X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=2b79256dd621e607d4c19534df4bf7a63aa65d3c;hb=7703a6a091c65e45bfb8f4d056cd2cbdb19b3535;hp=90d49089da8d0fd83b06b173b9586f04f218a205;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index 90d4908..2b79256 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.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. * @@ -20,21 +20,51 @@ */ package jalview.appletgui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.analysis.AlignmentSorter; -import jalview.commands.OrderCommand; -import jalview.datamodel.*; +import jalview.api.FeatureSettingsControllerI; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceFeature; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.GraduatedColor; import jalview.util.MessageManager; +import java.awt.BorderLayout; +import java.awt.Button; +import java.awt.Checkbox; +import java.awt.Color; +import java.awt.Component; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Frame; +import java.awt.Graphics; +import java.awt.GridLayout; +import java.awt.Image; +import java.awt.Label; +import java.awt.MenuItem; +import java.awt.Panel; +import java.awt.PopupMenu; +import java.awt.ScrollPane; +import java.awt.Scrollbar; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.AdjustmentEvent; +import java.awt.event.AdjustmentListener; +import java.awt.event.InputEvent; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.awt.event.WindowAdapter; +import java.awt.event.WindowEvent; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; + public class FeatureSettings extends Panel implements ItemListener, MouseListener, MouseMotionListener, ActionListener, - AdjustmentListener + AdjustmentListener, FeatureSettingsControllerI { FeatureRenderer fr; @@ -50,8 +80,6 @@ public class FeatureSettings extends Panel implements ItemListener, ScrollPane scrollPane; - boolean alignmentHasFeatures = false; - Image linkImage; Scrollbar transparency; @@ -64,9 +92,9 @@ public class FeatureSettings extends Panel implements ItemListener, fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); transparency = new Scrollbar(Scrollbar.HORIZONTAL, - 100 - (int) (fr.transparency * 100), 1, 1, 100); + 100 - (int) (fr.getTransparency() * 100), 1, 1, 100); - if (fr.transparencySetter != null) + if (fr.isTransparencyAvailable()) { transparency.addAdjustmentListener(this); } @@ -81,17 +109,17 @@ public class FeatureSettings extends Panel implements ItemListener, linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url); } - if (av.featuresDisplayed == null) + if (av.isShowSequenceFeatures() || !fr.hasRenderOrder()) { - fr.findAllFeatures(); + fr.findAllFeatures(true); // was default - now true to make all visible } - setTableData(); + discoverAllFeatureData(); this.setLayout(new BorderLayout()); scrollPane = new ScrollPane(); scrollPane.add(featurePanel); - if (alignmentHasFeatures) + if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0) { add(scrollPane, BorderLayout.CENTER); } @@ -104,7 +132,7 @@ public class FeatureSettings extends Panel implements ItemListener, Panel tPanel = new Panel(new BorderLayout()); - if (fr.transparencySetter != null) + if (fr.isTransparencyAvailable()) { tPanel.add(transparency, BorderLayout.CENTER); tPanel.add(new Label("Transparency"), BorderLayout.EAST); @@ -124,8 +152,8 @@ public class FeatureSettings extends Panel implements ItemListener, { groupPanel .setLayout(new GridLayout( - (fr.featureGroups.size() - fr.hiddenGroups.size()) / 4 + 1, - 4)); + (fr.getFeatureGroupsSize()) / 4 + 1, + 4)); // JBPNote - this was scaled on number of visible groups. seems broken groupPanel.validate(); add(groupPanel, BorderLayout.NORTH); @@ -150,16 +178,22 @@ public class FeatureSettings extends Panel implements ItemListener, height = Math.max(200, height); height = Math.min(400, height); int width = 300; - jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.feature_settings"), width, + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.feature_settings"), width, height); } public void paint(Graphics g) { g.setColor(Color.black); - g.drawString(MessageManager.getString("label.no_features_added_to_this_alignment"), 10, 20); - g.drawString(MessageManager.getString("label.features_can_be_added_from_searches_1"), 