X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=9a6749958481ff793d894fd3f4485998234bc010;hb=106a3890f956e2aa7780b2985f4326655912a558;hp=9e40b1a127d7fc03e12ad4dd6e5e2736f9e9161e;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 9e40b1a..9a67499 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -1,550 +1,861 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-
-public class FeatureSettings
- extends Panel implements ItemListener,
- MouseListener, MouseMotionListener, ActionListener, AdjustmentListener
-{
- FeatureRenderer fr;
- AlignmentPanel ap;
- AlignViewport av;
- Frame frame;
- Panel groupPanel;
- Panel featurePanel = new Panel();
- ScrollPane scrollPane;
- boolean alignmentHasFeatures = false;
- Image linkImage;
- Scrollbar transparency;
-
- public FeatureSettings(final AlignmentPanel ap)
- {
- this.ap = ap;
- this.av = ap.av;
- fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
-
- transparency = new Scrollbar(Scrollbar.HORIZONTAL,
- 100 - (int) (fr.transparency * 100), 1, 1, 100);
-
- if (fr.transparencySetter != null)
- {
- transparency.addAdjustmentListener(this);
- }
- else
- {
- transparency.setEnabled(false);
- }
-
- java.net.URL url = getClass().getResource("/images/link.gif");
- if (url != null)
- {
- linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
- }
-
- if (av.featuresDisplayed == null)
- {
- fr.findAllFeatures();
- }
-
- setTableData();
-
- this.setLayout(new BorderLayout());
- scrollPane = new ScrollPane();
- scrollPane.add(featurePanel);
- if (alignmentHasFeatures)
- {
- add(scrollPane, BorderLayout.CENTER);
- }
-
- Button invert = new Button("Invert Selection");
- invert.addActionListener(this);
-
- Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10));
- lowerPanel.add(invert);
-
- Panel tPanel = new Panel(new BorderLayout());
-
- if (fr.transparencySetter != null)
- {
- tPanel.add(transparency, BorderLayout.CENTER);
- tPanel.add(new Label("Transparency"), BorderLayout.EAST);
- }
- else
- {
- tPanel.add(new Label("Transparency not available in this web browser"),
- BorderLayout.CENTER);
- }
-
- lowerPanel.add(tPanel, BorderLayout.SOUTH);
-
- add(lowerPanel, BorderLayout.SOUTH);
-
- if (groupPanel != null)
- {
- groupPanel.setLayout(
- new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
- groupPanel.validate();
-
- add(groupPanel, BorderLayout.NORTH);
- }
- frame = new Frame();
- frame.add(this);
- int height = featurePanel.getComponentCount() * 50 + 60;
-
- height = Math.max(200, height);
- height = Math.min(400, height);
-
- jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 280,
- height);
- }
-
- public void paint(Graphics g)
- {
- g.setColor(Color.black);
- g.drawString("No Features added to this alignment!!", 10, 20);
- g.drawString("(Features can be added from searches or", 10, 40);
- g.drawString("from Jalview / GFF features files)", 10, 60);
- }
-
- void setTableData()
- {
- alignmentHasFeatures = false;
-
- if (fr.featureGroups == null)
- {
- fr.featureGroups = new Hashtable();
- }
-
- Vector allFeatures = new Vector();
- Vector allGroups = new Vector();
- SequenceFeature[] tmpfeatures;
- String group;
-
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
- {
- continue;
- }
-
- alignmentHasFeatures = true;
-
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
- int index = 0;
- while (index < tmpfeatures.length)
- {
- if (tmpfeatures[index].getFeatureGroup() != null)
- {
- group = tmpfeatures[index].featureGroup;
- if (!allGroups.contains(group))
- {
- allGroups.addElement(group);
-
- boolean visible = true;
- if (fr.featureGroups.containsKey(group))
