X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=46f574e03ec4d9f4c3b9f8183582c6aa80079767;hb=37e53fb916ef469eda6fd042701e116d56ff3c0b;hp=358798d8932450d5b89a7b9461af35c43709b345;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 358798d..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; @@ -179,15 +180,15 @@ public class FeatureRenderer 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) { @@ -204,28 +205,26 @@ public class FeatureRenderer } 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); + } + }); } } }); @@ -234,19 +233,26 @@ public class FeatureRenderer 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(); + 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); @@ -270,9 +276,8 @@ public class FeatureRenderer 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) @@ -386,7 +391,10 @@ public class FeatureRenderer 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 +403,7 @@ public class FeatureRenderer 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 +429,37 @@ public class FeatureRenderer { /* * 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 +474,18 @@ public class FeatureRenderer 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 +495,7 @@ public class FeatureRenderer } } - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); return true; }