X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=3c2715f28bb715abdaed3176ade207245f1eb59b;hb=fe654aee9b43fb9c9307830c277f1e63576826ae;hp=dd2b873926b02676a3171fd522a9cd5dd0838588;hpb=497958b4e5217efaa3ddeece38f38c3a6e98cb96;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index dd2b873..3c2715f 100644 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,15 +20,40 @@ */ package jalview.appletgui; -import java.util.*; -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.GraduatedColor; +import jalview.api.FeatureColourI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.io.FeaturesFile; +import jalview.schemes.FeatureColour; +import jalview.util.ColorUtils; import jalview.util.MessageManager; -import jalview.viewmodel.seqfeatures.FeaturesDisplayed; +import jalview.viewmodel.AlignmentViewport; + +import java.awt.BorderLayout; +import java.awt.Button; +import java.awt.Choice; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.FlowLayout; +import java.awt.Font; +import java.awt.Frame; +import java.awt.Graphics; +import java.awt.GridLayout; +import java.awt.Label; +import java.awt.Panel; +import java.awt.ScrollPane; +import java.awt.TextArea; +import java.awt.TextField; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.MouseAdapter; +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! @@ -36,8 +61,16 @@ import jalview.viewmodel.seqfeatures.FeaturesDisplayed; * @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 @@ -47,22 +80,13 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere * Creates a new FeatureRenderer object. * * @param av - * DOCUMENT ME! */ - public FeatureRenderer(AlignViewport av) + public FeatureRenderer(AlignmentViewport av) { - super(); - this.av = av; + super(av); - setTransparencyAvailable(!System.getProperty("java.version").startsWith("1.1")); } - static String lastFeatureAdded; - - static String lastFeatureGroupAdded; - - static String lastDescriptionAdded; - int featureIndex = 0; boolean deleteFeature = false; @@ -80,49 +104,35 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere /** * render a feature style in the amend feature dialog box */ - public void updateColor(Object newcol) + public void updateColor(FeatureColourI newcol) { - - Color bg, col = null; - GraduatedColor gcol = null; + Color bg = null; String vlabel = ""; - if (newcol instanceof Color) - { - isGcol = false; - col = (Color) newcol; - gcol = null; - } - else if (newcol instanceof GraduatedColor) + if (newcol.isSimpleColour()) { - isGcol = true; - gcol = (GraduatedColor) newcol; - col = null; + bg = newcol.getColour(); + setBackground(bg); } else { - throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox")); - } - if (col != null) - { - setBackground(bg = col); - } - else - { - if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) + if (newcol.isAboveThreshold()) + { + vlabel += " (>)"; + } + else if (newcol.isBelowThreshold()) { - vlabel += " " - + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)" - : "(<)"); + vlabel += " (<)"; } - if (isColourByLabel = gcol.isColourByLabel()) + + if (isColourByLabel = newcol.isColourByLabel()) { setBackground(bg = Color.white); vlabel += " (by Label)"; } else { - setBackground(bg = gcol.getMinColor()); - maxCol = gcol.getMaxColor(); + setBackground(bg = newcol.getMinColour()); + maxCol = newcol.getMaxColour(); } } label = vlabel; @@ -135,6 +145,7 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere super(null); } + @Override public void paint(Graphics g) { Dimension d = getSize(); @@ -160,13 +171,25 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere } - boolean amendFeatures(final SequenceI[] sequences, - final SequenceFeature[] features, boolean newFeatures, + /** + * Shows a dialog allowing the user to create, or amend or delete, sequence + * 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 + * @return + */ + boolean amendFeatures(final List sequences, + final List features, boolean create, final AlignmentPanel ap) { - Panel bigPanel = new Panel(new BorderLayout()); + final Panel bigPanel = new Panel(new BorderLayout()); final TextField name = new TextField(16); - final TextField source = new TextField(16); + final TextField group = new TextField(16); final TextArea description = new TextArea(3, 35); final TextField start = new TextField(8); final TextField end = new TextField(8); @@ -174,6 +197,22 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere Button deleteButton = new Button("Delete"); deleteFeature = false; + name.addTextListener(new