- {
- visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
- }
-
- fr.featureGroups.put(group, new Boolean(visible));
-
- if (groupPanel == null)
- {
- groupPanel = new Panel();
- }
-
- Checkbox check = new MyCheckbox(
- group,
- visible,
- (fr.featureLinks != null && fr.featureLinks.containsKey(group))
- );
-
- check.addMouseListener(this);
- check.setFont(new Font("Serif", Font.BOLD, 12));
- check.addItemListener(this);
- groupPanel.add(check);
- }
- }
-
- if (!allFeatures.contains(tmpfeatures[index].getType()))
- {
- allFeatures.addElement(tmpfeatures[index].getType());
- }
- index++;
- }
- }
-
- resetTable(false);
- }
-
- //This routine adds and removes checkboxes depending on
- //Group selection states
- void resetTable(boolean groupsChanged)
- {
- SequenceFeature[] tmpfeatures;
- String group = null, type;
- Vector visibleChecks = new Vector();
-
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
- {
- continue;
- }
-
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
- int index = 0;
- while (index < tmpfeatures.length)
- {
- group = tmpfeatures[index].featureGroup;
-
- if (group == null || fr.featureGroups.get(group) == null ||
- ( (Boolean) fr.featureGroups.get(group)).booleanValue())
- {
- type = tmpfeatures[index].getType();
- if (!visibleChecks.contains(type))
- {
- visibleChecks.addElement(type);
- }
- }
- index++;
- }
- }
-
- Component[] comps;
- int cSize = featurePanel.getComponentCount();
- Checkbox check;
- //This will remove any checkboxes which shouldn't be
- //visible
- for (int i = 0; i < cSize; i++)
- {
- comps = featurePanel.getComponents();
- check = (Checkbox) comps[i];
- if (!visibleChecks.contains(check.getLabel()))
- {
- featurePanel.remove(i);
- cSize--;
- i--;
- }
- }
-
- if (fr.renderOrder != 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--)
- {
- String item = fr.renderOrder[ro];
-
- if (!visibleChecks.contains(item))
- {
- continue;
- }
-
- visibleChecks.removeElement(item);
-
- addCheck(false, item);
- }
- }
-
- // now add checkboxes which should be visible,
- // if they have not already been added
- Enumeration en = visibleChecks.elements();
-
- while (en.hasMoreElements())
- {
- addCheck(groupsChanged, en.nextElement().toString());
- }
-
- featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1,
- 10, 5));
- featurePanel.validate();
-
- if (scrollPane != null)
- {
- scrollPane.validate();
- }
-
- itemStateChanged(null);
- }
-
- void addCheck(boolean groupsChanged, String type)
- {
- boolean addCheck;
- Component[] comps = featurePanel.getComponents();
- Checkbox check;
- addCheck = true;
- for (int i = 0; i < featurePanel.getComponentCount(); i++)
- {
- check = (Checkbox) comps[i];
- if (check.getLabel().equals(type))
- {
- addCheck = false;
- break;
- }
- }
-
- if (addCheck)
- {
- boolean selected = false;
- if (groupsChanged || av.featuresDisplayed.containsKey(type))
- {
- selected = true;
- }
-
- check = new MyCheckbox(type,
- selected,
- (fr.featureLinks != null &&
- fr.featureLinks.containsKey(type))
- );
-
- check.addMouseListener(this);
- check.addMouseMotionListener(this);
- check.setBackground(fr.getColour(type));
- check.addItemListener(this);
- featurePanel.add(check);
- }
- }
-
- public void actionPerformed(ActionEvent evt)
- {
- for (int i = 0; i < featurePanel.getComponentCount(); i++)
- {
- Checkbox check = (Checkbox) featurePanel.getComponent(i);
- check.setState(!check.getState());
- }
- selectionChanged();
- }
-
- public void itemStateChanged(ItemEvent evt)
- {
- if (evt != null)
- {
- //Is the source a top level featureGroup?
