X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=9c4b0094dfba47b2deeaf6f703d6336c721ab4fe;hb=106a3890f956e2aa7780b2985f4326655912a558;hp=55c4323e46597557dc6f5f8e4697a19e926f47cf;hpb=cd126a7085c5ebcfc8c05378c71bd862abc4fd91;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 55c4323..9c4b009 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 @@ -234,20 +235,26 @@ 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 +278,14 @@ 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 +322,8 @@ 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)); @@ -371,10 +377,11 @@ 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 @@ -386,7 +393,10 @@ public class FeatureRenderer extends FeaturesFile ffile = new FeaturesFile(); - String enteredType = name.getText().trim(); + 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) { /* @@ -395,7 +405,7 @@ public class FeatureRenderer extends if (useLastDefaults) { lastFeatureAdded = enteredType; - lastFeatureGroupAdded = group.getText().trim(); + lastFeatureGroupAdded = enteredGroup; // TODO: determine if the null feature group is valid if (lastFeatureGroupAdded.length() < 1) { @@ -421,26 +431,37 @@ 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 = enteredType; - 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(); @@ -455,19 +476,18 @@ public class FeatureRenderer extends for (int i = 0; i < sequences.size(); i++) { SequenceFeature sf = features.get(i); - sf.type = enteredType; - // 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(enteredType, fcol); featuresAdded(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); return true; } @@ -477,7 +497,7 @@ public class FeatureRenderer extends } } - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); return true; } @@ -514,7 +534,8 @@ 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); } }