } choosePanel.add(overlaps); @@ -271,14 +276,14 @@ public class FeatureRenderer extends highlight.addResult(sequences.get(0), sf.getBegin(), sf.getEnd()); - alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight); - + alignPanel.getSeqPanel().seqCanvas.highlightSearchResults( + highlight, false); } FeatureColourI col = getFeatureStyle(name.getText()); if (col == null) { - col = new FeatureColour(ColorUtils - .createColourFromName(name.getText())); + col = new FeatureColour( + ColorUtils.createColourFromName(name.getText())); } oldcol = fcol = col; updateColourButton(mainPanel, colour, col); @@ -315,9 +320,8 @@ public class FeatureRenderer extends mainPanel.add(gridPanel, BorderLayout.NORTH); JPanel descriptionPanel = new JPanel(); - descriptionPanel.add(new JLabel(MessageManager - .getString("label.description:"), - JLabel.RIGHT)); + descriptionPanel.add(new JLabel( + MessageManager.getString("label.description:"), JLabel.RIGHT)); description.setFont(JvSwingUtils.getTextAreaFont()); description.setLineWrap(true); descriptionPanel.add(new JScrollPane(description)); @@ -357,7 +361,7 @@ public class FeatureRenderer extends end.setValue(new Integer(firstFeature.getEnd())); description.setText(firstFeature.getDescription()); updateColourButton(mainPanel, colour, - (oldcol = fcol = getFeatureStyle(name.getText()))); + (oldcol = fcol = getFeatureStyle(featureType))); Object[] options; if (!create) { @@ -371,10 +375,11 @@ public class FeatureRenderer extends MessageManager.getString("action.cancel") }; } - String title = create ? MessageManager - .getString("label.create_new_sequence_features") + String title = create + ? MessageManager.getString("label.create_new_sequence_features") : MessageManager.formatMessage("label.amend_delete_features", - new String[] { sequences.get(0).getName() }); + new String[] + { sequences.get(0).getName() }); /* * show the dialog @@ -386,15 +391,19 @@ public class FeatureRenderer extends FeaturesFile ffile = new FeaturesFile(); - if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0) + final String enteredType = name.getText().trim(); + final String enteredGroup = group.getText().trim(); + final String enteredDescription = description.getText().replaceAll("\n", " "); + + if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0) { /* * update default values only if creating using default values */ if (useLastDefaults) { - lastFeatureAdded = name.getText().trim(); - lastFeatureGroupAdded = group.getText().trim(); + lastFeatureAdded = enteredType; + lastFeatureGroupAdded = enteredGroup; // TODO: determine if the null feature group is valid if (lastFeatureGroupAdded.length() < 1) { @@ -420,26 +429,37 @@ public class FeatureRenderer extends { /* * YES_OPTION corresponds to the Amend button - * need to refresh Feature Settings if type, group or colour changed + * need to refresh Feature Settings if type, group or colour changed; + * note we don't force the feature to be visible - the user has been + * warned if a hidden feature type or group was entered */ - sf.type = name.getText().trim(); - sf.featureGroup = group.getText().trim(); - sf.description = description.getText().replaceAll("\n", " "); - boolean refreshSettings = (!featureType.equals(sf.type) || !featureGroup - .equals(sf.featureGroup)); + boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup + .equals(enteredGroup)); refreshSettings |= (fcol != oldcol); - - setColour(sf.type, fcol); - + setColour(enteredType, fcol); + int newBegin = sf.begin; + int newEnd = sf.end; try { - sf.begin = ((Integer) start.getValue()).intValue(); - sf.end = ((Integer) end.getValue()).intValue(); + newBegin = ((Integer) start.getValue()).intValue(); + newEnd = ((Integer) end.getValue()).intValue(); } catch (NumberFormatException ex) { + // JSpinner doesn't accept invalid format data :-) } - ffile.parseDescriptionHTML(sf, false); + /* + * replace the feature by deleting it and adding a new one + * (to ensure integrity of SequenceFeatures data store) + */ + sequences.get(0).deleteFeature(sf); + SequenceFeature newSf = new SequenceFeature(sf, enteredType, + newBegin, newEnd, enteredGroup, sf.getScore()); + newSf.setDescription(enteredDescription); + ffile.parseDescriptionHTML(newSf, false); + // amend features dialog only updates one sequence at a time + sequences.get(0).addSequenceFeature(newSf); + if (refreshSettings) { featuresAdded(); @@ -449,24 +469,23 @@ public class FeatureRenderer extends else // NEW FEATURES ADDED { - if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0) + if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0) { for (int i = 0; i < sequences.size(); i++) { SequenceFeature sf = features.get(i); - sf.type = name.getText().trim(); - // fix for JAL-1538 - always set feature group here - sf.featureGroup = group.getText().trim(); - sf.description = description.getText().replaceAll("\n", " "); - sequences.get(i).addSequenceFeature(sf); - ffile.parseDescriptionHTML(sf, false); + SequenceFeature sf2 = new SequenceFeature(enteredType, + enteredDescription, sf.getBegin(), sf.getEnd(), + enteredGroup); + ffile.parseDescriptionHTML(sf2, false); + sequences.get(i).addSequenceFeature(sf2); } - setColour(lastFeatureAdded, fcol); + setColour(enteredType, fcol); featuresAdded(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); return true; } @@ -476,7 +495,7 @@ public class FeatureRenderer extends } } - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); return true; } @@ -513,7 +532,8 @@ public class FeatureRenderer extends { String msg = MessageManager.formatMessage("label.warning_hidden", MessageManager.getString("label.group"), group); - JvOptionPane.showMessageDialog(panel, msg, "", JvOptionPane.OK_OPTION); + JvOptionPane.showMessageDialog(panel, msg, "", + JvOptionPane.OK_OPTION); } }