- Checkbox source = (Checkbox) evt.getSource();
- if (fr.featureGroups.containsKey(source.getLabel()))
- {
- fr.featureGroups.put(source.getLabel(), new Boolean(source.getState()));
- ap.seqPanel.seqCanvas.repaint();
- if (ap.overviewPanel != null)
- {
- ap.overviewPanel.updateOverviewImage();
- }
-
- resetTable(true);
- return;
- }
- }
- selectionChanged();
- }
-
- void selectionChanged()
- {
- Component[] comps = featurePanel.getComponents();
- int cSize = comps.length;
-
- Object[][] tmp = new Object[cSize][3];
- int tmpSize = 0;
- for (int i = 0; i < cSize; i++)
- {
- Checkbox check = (Checkbox) comps[i];
- tmp[tmpSize][0] = check.getLabel();
- tmp[tmpSize][1] = fr.getColour(check.getLabel());
- tmp[tmpSize][2] = new Boolean(check.getState());
- tmpSize++;
- }
-
- Object[][] data = new Object[tmpSize][3];
- System.arraycopy(tmp, 0, data, 0, tmpSize);
-
- fr.setFeaturePriority(data);
- ap.seqPanel.seqCanvas.repaint();
- if (ap.overviewPanel != null)
- {
- ap.overviewPanel.updateOverviewImage();
- }
- }
-
- MyCheckbox selectedCheck;
- boolean dragging = false;
-
- public void mousePressed(MouseEvent evt)
- {
-
- selectedCheck = (MyCheckbox) evt.getSource();
-
- if (fr.featureLinks != null
- && fr.featureLinks.containsKey(selectedCheck.getLabel())
- )
- {
- if (evt.getX() > selectedCheck.stringWidth + 20)
- {
- evt.consume();
- }
- }
-
- }
-
- public void mouseDragged(MouseEvent evt)
- {
- if ( ( (Component) evt.getSource()).getParent() != featurePanel)
- {
- return;
- }
- dragging = true;
- }
-
- public void mouseReleased(MouseEvent evt)
- {
- if ( ( (Component) evt.getSource()).getParent() != featurePanel)
- {
- return;
- }
-
- Component comp = null;
- Checkbox target = null;
-
- int height = evt.getY() + evt.getComponent().getLocation().y;
-
- if (height > featurePanel.getSize().height)
- {
-
- comp = featurePanel.getComponent(featurePanel.getComponentCount() - 1);
- }
- else if (height < 0)
- {
- comp = featurePanel.getComponent(0);
- }
- else
- {
- comp = featurePanel.getComponentAt(evt.getX(),
- evt.getY() +
- evt.getComponent().getLocation().y);
- }
-
- if (comp != null && comp instanceof Checkbox)
- {
- target = (Checkbox) comp;
- }
-
- if (selectedCheck != null
- && target != null
- && selectedCheck != target)
- {
- int targetIndex = -1;
- for (int i = 0; i < featurePanel.getComponentCount(); i++)
- {
- if (target == featurePanel.getComponent(i))
- {
- targetIndex = i;
- break;
- }
- }
-
- featurePanel.remove(selectedCheck);
- featurePanel.add(selectedCheck, targetIndex);
- featurePanel.validate();
- itemStateChanged(null);
- }
- }
-
- public void setUserColour(String feature, Color col)
- {
- fr.setColour(feature, col);
- featurePanel.removeAll();
- resetTable(false);
- ap.repaint();
- }
-
- public void mouseEntered(MouseEvent evt)
- {}
-
- public void mouseExited(MouseEvent evt)
- {}
-
- public void mouseClicked(MouseEvent evt)
- {
- MyCheckbox check = (MyCheckbox) evt.getSource();
-
- if (fr.featureLinks != null
- && fr.featureLinks.containsKey(check.getLabel()))
- {
- if (evt.getX() > check.stringWidth + 20)
- {
- evt.consume();
- String link = fr.featureLinks.get(check.getLabel()).toString();
- ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1),
- link.substring(0, link.indexOf("|")));
- }
- }
-
- if (check.getParent() != featurePanel)
- {
- return;
- }
-