TextListener() + { + @Override + public void textValueChanged(TextEvent e) + { + warnIfTypeHidden(ap.alignFrame, name.getText()); + } + }); + group.addTextListener(new TextListener() + { + @Override + public void textValueChanged(TextEvent e) + { + warnIfGroupHidden(ap.alignFrame, group.getText()); + } + }); colourPanel = new FeatureColourPanel(); colourPanel.setSize(110, 15); final FeatureRenderer fr = this; @@ -185,20 +224,20 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere // ///////////////////////////////////// // /MULTIPLE FEATURES AT SELECTED RESIDUE - if (!newFeatures && 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) - item += " (" + features[i].getFeatureGroup() + ")"; - + String item = sf.getType() + "/" + sf.getBegin() + "-" + + sf.getEnd(); + if (sf.getFeatureGroup() != null) + { + item += " (" + sf.getFeatureGroup() + ")"; + } overlaps.addItem(item); } @@ -206,30 +245,33 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere overlaps.addItemListener(new java.awt.event.ItemListener() { + @Override public void itemStateChanged(java.awt.event.ItemEvent e) { int index = overlaps.getSelectedIndex(); if (index != -1) { featureIndex = index; - name.setText(features[index].getType()); - description.setText(features[index].getDescription()); - source.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() + ""); - SearchResults highlight = new SearchResults(); - highlight.addResult(sequences[0], features[index].getBegin(), - features[index].getEnd()); + SearchResultsI highlight = new SearchResults(); + highlight.addResult(sequences.get(0), sf.getBegin(), + sf.getEnd()); ap.seqPanel.seqCanvas.highlightSearchResults(highlight); } - Object col = getFeatureStyle(name.getText()); + FeatureColourI col = getFeatureStyle(name.getText()); if (col == null) { - col = new jalview.schemes.UserColourScheme() - .createColourFromName(name.getText()); + Color generatedColour = ColorUtils.createColourFromName(name + .getText()); + col = new FeatureColour(generatedColour); } colourPanel.updateColor(col); @@ -243,33 +285,36 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere tmp = new Panel(); panel.add(tmp); - tmp.add(new 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("Group: ", Label.RIGHT)); - tmp.add(source); + tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT)); + tmp.add(group); tmp = new Panel(); panel.add(tmp); - tmp.add(new Label("Colour: ", Label.RIGHT)); + tmp.add(new Label(MessageManager.getString("label.colour"), Label.RIGHT)); tmp.add(colourPanel); bigPanel.add(panel, BorderLayout.NORTH); panel = new Panel(); - panel.add(new Label("Description: ", Label.RIGHT)); + panel.add(new Label(MessageManager.getString("label.description:"), + Label.RIGHT)); panel.add(new ScrollPane().add(description)); - if (!newFeatures) + if (!create) { bigPanel.add(panel, BorderLayout.SOUTH); panel = new Panel(); - panel.add(new Label(" Start:", Label.RIGHT)); + panel.add(new Label(MessageManager.getString("label.start"), + Label.RIGHT)); panel.add(start); - panel.add(new Label(" End:", Label.RIGHT)); + panel.add(new Label(MessageManager.getString("label.end"), + Label.RIGHT)); panel.add(end); bigPanel.add(panel, BorderLayout.CENTER); } @@ -278,76 +323,59 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere bigPanel.add(panel, BorderLayout.CENTER); } - 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 = newFeatures ? MessageManager.getString("label.create_new_sequence_features") - : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()}); + /* + * 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.get(0).getName() }); final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385, 240); dialog.setMainPanel(bigPanel); - if (newFeatures) - { - name.setText(lastFeatureAdded); - source.setText(lastFeatureGroupAdded); - } - else + name.setText(featureType); + group.setText(featureGroup); + + if (!create) { dialog.ok.setLabel(MessageManager.getString("label.amend")); dialog.buttonPanel.add(deleteButton, 1); deleteButton.