X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=5f5e8e0c42abd6069ff5b9d6ce22a844e44a83d5;hb=HEAD;hp=2db2cabba74768e496252f0c30990ff855a4bdab;hpb=19e044a2ce25aa395f9cf22f15c7378221636d21;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index 2db2cab..5f5e8e0 100644 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -53,6 +53,7 @@ import java.awt.event.MouseEvent; import java.awt.event.TextEvent; import java.awt.event.TextListener; import java.util.Hashtable; +import java.util.List; /** * DOCUMENT ME! @@ -60,9 +61,16 @@ import java.util.Hashtable; * @author $author$ * @version $Revision$ */ -public class FeatureRenderer extends - jalview.renderer.seqfeatures.FeatureRenderer +public class FeatureRenderer + extends jalview.renderer.seqfeatures.FeatureRenderer { + /* + * creating a new feature defaults to the type and group as + * the last one created + */ + static String lastFeatureAdded = "feature_1"; + + static String lastFeatureGroupAdded = "Jalview"; // Holds web links for feature groups and feature types // in the form label|link @@ -79,12 +87,6 @@ public class FeatureRenderer extends } - static String lastFeatureAdded; - - static String lastFeatureGroupAdded; - - static String lastDescriptionAdded; - int featureIndex = 0; boolean deleteFeature = false; @@ -171,18 +173,19 @@ public class FeatureRenderer extends /** * Shows a dialog allowing the user to create, or amend or delete, sequence - * features. + * features. If null in the supplied feature(s), feature type and group + * default to those for the last feature created (with initial defaults of + * "feature_1" and "Jalview"). * * @param sequences * @param features * @param create * @param ap - * @param featureType * @return */ - boolean amendFeatures(final SequenceI[] sequences, - final SequenceFeature[] features, boolean create, - final AlignmentPanel ap, String featureType) + boolean amendFeatures(final List sequences, + final List features, boolean create, + final AlignmentPanel ap) { final Panel bigPanel = new Panel(new BorderLayout()); final TextField name = new TextField(16); @@ -221,22 +224,20 @@ public class FeatureRenderer extends // ///////////////////////////////////// // /MULTIPLE FEATURES AT SELECTED RESIDUE - if (!create && features.length > 1) + if (!create && features.size() > 1) { panel = new Panel(new GridLayout(4, 1)); tmp = new Panel(); tmp.add(new Label("Select Feature: ")); overlaps = new Choice(); - for (int i = 0; i < features.length; i++) + for (SequenceFeature sf : features) { - String item = features[i].getType() + "/" + features[i].getBegin() - + "-" + features[i].getEnd(); - - if (features[i].getFeatureGroup() != null) + String item = sf.getType() + "/" + sf.getBegin() + "-" + + sf.getEnd(); + if (sf.getFeatureGroup() != null) { - item += " (" + features[i].getFeatureGroup() + ")"; + item += " (" + sf.getFeatureGroup() + ")"; } - overlaps.addItem(item); } @@ -251,15 +252,16 @@ public class FeatureRenderer extends if (index != -1) { featureIndex = index; - name.setText(features[index].getType()); - description.setText(features[index].getDescription()); - group.setText(features[index].getFeatureGroup()); - start.setText(features[index].getBegin() + ""); - end.setText(features[index].getEnd() + ""); + SequenceFeature sf = features.get(index); + name.setText(sf.getType()); + description.setText(sf.getDescription()); + group.setText(sf.getFeatureGroup()); + start.setText(sf.getBegin() + ""); + end.setText(sf.getEnd() + ""); SearchResultsI highlight = new SearchResults(); - highlight.addResult(sequences[0], features[index].getBegin(), - features[index].getEnd()); + highlight.addResult(sequences.get(0), sf.getBegin(), + sf.getEnd()); ap.seqPanel.seqCanvas.highlightSearchResults(highlight); @@ -283,17 +285,20 @@ public class FeatureRenderer extends tmp = new Panel(); panel.add(tmp); - tmp.add(new Label(MessageManager.getString("label.name:"), Label.RIGHT)); + tmp.add(new Label(MessageManager.getString("label.name:"), + Label.RIGHT)); tmp.add(name); tmp = new Panel(); panel.add(tmp); - tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT)); + tmp.add(new Label(MessageManager.getString("label.group:"), + Label.RIGHT)); tmp.add(group); tmp = new Panel(); panel.add(tmp); - tmp.add(new Label(MessageManager.getString("label.colour"), Label.RIGHT)); + tmp.add(new Label(MessageManager.getString("label.colour"), + Label.RIGHT)); tmp.add(colourPanel); bigPanel.add(panel, BorderLayout.NORTH); @@ -321,53 +326,33 @@ public class FeatureRenderer extends bigPanel.add(panel, BorderLayout.CENTER); } - if (featureType != null) - { - lastFeatureAdded = featureType; - } - else - { - if (lastFeatureAdded == null) - { - if (features[0].type != null) - { - lastFeatureAdded = features[0].type; - } - else - { - lastFeatureAdded = "feature_1"; - } - } - } - - if (lastFeatureGroupAdded == null) - { - if (features[0].featureGroup != null) - { - lastFeatureGroupAdded = features[0].featureGroup; - } - else - { - lastFeatureAdded = "Jalview"; - } - } - - String title = create ? MessageManager - .getString("label.create_new_sequence_features") + /* + * use