- if (evt.getClickCount() > 1)
- {
- new UserDefinedColours(this, check.getLabel(),
- fr.getColour(check.getLabel()));
- }
- }
-
- public void mouseMoved(MouseEvent evt)
- {}
-
- public void adjustmentValueChanged(AdjustmentEvent evt)
- {
- fr.transparency = ( (float) (100 - transparency.getValue()) / 100f);
- ap.seqPanel.seqCanvas.repaint();
-
- }
-
- class MyCheckbox
- extends Checkbox
- {
- public int stringWidth;
- boolean hasLink;
- public MyCheckbox(String label, boolean checked, boolean haslink)
- {
- super(label, checked);
-
- FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());
- stringWidth = fm.stringWidth(label);
- this.hasLink = haslink;
- }
-
- public void paint(Graphics g)
- {
- if (hasLink)
- {
- g.drawImage(linkImage, stringWidth + 25, (
- getSize().height - linkImage.getHeight(this)) / 2,
- this);
- }
- }
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+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.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+public class FeatureSettings extends Panel
+ implements ItemListener, MouseListener, MouseMotionListener,
+ ActionListener, AdjustmentListener, FeatureSettingsControllerI
+{
+ FeatureRenderer fr;
+
+ AlignmentPanel ap;
+
+ AlignViewport av;
+
+ Frame frame;
+
+ Panel groupPanel;
+
+ Panel featurePanel = new Panel();
+
+ ScrollPane scrollPane;
+
+ Image linkImage;
+
+ Scrollbar transparency;
+
+ public FeatureSettings(final AlignmentPanel ap)
+ {
+ this.ap = ap;
+ this.av = ap.av;
+ ap.av.featureSettings = this;
+ fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
+
+ transparency = new Scrollbar(Scrollbar.HORIZONTAL,
+ 100 - (int) (fr.getTransparency() * 100), 1, 1, 100);
+
+ transparency.addAdjustmentListener(this);
+
+ java.net.URL url = getClass().getResource("/images/link.gif");
+ if (url != null)
+ {
+ linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
+ }
+
+ if (av.isShowSequenceFeatures() || !fr.hasRenderOrder())
+ {
+ fr.findAllFeatures(true); // was default - now true to make all visible
+ }
+ groupPanel = new Panel();
+
+ discoverAllFeatureData();
+
+ this.setLayout(new BorderLayout());
+ scrollPane = new ScrollPane();
+ scrollPane.add(featurePanel);
+ if (fr.getAllFeatureColours() != null
+ && fr.getAllFeatureColours().size() > 0)
+ {
+ add(scrollPane, BorderLayout.CENTER);
+ }
+
+ Button invert = new Button("Invert Selection");
+ invert.addActionListener(this);
+
+ Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10));
+ lowerPanel.add(invert);
+
+ Panel tPanel = new Panel(new BorderLayout());
+
+ tPanel.add(transparency, BorderLayout.CENTER);
+ tPanel.add(new Label("Transparency"), BorderLayout.EAST);
+
+ lowerPanel.add(tPanel, BorderLayout.SOUTH);
+
+ add(lowerPanel, BorderLayout.SOUTH);
+
+ 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);
+
+ frame = new Frame();
+ frame.add(this);
+ final FeatureSettings me = this;
+ frame.addWindowListener(new WindowAdapter()
+ {
+ @Override
+ public void windowClosing(WindowEvent e)
+ {
+ if (me.av.featureSettings == me)
+ {
+ me.av.featureSettings = null;
+ me.ap = null;
+ me.av = null;
+ }
+ }
+ });
+ int height = featurePanel.getComponentCount() * 50 + 60;
+
+ height = Math.max(200, height);
+ height = Math.min(400, height);
+ int width = 300;
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ width, height);
+ }
+
+ @Override
