X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=9c4b0094dfba47b2deeaf6f703d6336c721ab4fe;hb=106a3890f956e2aa7780b2985f4326655912a558;hp=0779760ee559d170332a50adf13b22ba6c346aba;hpb=691e7f3e04f4ddc3ae858257f063a0b01be265fc;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 0779760..9c4b009 100644 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -41,9 +41,9 @@ 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.HashMap; import java.util.List; import javax.swing.JColorChooser; @@ -64,8 +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 @@ -200,7 +200,7 @@ public class FeatureRenderer extends if (col != null) { fcol = new FeatureColour(col); - updateColourButton(mainPanel, colour, new FeatureColour(col)); + updateColourButton(mainPanel, colour, fcol); } } else @@ -235,20 +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); @@ -272,14 +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); @@ -316,9 +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)); @@ -358,7 +363,7 @@ 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) { @@ -372,10 +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 @@ -387,15 +393,19 @@ 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) { @@ -421,16 +431,14 @@ 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 */ - String newType = name.getText().trim(); - String newFeatureGroup = group.getText().trim(); - String newDescription = 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(newType, fcol); -/*?*/ getFeaturesDisplayed().setVisible(newType); + setColour(enteredType, fcol); int newBegin = sf.begin; int newEnd = sf.end; try @@ -447,24 +455,11 @@ public class FeatureRenderer extends * (to ensure integrity of SequenceFeatures data store) */ sequences.get(0).deleteFeature(sf); - SequenceFeature newSf = new SequenceFeature(newType, - newDescription, newBegin, newEnd, sf.getScore(), - newFeatureGroup); - // ensure any additional properties are copied - if (sf.otherDetails != null) - { - newSf.otherDetails = new HashMap(sf.otherDetails); - } + SequenceFeature newSf = new SequenceFeature(sf, enteredType, + newBegin, newEnd, enteredGroup, sf.getScore()); + newSf.setDescription(enteredDescription); ffile.parseDescriptionHTML(newSf, false); - // add any additional links not parsed from description - if (sf.links != null) - { - for (String link : sf.links) - { - newSf.addLink(link); - } - } - // amend features only gets one sequence to act on + // amend features dialog only updates one sequence at a time sequences.get(0).addSequenceFeature(newSf); if (refreshSettings) @@ -476,24 +471,23 @@ 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; } @@ -503,7 +497,7 @@ public class FeatureRenderer extends } } - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); return true; } @@ -540,7 +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); } }