defaults for type and group (and update them on Confirm) only + * if feature type has not been supplied by the caller + * (e.g. for Amend, or create features from Find) + */ + SequenceFeature firstFeature = features.get(0); + boolean useLastDefaults = firstFeature.getType() == null; + String featureType = useLastDefaults ? lastFeatureAdded + : firstFeature.getType(); + String featureGroup = useLastDefaults ? lastFeatureGroupAdded + : firstFeature.getFeatureGroup(); + + String title = create + ? MessageManager.getString("label.create_new_sequence_features") : MessageManager.formatMessage("label.amend_delete_features", - new String[] { sequences[0].getName() }); + new String[] + { sequences.get(0).getName() }); final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385, 240); dialog.setMainPanel(bigPanel); - if (create) - { - name.setText(lastFeatureAdded); - group.setText(lastFeatureGroupAdded); - } - else + name.setText(featureType); + group.setText(featureGroup); + + if (!create) { dialog.ok.setLabel(MessageManager.getString("label.amend")); dialog.buttonPanel.add(deleteButton, 1); @@ -380,13 +365,11 @@ public class FeatureRenderer extends dialog.setVisible(false); } }); - name.setText(features[0].getType()); - group.setText(features[0].getFeatureGroup()); } - start.setText(features[0].getBegin() + ""); - end.setText(features[0].getEnd() + ""); - description.setText(features[0].getDescription()); + start.setText(firstFeature.getBegin() + ""); + end.setText(firstFeature.getEnd() + ""); + description.setText(firstFeature.getDescription()); // lookup (or generate) the feature colour FeatureColourI fcol = getFeatureStyle(name.getText()); // simply display the feature color in a box @@ -413,42 +396,55 @@ public class FeatureRenderer extends FeaturesFile ffile = new FeaturesFile(); - if (dialog.accept) - { - lastFeatureAdded = name.getText().trim(); - lastFeatureGroupAdded = group.getText().trim(); - lastDescriptionAdded = description.getText().replace('\n', ' '); - } + /* + * only update default type and group if we used defaults + */ + final String enteredType = name.getText().trim(); + final String enteredGroup = group.getText().trim(); + final String enteredDesc = description.getText().replace('\n', ' '); - if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1) + if (dialog.accept && useLastDefaults) { - lastFeatureGroupAdded = null; + lastFeatureAdded = enteredType; + lastFeatureGroupAdded = enteredGroup; } if (!create) { - - SequenceFeature sf = features[featureIndex]; + SequenceFeature sf = features.get(featureIndex); if (dialog.accept) { - boolean typeOrGroupChanged = (!lastFeatureAdded.equals(sf.type) || !lastFeatureGroupAdded - .equals(sf.featureGroup)); - sf.type = lastFeatureAdded; - sf.featureGroup = lastFeatureGroupAdded; - sf.description = lastDescriptionAdded; if (!colourPanel.isGcol) { // update colour - otherwise its already done. - setColour(sf.type, new FeatureColour(colourPanel.getBackground())); + setColour(enteredType, + new FeatureColour(colourPanel.getBackground())); } + int newBegin = sf.begin; + int newEnd = sf.end; try { - sf.begin = Integer.parseInt(start.getText()); - sf.end = Integer.parseInt(end.getText()); + newBegin = Integer.parseInt(start.getText()); + newEnd = Integer.parseInt(end.getText()); } catch (NumberFormatException ex) { + // } + /* + * 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(enteredDesc); + ffile.parseDescriptionHTML(newSf, false); + // amend features dialog only updates one sequence at a time + sequences.get(0).addSequenceFeature(newSf); + boolean typeOrGroupChanged = (!featureType.equals(newSf.getType()) + || !featureGroup.equals(newSf.getFeatureGroup())); + ffile.parseDescriptionHTML(sf, false); if (typeOrGroupChanged) { @@ -457,11 +453,10 @@ public class FeatureRenderer extends } if (deleteFeature) { - sequences[0].deleteFeature(sf); + sequences.get(0).deleteFeature(sf); // ensure Feature Settings reflects removal of feature / group featuresAdded(); } - } else { @@ -470,19 +465,19 @@ public class FeatureRenderer extends */ if (dialog.accept && name.getText().length() > 0) { - for (int i = 0; i < sequences.length; i++) + for (int i = 0; i < sequences.size(); i++) { - features[i].type = lastFeatureAdded; - features[i].featureGroup = lastFeatureGroupAdded; - features[i].description = lastDescriptionAdded; - sequences[i].addSequenceFeature(features[i]); - ffile.parseDescriptionHTML(features[i], false); + SequenceFeature sf = features.get(i); + SequenceFeature sf2 = new SequenceFeature(enteredType, + enteredDesc, sf.getBegin(), sf.getEnd(), enteredGroup); + ffile.parseDescriptionHTML(sf2, false); + sequences.get(i).addSequenceFeature(sf2); } Color newColour = colourPanel.getBackground(); // setColour(lastFeatureAdded, fcol); - setColour(lastFeatureAdded, new FeatureColour(newColour)); // was fcol + setColour(enteredType, new FeatureColour(newColour)); // was fcol featuresAdded(); } else @@ -498,7 +493,7 @@ public class FeatureRenderer extends } // findAllFeatures(); - ap.paintAlignment(true); + ap.paintAlignment(true, true); return true; }