X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=5f5e8e0c42abd6069ff5b9d6ce22a844e44a83d5;hb=56d72101b0584635cf539d5413db27abc8deb575;hp=a6d0d99da0f794778c529205dfe94d75b5371bd6;hpb=268dfe33ea14bbcdfb0671a1ec8acc5e9c423426;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index a6d0d99..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! @@ -60,8 +61,8 @@ 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 @@ -182,8 +183,8 @@ public class FeatureRenderer extends * @param ap * @return */ - boolean amendFeatures(final SequenceI[] sequences, - final SequenceFeature[] features, boolean create, + boolean amendFeatures(final List sequences, + final List features, boolean create, final AlignmentPanel ap) { final Panel bigPanel = new Panel(new BorderLayout()); @@ -223,22 +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); } @@ -253,15 +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); @@ -285,17 +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); @@ -328,16 +331,18 @@ public class FeatureRenderer extends * if feature type has not been supplied by the caller * (e.g. for Amend, or create features from Find) */ - boolean useLastDefaults = features[0].getType() == null; - String featureType = useLastDefaults ? lastFeatureAdded : features[0] - .getType(); + SequenceFeature firstFeature = features.get(0); + boolean useLastDefaults = firstFeature.getType() == null; + String featureType = useLastDefaults ? lastFeatureAdded + : firstFeature.getType(); String featureGroup = useLastDefaults ? lastFeatureGroupAdded - : features[0].getFeatureGroup(); + : firstFeature.getFeatureGroup(); - 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[0].getName() }); + new String[] + { sequences.get(0).getName() }); final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385, 240); @@ -362,9 +367,9 @@ public class FeatureRenderer extends }); } - 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 @@ -394,39 +399,51 @@ public class FeatureRenderer extends /* * 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 (dialog.accept && useLastDefaults) { - lastFeatureAdded = name.getText().trim(); - lastFeatureGroupAdded = group.getText().trim(); + lastFeatureAdded = enteredType; + lastFeatureGroupAdded = enteredGroup; } if (!create) { - SequenceFeature sf = features[featureIndex]; + SequenceFeature sf = features.get(featureIndex); if (dialog.accept) { - sf.type = name.getText().trim(); - sf.featureGroup = group.getText().trim(); - if (sf.featureGroup != null && sf.featureGroup.length() < 1) - { - sf.featureGroup = null; - } - sf.description = description.getText().replace('\n', ' '); 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) { // } - boolean typeOrGroupChanged = (!featureType.equals(sf.type) || !featureGroup - .equals(sf.featureGroup)); + + /* + * 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) @@ -436,7 +453,7 @@ public class FeatureRenderer extends } if (deleteFeature) { - sequences[0].deleteFeature(sf); + sequences.get(0).deleteFeature(sf); // ensure Feature Settings reflects removal of feature / group featuresAdded(); } @@ -448,20 +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 = name.getText().trim(); - features[i].featureGroup = group.getText().trim(); - features[i].description = description.getText() - .replace('\n', ' '); - 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 @@ -477,7 +493,7 @@ public class FeatureRenderer extends } // findAllFeatures(); - ap.paintAlignment(true); + ap.paintAlignment(true, true); return true; }