X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=584a69a52c46ece5053ac47db499157610eab73b;hb=c6c67aaa8e2d236305a3495f4edfc8cc88e22b79;hp=cd998b1e61bebf1bd80bb2335d85fcec5d3eb94c;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index cd998b1..584a69a 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 2.8.2b1) - * 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 +20,52 @@ */ package jalview.appletgui; -import java.util.*; -import java.util.List; -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.Arrays; +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; @@ -84,12 +115,13 @@ public class FeatureSettings extends Panel implements ItemListener, fr.findAllFeatures(true); // was default - now true to make all visible } - setTableData(); + discoverAllFeatureData(); this.setLayout(new BorderLayout()); scrollPane = new ScrollPane(); scrollPane.add(featurePanel); - if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0) + if (fr.getAllFeatureColours() != null + && fr.getAllFeatureColours().size() > 0) { add(scrollPane, BorderLayout.CENTER); } @@ -120,10 +152,11 @@ public class FeatureSettings extends Panel implements ItemListener, if (groupPanel != null) { - groupPanel - .setLayout(new GridLayout( - (fr.getFeatureGroupsSize()) / 4 + 1, - 4)); // JBPNote - this was scaled on number of visible groups. seems broken + groupPanel.setLayout(new GridLayout( + (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was + // scaled on number of + // visible groups. seems + // broken groupPanel.validate(); add(groupPanel, BorderLayout.NORTH); @@ -133,6 +166,7 @@ public class FeatureSettings extends Panel implements ItemListener, final FeatureSettings me = this; frame.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent e) { if (me.av.featureSettings == me) @@ -149,10 +183,11 @@ public class FeatureSettings extends Panel implements ItemListener, height = Math.min(400, height); int width = 300; jalview.bin.JalviewLite.addFrame(frame, - MessageManager.getString("label.feature_settings"), width, - height); + MessageManager.getString("label.sequence_feature_settings"), + width, height); } + @Override public void paint(Graphics g) { g.setColor(Color.black); @@ -172,8 +207,7 @@ 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 })); + "label.settings_for_type", new String[] { type })); java.awt.MenuItem scr = new MenuItem( MessageManager.getString("label.sort_by_score")); men.add(scr); @@ -181,10 +215,11 @@ public class FeatureSettings extends Panel implements ItemListener, scr.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - me.ap.alignFrame.avc.sortAlignmentByFeatureScore(new String[] - { type }); + me.ap.alignFrame.avc.sortAlignmentByFeatureScore(Arrays + .asList(new String[] { type })); } }); @@ -193,10 +228,11 @@ public class FeatureSettings extends Panel implements ItemListener, dens.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(new String[] - { type }); + me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(Arrays + .asList(new String[] { type })); } }); @@ -227,6 +263,7 @@ public class FeatureSettings extends Panel implements ItemListener, mxcol.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { if (typeCol instanceof Color) @@ -249,9 +286,11 @@ public class FeatureSettings extends Panel implements ItemListener, men.show(this.featurePanel, x, y); } - public void setTableData() + @Override + public void discoverAllFeatureData() { - if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0) + if (fr.getAllFeatureColours() != null + && fr.getAllFeatureColours().size() > 0) { rebuildGroups(); @@ -276,12 +315,10 @@ public class FeatureSettings extends Panel implements ItemListener, } // TODO: JAL-964 - smoothly incorporate new group entries if panel already // displayed and new groups present - for (String group:(List)fr.getFeatureGroups()) + for (String group : fr.getFeatureGroups()) { boolean vis = fr.checkGroupVisibility(group, false); - Checkbox check = new MyCheckbox(group, vis, - (fr.featureLinks != null && fr.featureLinks - .containsKey(group))); + Checkbox check = new MyCheckbox(group, vis, false); check.addMouseListener(this); check.setFont(new Font("Serif", Font.BOLD, 12)); check.addItemListener(groupItemListener); @@ -294,6 +331,7 @@ public class FeatureSettings extends Panel implements