10, 40); - g.drawString(MessageManager.getString("label.features_can_be_added_from_searches_2"), 10, 60); + g.drawString(MessageManager + .getString("label.no_features_added_to_this_alignment"), 10, 20); + g.drawString(MessageManager + .getString("label.features_can_be_added_from_searches_1"), 10, + 40); + g.drawString(MessageManager + .getString("label.features_can_be_added_from_searches_2"), 10, + 60); } protected void popupSort(final MyCheckbox check, final Hashtable minmax, @@ -167,8 +201,11 @@ public class FeatureSettings extends Panel implements ItemListener, { final String type = check.type; final Object typeCol = fr.getFeatureStyle(type); - java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage("label.settings_for_type", new String[]{type})); - java.awt.MenuItem scr = new MenuItem(MessageManager.getString("label.sort_by_score")); + java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage( + "label.settings_for_type", new String[] + { type })); + java.awt.MenuItem scr = new MenuItem( + MessageManager.getString("label.sort_by_score")); men.add(scr); final FeatureSettings me = this; scr.addActionListener(new ActionListener() @@ -176,18 +213,19 @@ public class FeatureSettings extends Panel implements ItemListener, public void actionPerformed(ActionEvent e) { - me.sortByScore(new String[] + me.ap.alignFrame.avc.sortAlignmentByFeatureScore(new String[] { type }); } }); - MenuItem dens = new MenuItem(MessageManager.getString("label.sort_by_density")); + MenuItem dens = new MenuItem( + MessageManager.getString("label.sort_by_density")); dens.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - me.sortByDens(new String[] + me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(new String[] { type }); } @@ -241,10 +279,10 @@ public class FeatureSettings extends Panel implements ItemListener, men.show(this.featurePanel, x, y); } - public void setTableData() + @Override + public void discoverAllFeatureData() { - alignmentHasFeatures = fr.buildGroupHash(); - if (alignmentHasFeatures) + if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0) { rebuildGroups(); @@ -269,18 +307,17 @@ public class FeatureSettings extends Panel implements ItemListener, } // TODO: JAL-964 - smoothly incorporate new group entries if panel already // displayed and new groups present - Enumeration gps = fr.featureGroups.keys(); - while (gps.hasMoreElements()) + for (String group:fr.getFeatureGroups()) { - String group = (String) gps.nextElement(); - Boolean vis = (Boolean) fr.featureGroups.get(group); - Checkbox check = new MyCheckbox(group, vis.booleanValue(), + boolean vis = fr.checkGroupVisibility(group, false); + Checkbox check = new MyCheckbox(group, vis, (fr.featureLinks != null && fr.featureLinks .containsKey(group))); check.addMouseListener(this); check.setFont(new Font("Serif", Font.BOLD, 12)); - check.addItemListener(this); - check.setVisible(fr.hiddenGroups.contains(group)); + check.addItemListener(groupItemListener); + // note - visibility seems to correlate with displayed. ???wtf ?? + check.setVisible(vis); groupPanel.add(check); } if (rdrw) @@ -288,7 +325,6 @@ public class FeatureSettings extends Panel implements ItemListener, groupPanel.validate(); } } - // This routine adds and removes checkboxes depending on // Group selection states void resetTable(boolean groupsChanged) @@ -310,8 +346,7 @@ public class FeatureSettings extends Panel implements ItemListener, { group = tmpfeatures[index].featureGroup; - if (group == null || fr.featureGroups.get(group) == null - || ((Boolean) fr.featureGroups.get(group)).booleanValue()) + if (group == null || fr.checkGroupVisibility(group, true)) { type = tmpfeatures[index].getType(); if (!visibleChecks.contains(type)) @@ -340,13 +375,14 @@ public class FeatureSettings extends Panel implements ItemListener, } } - if (fr.renderOrder != null) + if (fr.getRenderOrder() != null) { // First add the checks in the previous render order, // in case the window has been closed and reopened - for (int ro = fr.renderOrder.length - 1; ro > -1; ro--) + List rol = fr.getRenderOrder(); + for (int ro = rol.size() - 1; ro > -1; ro--) { - String item = fr.renderOrder[ro]; + String item = rol.get(ro); if (!visibleChecks.contains(item)) { @@ -408,7 +444,7 @@ public class FeatureSettings extends Panel implements ItemListener, if (addCheck) { boolean selected = false; - if (groupsChanged || av.featuresDisplayed.containsKey(type)) + if (groupsChanged || av.getFeaturesDisplayed().isVisible(type)) { selected = true; } @@ -445,26 +481,22 @@ public class FeatureSettings extends Panel implements ItemListener, selectionChanged(); } - public void itemStateChanged(ItemEvent evt) - { - if (evt != null) - { - // Is the source a top level featureGroup? + private ItemListener groupItemListener = new ItemListener() { + public void itemStateChanged(ItemEvent evt) { Checkbox source = (Checkbox) evt.getSource(); - if (fr.featureGroups.containsKey(source.getLabel())) + fr.setGroupVisibility(source.getLabel(), + source.getState()); + ap.seqPanel.seqCanvas.repaint(); + if (ap.overviewPanel != null) { - fr.featureGroups.put(source.getLabel(), - new Boolean(source.getState())); - ap.seqPanel.seqCanvas.repaint(); - if (ap.overviewPanel != null) - { - ap.overviewPanel.updateOverviewImage(); - } - - resetTable(true); - return; + ap.overviewPanel.updateOverviewImage(); } - } + resetTable(true); + return; + }; + }; + public void itemStateChanged(ItemEvent evt) + { selectionChanged(); } @@ -582,8 +614,7 @@ public class FeatureSettings extends Panel implements ItemListener, } else { - throw new Error( - "Implementation error: Unsupported feature colour object."); + throw new Error(MessageManager.getString("error.implementation_error_unsupported_feature_colour_object")); } refreshTable(); } @@ -608,7 +639,7 @@ public class FeatureSettings extends Panel implements ItemListener, MyCheckbox check = (MyCheckbox) evt.getSource(); if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0) { - this.popupSort(check, fr.minmax, evt.getX(), evt.getY()); + this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY()); } if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type)) { @@ -648,7 +679,7 @@ public class FeatureSettings extends Panel implements ItemListener, public void adjustmentValueChanged(AdjustmentEvent evt) { - fr.transparency = ((float) (100 - transparency.getValue()) / 100f); + fr.setTransparency((100 - transparency.getValue()) / 100f); ap.seqPanel.seqCanvas.repaint(); } @@ -679,7 +710,7 @@ public class FeatureSettings extends Panel implements ItemListener, } else { - throw new Error("Invalid color for MyCheckBox"); + throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox")); } if (col != null) { @@ -762,81 +793,4 @@ public class FeatureSettings extends Panel implements ItemListener, } } - protected void sortByDens(String[] typ) - { - sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY); - } - - private String[] getDisplayedFeatureTypes() - { - String[] typ = null; - if (fr != null) - { - synchronized (fr.renderOrder) - { - typ = new String[fr.renderOrder.length]; - System.arraycopy(fr.renderOrder, 0, typ, 0, typ.length); - for (int i = 0; i < typ.length; i++) - { - if (av.featuresDisplayed.get(typ[i]) == null) - { - typ[i] = null; - } - } - } - } - return typ; - } - - protected void sortBy(String[] typ, String methodText, final String method) - { - if (typ == null) - { - typ = getDisplayedFeatureTypes(); - } - String gps[] = null; - gps = fr.getGroups(true); - if (typ != null) - { - for (int i = 0; i < typ.length; i++) - { - System.err.println("Sorting on Types:" + typ[i]); - } - } - if (gps != null) - { - - for (int i = 0; i < gps.length; i++) - { - System.err.println("Sorting on groups:" + gps[i]); - } - } - AlignmentPanel alignPanel = ap; - AlignmentI al = alignPanel.av.getAlignment(); - - int start, stop; - SequenceGroup sg = alignPanel.av.getSelectionGroup(); - if (sg != null) - { - start = sg.getStartRes(); - stop = sg.getEndRes(); - } - else - { - start = 0; - stop = al.getWidth(); - } - SequenceI[] oldOrder = al.getSequencesArray(); - AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method); - this.ap.alignFrame.addHistoryItem(new OrderCommand(methodText, - oldOrder, alignPanel.av.getAlignment())); - alignPanel.paintAlignment(true); - - } - - protected void sortByScore(String[] typ) - { - sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE); - } - }