+ 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);
+ }
+
+ protected void popupSort(final MyCheckbox check,
+ final Map minmax, int x, int y)
+ {
+ final String type = check.type;
+ final FeatureColourI typeCol = fr.getFeatureStyle(type);
+ 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()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc
+ .sortAlignmentByFeatureScore(Arrays.asList(new String[]
+ { type }));
+ }
+
+ });
+ MenuItem dens = new MenuItem(
+ MessageManager.getString("label.sort_by_density"));
+ dens.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc
+ .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
+ { type }));
+ }
+
+ });
+ men.add(dens);
+
+ if (minmax != null)
+ {
+ final float[][] typeMinMax = minmax.get(type);
+ /*
+ * final java.awt.CheckboxMenuItem chb = new
+ * java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the
+ * moment chb.setState(minmax.get(type) != null);
+ * chb.addActionListener(new ActionListener() {
+ *
+ * public void actionPerformed(ActionEvent e) {
+ * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type,
+ * null); } else { minmax.put(type, typeMinMax); } }
+ *
+ * }); men.add(chb);
+ */
+ if (typeMinMax != null && typeMinMax[0] != null)
+ {
+ // graduated colourschemes for those where minmax exists for the
+ // positional features
+ MenuItem mxcol = new MenuItem(
+ (typeCol.isSimpleColour()) ? "Graduated Colour"
+ : "Single Colour");
+ men.add(mxcol);
+ mxcol.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (typeCol.isSimpleColour())
+ {
+ new FeatureColourChooser(me, type);
+ // write back the current colour object to update the table
+ check.updateColor(fr.getFeatureStyle(type));
+ }
+ else
+ {
+ new UserDefinedColours(me, check.type, typeCol);
+ }
+ }
+
+ });
+ }
+ }
+
+ MenuItem selectContaining = new MenuItem(
+ MessageManager.getString("label.select_columns_containing"));
+ selectContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
+ false, type);
+ }
+ });
+ men.add(selectContaining);
+
+ MenuItem selectNotContaining = new MenuItem(MessageManager
+ .getString("label.select_columns_not_containing"));
+ selectNotContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ me.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
+ false, type);
+ }
+ });
+ men.add(selectNotContaining);
+
+ MenuItem hideContaining = new MenuItem(
+ MessageManager.getString("label.hide_columns_containing"));
+ hideContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideFeatureColumns(type, true);
+ }
+ });
+ men.add(hideContaining);
+
+ MenuItem hideNotContaining = new MenuItem(
+ MessageManager.getString("label.hide_columns_not_containing"));
+ hideNotContaining.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideFeatureColumns(type, false);
+ }
+ });
+ men.add(hideNotContaining);
+
+ this.featurePanel.add(men);
+ men.show(this.featurePanel, x, y);
+ }
+
+ @Override
+ public void discoverAllFeatureData()
+ {
+ if (fr.getAllFeatureColours() != null
+ && fr.getAllFeatureColours().size() > 0)
+ {
+ // rebuildGroups();
+
+ }
+ resetTable(false);
+ }
+
+ /**
+ * Answers the visibility of the given group, and adds a checkbox for it if
+ * there is not one already
+ */
+ public boolean checkGroupState(String group)
+ {
+ boolean visible = fr.checkGroupVisibility(group, true);
+
+ /*
+ * is there already a checkbox for this group?