ItemListener, groupPanel.validate(); } } + // This routine adds and removes checkboxes depending on // Group selection states void resetTable(boolean groupsChanged) @@ -418,10 +456,7 @@ public class FeatureSettings extends Panel implements ItemListener, selected = true; } - check = new MyCheckbox( - type, - selected, - (fr.featureLinks != null && fr.featureLinks.containsKey(type)), + check = new MyCheckbox(type, selected, false, fr.getFeatureStyle(type)); check.addMouseListener(this); @@ -440,6 +475,7 @@ public class FeatureSettings extends Panel implements ItemListener, } } + @Override public void actionPerformed(ActionEvent evt) { for (int i = 0; i < featurePanel.getComponentCount(); i++) @@ -450,11 +486,13 @@ public class FeatureSettings extends Panel implements ItemListener, selectionChanged(); } - private ItemListener groupItemListener = new ItemListener() { - public void itemStateChanged(ItemEvent evt) { + private ItemListener groupItemListener = new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent evt) + { Checkbox source = (Checkbox) evt.getSource(); - fr.setGroupVisibility(source.getLabel(), - source.getState()); + fr.setGroupVisibility(source.getLabel(), source.getState()); ap.seqPanel.seqCanvas.repaint(); if (ap.overviewPanel != null) { @@ -464,6 +502,8 @@ public class FeatureSettings extends Panel implements ItemListener, return; }; }; + + @Override public void itemStateChanged(ItemEvent evt) { selectionChanged(); @@ -497,22 +537,7 @@ public class FeatureSettings extends Panel implements ItemListener, boolean dragging = false; - public void mousePressed(MouseEvent evt) - { - - selectedCheck = (MyCheckbox) evt.getSource(); - - if (fr.featureLinks != null - && fr.featureLinks.containsKey(selectedCheck.type)) - { - if (evt.getX() > selectedCheck.stringWidth + 20) - { - evt.consume(); - } - } - - } - + @Override public void mouseDragged(MouseEvent evt) { if (((Component) evt.getSource()).getParent() != featurePanel) @@ -522,6 +547,7 @@ public class FeatureSettings extends Panel implements ItemListener, dragging = true; } + @Override public void mouseReleased(MouseEvent evt) { if (((Component) evt.getSource()).getParent() != featurePanel) @@ -583,7 +609,9 @@ public class FeatureSettings extends Panel implements ItemListener, } else { - throw new Error(MessageManager.getString("error.implementation_error_unsupported_feature_colour_object")); + throw new Error( + MessageManager + .getString("error.implementation_error_unsupported_feature_colour_object")); } refreshTable(); } @@ -595,14 +623,17 @@ public class FeatureSettings extends Panel implements ItemListener, ap.paintAlignment(true); } + @Override public void mouseEntered(MouseEvent evt) { } + @Override public void mouseExited(MouseEvent evt) { } + @Override public void mouseClicked(MouseEvent evt) { MyCheckbox check = (MyCheckbox) evt.getSource(); @@ -610,16 +641,6 @@ public class FeatureSettings extends Panel implements ItemListener, { this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY()); } - if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type)) - { - if (evt.getX() > check.stringWidth + 20) - { - evt.consume(); - String link = fr.featureLinks.get(check.type).toString(); - ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1), - link.substring(0, link.indexOf("|"))); - } - } if (check.getParent() != featurePanel) { @@ -642,13 +663,15 @@ public class FeatureSettings extends Panel implements ItemListener, } } + @Override public void mouseMoved(MouseEvent evt) { } + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { - fr.setTransparency((float) (100 - transparency.getValue()) / 100f); + fr.setTransparency((100 - transparency.getValue()) / 100f); ap.seqPanel.seqCanvas.repaint(); } @@ -679,7 +702,9 @@ public class FeatureSettings extends Panel implements ItemListener, } else { - throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox")); + throw new Error( + MessageManager + .getString("error.invalid_colour_for_mycheckbox")); } if (col != null) { @@ -724,6 +749,7 @@ public class FeatureSettings extends Panel implements ItemListener, updateColor(featureStyle); } + @Override public void paint(Graphics g) { Dimension d = getSize(); @@ -762,4 +788,9 @@ public class FeatureSettings extends Panel implements ItemListener, } } + @Override + public void mousePressed(MouseEvent e) + { + } + }