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { deleteFeature = true; dialog.setVisible(false); } }); - name.setText(features[0].getType()); - source.setText(features[0].getFeatureGroup()); } - start.setText(features[0].getBegin() + ""); - end.setText(features[0].getEnd() + ""); - description.setText(features[0].getDescription()); - Color col = getColour(name.getText()); - if (col == null) - { - col = new jalview.schemes.UserColourScheme() - .createColourFromName(name.getText()); - } - Object fcol = getFeatureStyle(name.getText()); + 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 colourPanel.updateColor(fcol); dialog.setResizable(true); // TODO: render the graduated color in the box. - colourPanel.addMouseListener(new java.awt.event.MouseAdapter() + colourPanel.addMouseListener(new MouseAdapter() { - public void mousePressed(java.awt.event.MouseEvent evt) + @Override + public void mousePressed(MouseEvent evt) { if (!colourPanel.isGcol) { @@ -355,42 +383,41 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere } else { - FeatureColourChooser fcc = new FeatureColourChooser( - ap.alignFrame, name.getText()); + new FeatureColourChooser(ap.alignFrame, name.getText()); dialog.transferFocus(); } } }); dialog.setVisible(true); - jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); + FeaturesFile ffile = new FeaturesFile(); - if (dialog.accept) + /* + * only update default type and group if we used defaults + */ + String enteredType = name.getText().trim(); + if (dialog.accept && useLastDefaults) { - // This ensures that the last sequence - // is refreshed and new features are rendered - lastSeq = null; - lastFeatureAdded = name.getText().trim(); - lastFeatureGroupAdded = source.getText().trim(); - lastDescriptionAdded = description.getText().replace('\n', ' '); + lastFeatureAdded = enteredType; + lastFeatureGroupAdded = group.getText().trim(); } - if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1) - lastFeatureGroupAdded = null; - - if (!newFeatures) + if (!create) { - - SequenceFeature sf = features[featureIndex]; + SequenceFeature sf = features.get(featureIndex); if (dialog.accept) { - sf.type = lastFeatureAdded; - sf.featureGroup = lastFeatureGroupAdded; - sf.description = lastDescriptionAdded; + sf.type = enteredType; + 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, colourPanel.getBackground()); + setColour(sf.type, new FeatureColour(colourPanel.getBackground())); } try { @@ -398,41 +425,46 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere sf.end = Integer.parseInt(end.getText()); } catch (NumberFormatException ex) { + // } + boolean typeOrGroupChanged = (!featureType.equals(sf.type) || !featureGroup + .equals(sf.featureGroup)); ffile.parseDescriptionHTML(sf, false); - setVisible(lastFeatureAdded); // if user edited name then make sure new type is visible + if (typeOrGroupChanged) + { + featuresAdded(); + } } if (deleteFeature) { - sequences[0].deleteFeature(sf); + sequences.get(0).deleteFeature(sf); + // ensure Feature Settings reflects removal of feature / group + featuresAdded(); } - } else { + /* + * adding feature(s) + */ 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); + features.get(i).type = enteredType; + features.get(i).featureGroup = group.getText().trim(); + features.get(i).description = description.getText() + .replace('\n', ' '); + sequences.get(i).addSequenceFeature(features.get(i)); + ffile.parseDescriptionHTML(features.get(i), false); } - col = colourPanel.getBackground(); + Color newColour = colourPanel.getBackground(); // setColour(lastFeatureAdded, fcol); - if (lastFeatureGroupAdded != null) - { - setGroupVisibility(lastFeatureGroupAdded, true); - } - setColour(lastFeatureAdded, fcol); - setVisible(lastFeatureAdded); - findAllFeatures(false); // different to original applet behaviour ? - // findAllFeatures(); + setColour(enteredType, new FeatureColour(newColour)); // was fcol + featuresAdded(); } else { @@ -451,4 +483,43 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere return true; } + + protected void warnIfGroupHidden(Frame frame, String group) + { + if (featureGroups.containsKey(group) && !featureGroups.get(group)) + { + String msg = MessageManager.formatMessage("label.warning_hidden", + MessageManager.getString("label.group"), group); + showWarning(frame, msg); + } + } + + protected void warnIfTypeHidden(Frame frame, String type) + { + if (getRenderOrder().contains(type)) + { + if (!showFeatureOfType(type)) + { + String msg = MessageManager.formatMessage("label.warning_hidden", + MessageManager.getString("label.feature_type"), type); + showWarning(frame, msg); + } + } + } + + /** + * @param frame + * @param msg + */ + protected void showWarning(Frame frame, String msg) + { + JVDialog d = new JVDialog(frame, "", true, 350, 200); + Panel mp = new Panel(); + d.ok.setLabel(MessageManager.getString("action.ok")); + d.cancel.setVisible(false); + mp.setLayout(new FlowLayout()); + mp.add(new Label(msg)); + d.setMainPanel(mp); + d.setVisible(true); + } }