+ */
+ for (int g = 0; g < groupPanel.getComponentCount(); g++)
+ {
+ if (((Checkbox) groupPanel.getComponent(g)).getLabel().equals(group))
+ {
+ ((Checkbox) groupPanel.getComponent(g)).setState(visible);
+ return visible;
+ }
+ }
+
+ /*
+ * add a new checkbox
+ */
+ Checkbox check = new MyCheckbox(group, visible, false);
+ check.addMouseListener(this);
+ check.setFont(new Font("Serif", Font.BOLD, 12));
+ check.addItemListener(groupItemListener);
+ groupPanel.add(check);
+
+ groupPanel.validate();
+ return visible;
+ }
+
+ // This routine adds and removes checkboxes depending on
+ // Group selection states
+ void resetTable(boolean groupsChanged)
+ {
+ List displayableTypes = new ArrayList<>();
+ Set foundGroups = new HashSet<>();
+
+ AlignmentI alignment = av.getAlignment();
+
+ for (int i = 0; i < alignment.getHeight(); i++)
+ {
+ SequenceI seq = alignment.getSequenceAt(i);
+
+ /*
+ * get the sequence's groups for positional features
+ * and keep track of which groups are visible
+ */
+ Set groups = seq.getFeatures().getFeatureGroups(true);
+ Set visibleGroups = new HashSet<>();
+ for (String group : groups)
+ {
+ // if (group == null || fr.checkGroupVisibility(group, true))
+ if (group == null || checkGroupState(group))
+ {
+ visibleGroups.add(group);
+ }
+ }
+ foundGroups.addAll(groups);
+
+ /*
+ * get distinct feature types for visible groups
+ * record distinct visible types
+ */
+ Set types = seq.getFeatures().getFeatureTypesForGroups(true,
+ visibleGroups.toArray(new String[visibleGroups.size()]));
+ displayableTypes.addAll(types);
+ }
+
+ /*
+ * remove any checkboxes for groups not present
+ */
+ pruneGroups(foundGroups);
+
+ Component[] comps;
+ int cSize = featurePanel.getComponentCount();
+ MyCheckbox check;
+ // This will remove any checkboxes which shouldn't be
+ // visible
+ for (int i = 0; i < cSize; i++)
+ {
+ comps = featurePanel.getComponents();
+ check = (MyCheckbox) comps[i];
+ if (!displayableTypes.contains(check.type))
+ {
+ featurePanel.remove(i);
+ cSize--;
+ i--;
+ }
+ }
+
+ if (fr.getRenderOrder() != null)
+ {
+ // First add the checks in the previous render order,
+ // in case the window has been closed and reopened
+ List rol = fr.getRenderOrder();
+ for (int ro = rol.size() - 1; ro > -1; ro--)
+ {
+ String item = rol.get(ro);
+
+ if (!displayableTypes.contains(item))
+ {
+ continue;
+ }
+
+ displayableTypes.remove(item);
+
+ addCheck(false, item);
+ }
+ }
+
+ /*
+ * now add checkboxes which should be visible,
+ * if they have not already been added
+ */
+ for (String type : displayableTypes)
+ {
+ addCheck(groupsChanged, type);
+ }
+
+ featurePanel.setLayout(
+ new GridLayout(featurePanel.getComponentCount(), 1, 10, 5));
+ featurePanel.validate();
+
+ if (scrollPane != null)
+ {
+ scrollPane.validate();
+ }
+
+ itemStateChanged(null);
+ }
+
+ /**
+ * Remove from the groups panel any checkboxes for groups that are not in the
+ * foundGroups set. This enables removing a group from the display when the
+ * last feature in that group is deleted.
+ *
+ * @param foundGroups
+ */
+ protected void pruneGroups(Set foundGroups)
+ {
+ for (int g = 0; g < groupPanel.getComponentCount(); g++)
+ {
+ Checkbox checkbox = (Checkbox) groupPanel.getComponent(g);
+ if (!foundGroups.contains(checkbox.getLabel()))
+ {
+ groupPanel.remove(checkbox);
+ }
+ }
+ }
+
+ /**
+ * update the checklist of feature types with the given type
+ *
+ * @param groupsChanged
+ * true means if the type is not in the display list then it will be
+ * added and displayed
+ * @param type
+ * feature type to be checked for in the list.
+ */
+ void addCheck(boolean groupsChanged, String type)
+ {
+ boolean addCheck;
+ Component[] comps = featurePanel.getComponents();
+ MyCheckbox check;
+ addCheck = true;
+ for (int i = 0; i < featurePanel.getComponentCount(); i++)
+ {
+ check = (MyCheckbox) comps[i];
+ if (check.type.equals(type))
+ {
+ addCheck = false;
+ break;
+ }
+ }
+
+ if (addCheck)
+ {
+ boolean selected = false;
+ if (groupsChanged || av.getFeaturesDisplayed().isVisible(type))
+ {
+ selected = true;
+ }
+
+ check = new MyCheckbox(type, selected, false,
+ fr.getFeatureStyle(type));
+
+ check.addMouseListener(this);
+ check.addMouseMotionListener(this);
+ check.addItemListener(this);
+ if (groupsChanged)
+ {
+ // add at beginning of stack.
+ featurePanel.add(check, 0);
+ }
+ else
+ {
+ // add at end of stack.
+ featurePanel.add(check);
+ }
+ }
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ for (int i = 0; i < featurePanel.getComponentCount(); i++)
+ {
+ Checkbox check = (Checkbox) featurePanel.getComponent(i);
+ check.setState(!check.getState());
+ }
+ selectionChanged(true);
+ }
+
+ private ItemListener groupItemListener = new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent evt)
+ {
+ Checkbox source = (Checkbox) evt.getSource();
+ fr.setGroupVisibility(source.getLabel(), source.getState());
+ ap.seqPanel.seqCanvas.repaint();
+ if (ap.overviewPanel != null)
+ {
+ ap.overviewPanel.updateOverviewImage();
+ }
+ resetTable(true);
+ return;
+ };
+ };
+
+ @Override
+ public void itemStateChanged(ItemEvent evt)
+ {
+ selectionChanged(true);
+ }
+
+ void selectionChanged(boolean updateOverview)
+ {
+ Component[] comps = featurePanel.getComponents();
+ int cSize = comps.length;
+
+ Object[][] tmp = new Object[cSize][3];
+ int tmpSize = 0;
+ for (int i = 0; i < cSize; i++)
+ {
+ MyCheckbox check = (MyCheckbox) comps[i];
+ tmp[tmpSize][0] = check.type;
+ tmp[tmpSize][1] = fr.getFeatureStyle(check.type);
+ tmp[tmpSize][2] = new Boolean(check.getState());
+ tmpSize++;
+ }
+
+ Object[][] data = new Object[tmpSize][3];
+ System.arraycopy(tmp, 0, data, 0, tmpSize);
+
+ fr.setFeaturePriority(data);
+
+ ap.paintAlignment(updateOverview, updateOverview);
+ }
+
+ MyCheckbox selectedCheck;
+
+ boolean dragging = false;
+
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ if (((Component) evt.getSource()).getParent() != featurePanel)
+ {
+ return;
+ }
+ dragging = true;
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (((Component) evt.getSource()).getParent() != featurePanel)
+ {
+ return;
+ }
+
+ Component comp = null;
+ Checkbox target = null;
+
+ int height = evt.getY() + evt.getComponent().getLocation().y;
+
+ if (height > featurePanel.getSize().height)
+ {
+
+ comp = featurePanel
+ .getComponent(featurePanel.getComponentCount() - 1);
+ }
+ else if (height < 0)
+ {
+ comp = featurePanel.getComponent(0);
+ }
+ else
+ {
+ comp = featurePanel.getComponentAt(evt.getX(),
+ evt.getY() + evt.getComponent().getLocation().y);
+ }
+
+ if (comp != null && comp instanceof Checkbox)
+ {
+ target = (Checkbox) comp;
+ }
+
+ if (selectedCheck != null && target != null && selectedCheck != target)
+ {
+ int targetIndex = -1;
+ for (int i = 0; i < featurePanel.getComponentCount(); i++)
+ {
+ if (target == featurePanel.getComponent(i))
+ {
+ targetIndex = i;
+ break;
+ }
+ }
+
+ featurePanel.remove(selectedCheck);
+ featurePanel.add(selectedCheck, targetIndex);
+ featurePanel.validate();
+ itemStateChanged(null);
+ }
+ }
+
+ public void setUserColour(String feature, FeatureColourI originalColour)
+ {
+ fr.setColour(feature, originalColour);
+ refreshTable();
+ }
+
+ public void refreshTable()
+ {
+ featurePanel.removeAll();
+ resetTable(false);
+ ap.paintAlignment(true, true);
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent evt)
+ {
+ }
+
+ @Override
+ public void mouseExited(MouseEvent evt)
+ {
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ MyCheckbox check = (MyCheckbox) evt.getSource();
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
+ {
+ this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
+ }
+
+ if (check.getParent() != featurePanel)
+ {
+ return;
+ }
+
+ if (evt.getClickCount() > 1)
+ {
+ FeatureColourI fcol = fr.getFeatureStyle(check.type);
+ if (fcol.isSimpleColour())
+ {
+ new UserDefinedColours(this, check.type, fcol.getColour());
+ }
+ else
+ {
+ new FeatureColourChooser(this, check.type);
+ // write back the current colour object to update the table
+ check.updateColor(fr.getFeatureStyle(check.type));
+ }
+ }
+ }
+
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ }
+
+ @Override
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ fr.setTransparency((100 - transparency.getValue()) / 100f);
+ ap.paintAlignment(true, true);
+ }
+
+ class MyCheckbox extends Checkbox
+ {
+ public String type;
+
+ public int stringWidth;
+
+ boolean hasLink;
+
+ FeatureColourI col;
+
+ public void updateColor(FeatureColourI newcol)
+ {
+ col = newcol;
+ if (col.isSimpleColour())
+ {
+ setBackground(col.getColour());
+ }
+ else
+ {
+ String vlabel = type;
+ if (col.isAboveThreshold())
+ {
+ vlabel += " (>)";
+ }
+ else if (col.isBelowThreshold())
+ {
+ vlabel += " (<)";
+ }
+ if (col.isColourByLabel())
+ {
+ setBackground(Color.white);
+ vlabel += " (by Label)";
+ }
+ else
+ {
+ setBackground(col.getMinColour());
+ }
+ this.setLabel(vlabel);
+ }
+ repaint();
+ }
+
+ public MyCheckbox(String label, boolean checked, boolean haslink)
+ {
+ super(label, checked);
+ type = label;
+ FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());
+ stringWidth = fm.stringWidth(label);
+ this.hasLink = haslink;
+ }
+
+ public MyCheckbox(String type, boolean selected, boolean b,
+ FeatureColourI featureStyle)
+ {
+ this(type, selected, b);
+ updateColor(featureStyle);
+ }
+
+ @Override
+ public void paint(Graphics g)
+ {
+ Dimension d = getSize();
+ if (col != null)
+ {
+ if (col.isColourByLabel())
+ {
+ g.setColor(Color.white);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+ /*
+ * g.setColor(Color.black); Font f=g.getFont().deriveFont(9);
+ * g.setFont(f);
+ *
+ * // g.setFont(g.getFont().deriveFont( //
+ * AffineTransform.getScaleInstance( //
+ * width/g.getFontMetrics().stringWidth("Label"), //
+ * height/g.getFontMetrics().getHeight()))); g.drawString("Label",
+ * width/2, 0);
+ */
+
+ }
+ else if (col.isGraduatedColour())
+ {
+ Color maxCol = col.getMaxColour();
+ g.setColor(maxCol);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+
+ }
+ }
+
+ if (hasLink)
+ {
+ g.drawImage(linkImage, stringWidth + 25,
+ (getSize().height - linkImage.getHeight(this)) / 2, this);
+ }
+ }
+ }
+
+ /**
+ * Hide columns containing (or not containing) a given feature type
+ *
+ * @param type
+ * @param columnsContaining
+ */
+ void hideFeatureColumns(final String type, boolean columnsContaining)
+ {
+ if (ap.alignFrame.avc.markColumnsContainingFeatures(columnsContaining,
+ false, false, type))
+ {
+ if (ap.alignFrame.avc.markColumnsContainingFeatures(
+ !columnsContaining, false, false, type))
+ {
+ ap.alignFrame.viewport.hideSelectedColumns();
+ }
+ }
+ }
+
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+}